bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive response to a future life challenge: consequences of early-life environmental complexity in dual-purpose chicks
Authors: Yan Chao , Hartcher Kate , Liu Wen , Xiao Jinlong , Xiang Hai , Wang Jikun , Liu Hao , Zhang Hui , Liu Jian , Chen Siyu , Zhao Xingbo
Published: October 2020

Conditions in early life play profound and long-lasting effects on the welfare and adaptability to stress of chickens. This study aimed to explore the hypothesis that the provision of environmental complexity in early life improves birds’ adaptive plasticity and ability to cope with a challenge later in life. It also tried to investigate the effect of the gut-brain axis by measuring behavior, stress hormone, gene expression, and gut microbiota. One-day-old chicks were split into 3 groups: (1) a barren environment (without enrichment items) group (BG, n = 40), (2) a litter materials group (LG, n = 40), and (3) a perches with litter materials group (PLG, n = 40). Then, enrichment items were removed and simulated as an environmental challenge at 31 to 53 d of age. Birds were subjected to a predator test at 42 d of age. In the environmental challenge, when compared with LG, PLG birds were characterized by decreased fearfulness, lower plasma corticosterone, improved gut microbial functions, lower relative mRNA expression of GR, and elevated mRNA expressions of stress-related genes CRH, BDNF, and NR2A in the hypothalamus (all P < 0.05). Unexpectedly, the opposite was true for the LG birds when compared with the BG (P < 0.05). Decreased plasma corticosterone and fearfulness were accompanied by altered hypothalamic gene mRNA expressions of BDNF, NR2A, GR, and CRH through the HPA axis in response to altered gut microbial compositions and functions. The findings suggest that gut microbiota may integrate fearfulness, plasma corticosterone, and gene expression in the hypothalamus to provide an insight into the gut-brain axis in chicks. In conclusion, having access to both perches and litter materials in early life allowed birds to cope better with a future challenge. Birds in perches and litter materials environment may have optimal development and adaptive plasticity through the gut-brain axis.
A Novel Marker, Based on Ultrasound Tomography, for Monitoring Early Response to Neoadjuvant Chemotherapy
Authors: Duric Neb , Littrup Peter , Sak Mark , Li Cuiping , Chen Di , Roy Olivier , Bey-Knight Lisa , Brem Rachel
Published: October 2020

Objective

To evaluate the combination of tumor volume and sound speed as a potential imaging marker for assessing neoadjuvant chemotherapy (NAC) response.

Methods

This study was carried out under an IRB-approved protocol (written consent required). Fourteen patients undergoing NAC for invasive breast cancer were examined with ultrasound tomography (UST) throughout their treatment. The volume (V) and the volume-averaged sound speed (VASS) of the tumors and their changes were measured for each patient. Time-dependent response curves of V and VASS were constructed individually for each patient and then as averages for the complete versus partial response groups in order to characterize differences between the two groups. Differences in group means were assessed for statistical significance using t-tests. Differences in shapes of group curves were evaluated with Kolmogorov–Smirnoff tests.

Results

On average, tumor volume and sound speed in the partial response group showed a gradual decline in the first 60 days of treatment, while the complete response group showed a much steeper decline (P < 0.05). The shapes of the response curves of the two groups, corresponding to the entire treatment period, were also found to be significantly different (P < 0.05). Furthermore, large simultaneous drops in volume and sound speed in the first 3 weeks of treatment were characteristic only of the complete responders (P < 0.05).

Conclusion

This study demonstrates the feasibility of using UST to monitor NAC response, warranting future studies to better define the potential of UST for noninvasive, rapid identification of partial versus complete responders in women undergoing NAC.
An analysis of the genus Leucothoe Leach, 1814 (Amphipoda: Leucothoidae) in New Zealand, with the description of two new species symbiotic with ascidians and sponges
Authors: Hauke Ronja , Peart Rachael A , Ryan Ken G
Published: October 2020

Leucothoids (family Leucothoidae Dana, 1852) are amphipods often associated with sponges and are relatively poorly recorded in New Zealand waters, with only four species previously recorded. Two newly discovered species, Leucothoe agripeta  sp. nov. and L. tumultus  sp. nov. are described from a sponge off Aotea Quay, Wellington, New Zealand and an ascidian from the Chatham Rise, eastern New Zealand, respectively. Leucothoe traillii  Thomson, 1881 is redescribed and a neotype assigned. A key to the New Zealand species of Leucothoe as well as a discussion of their host-specificity and ecology are also provided.
Age-Dependent Functional and Numerical Responses ofNeoseiulus cucumeris(Acari: Phytoseiidae) on Two-Spotted Spider Mite (Acari: Tetranychidae)
Authors: Dalir Sajjad , Hajiqanbar Hamidreza , Fathipour Yaghoub , Khanamani Mostafa
Published: October 2020

The age-specific functional and numerical responses of Neoseiulus cucumeris Oudemans (Mesostigmata: Phytoseiidae) on eggs of the two-spotted spider mite, Tetranychus urticae Koch (Prostigmata: Tetranychidae), were assessed in the laboratory using bean leaf discs. Densities of 2, 4, 8, 16, 32, 64, and 128 prey were provided to 4- (protonymph), 6- (deutonymph), 8-, 13-, 18-, 23-, 28-, 33-, and 40-d-old N. cucumeris individuals. The functional response of 28- and 40-d-old N. cucumeris fitted type II, whereas the other ages displayed a type III functional response. The longest handling time observed at the age of 4 d was 0.515 h, whereas the shortest handling time and highest value of maximum attack rate (T/Th) were associated with the age of the 28-d-old treatment (0.261 h and 91.95 prey/d, respectively). The numerical response of N. cucumeris showed a significant increase with increasing prey density, but its rate gradually decreased at higher densities. Therefore, the efficiency of conversion of ingested food was relatively higher at low two-spotted spider mite densities, whereas it was reduced at high two-spotted spider mite densities. The stronger functional response and predation capacity of N. cucumeris on two-spotted spider mite eggs indicated the high potential of this predatory mite as an effective biological control agent against two-spotted spider mite especially at its early and middle ages and also when higher prey densities are present.
The Right to Seeds and Legal Mobilization for the Protection of Peasant Seed Systems in Mali
Authors: Coulibaly Mohamed , Claeys Priscilla , Berson Anne
Published: October 2020

This article discusses the right to seeds and legal mobilization for the protection of peasant seed systems in Mali. It centres on the ongoing ‘Seed, Norms and Peasants’ process (‘Semences, Normes et Paysans’, SNP), the goal of which is to achieve the recognition of peasant seed systems in the law. Through the lens of human rights practice, the article explores how peasant organizations and allied NGOs have: a) converged around a shared political agenda despite initial disagreement on the role of certified seeds; b) framed the right to seeds as a collective right, grounded in customary regimes for the governance of land and natural resources; and c) engaged in dialogue with the state to push for legal reform. It further discusses processes of legal transfers and seed aid that have ushered the development of a commercial seed sector in Mali and locates peasant seed systems within the political economy of seeds in the country.
Sufi Asceticism and the Sunna of the Prophet in al-Junayd’s Adab al-Muftaqir ilā Allāh
Authors: Zaleski John
Published: October 2020

One of the central claims of early Sufis was the harmony of the Sufi path with the sunna of the Prophet Muḥammad. It remains to be explored, however, how early Sufis related to the sunna as an authoritative model. Focusing on the writings of al-Junayd al-Baghdādī (d. 298/910–11), in particular the understudied Adab al-Muftaqir ilā Allāh, this article argues that al-Junayd sought to resolve a tension between anti-ascetic aspects of the sunna and the ascetic practices undertaken by Sufis. By attributing appeals to anti-ascetic ḥadīths to the influence of the lower-soul (nafs), al-Junayd made room for Sufis to undertake practices, including celibacy, that ran counter to the widely accepted sense of sayings of the Prophet. In so doing, he intervened in ongoing discussions concerning the value of asceticism and sexual abstinence. Al-Junayd’s writings reveal a nuanced approach to the sunna, whereby Sufis must identify those aspects of the sunna that would help rather than hinder their spiritual path. His writings thus take us beyond the (correct) affirmation that early Sufis upheld the law and sunna and allow us to see how Sufis wrestled with the example of the Prophet and the meaning of his life and words for their path to God.
Disease Vector Relative Spatio-Temporal Abundances to Water Bodies and Thermal Fitness Across Malaria Endemic Semi-Arid Areas
Authors: Buxton Mmabaledi , Wasserman Ryan J , Nyamukondiwa Casper
Published: October 2020

The biophysical environment plays an important role in the spatio-temporal abundance and distribution of mosquitoes. This has implications for the spread of vectors and diseases they cause across diverse landscapes. Here, we assessed vector mosquito abundances in relation to large water bodies, from three malaria districts in a semi-arid environment. Furthermore, we explored thermal limits to activity of the dominant and most medically important malaria vector across malaria-endemic areas. Mosquitoes were trapped near permanent water bodies across different districts. Critical thermal limits (critical thermal-maxima and -minima) to activity of wild adults and 4th instar larvae Anopheles arabiensis (Diptera: Culicidae) were assessed. Our results showed that Anopheles spp. dominate mosquito communities across all three districts, but that their numbers were far greater in Okavango than in other regions. At the Okavango sites, the numbers of Anopheles spp. decreased with distance from main water source. Anopheles spp. sampled in this region comprised Anopheles gambiae (Giles,1902) and Anopheles funestus (Giles, 1900) species complexes, with the former dominating in numbers. Thermal activity assays showed An. arabiensis females had wider thermal tolerance windows than males while larval thermal activity limits differed significantly across space. These results confirm that the Okavango district should be prioritized for vector control measures. Moreover, intervention strategies should consider recommendations for proximity effects to large water bodies, given the differential risk associated with distance from water. The wider thermal window on female vectors has implications for possible future malaria transmission and diverse habitat utilization under changing environments.
Unaccompanied Girls with Precarious Odds
Authors: Hedlund Daniel , Salmonsson Lisa , Sohlberg Tove
Published: October 2020

Statistics made available by the Swedish Migration Agency (SMA) make it possible to follow first-decision outcomes in asylum cases concerning unaccompanied children (types of residence permits granted, percentage of rejections, etc.). Yet, we know little about differences in asylum decision outcomes for unaccompanied children coming to Sweden. Therefore, we wanted to find out how gender, country of origin, and asylum reports are associated with the likelihood of being granted residency. Asylum decisions concerning unaccompanied children were first coded inductively. These codes were later merged into larger categories that were analyzed quantitatively by logistic regression analysis. The data sample consisted of one calendar year of asylum decisions issued by the SMA. Results show that fewer girls than boys were granted asylum, and in fact, girls have an overall lower prospect of being granted residency. Results also display statistically significant gender differences in reported reasons for seeking asylum.
Expanding Refugee Ineligibility: Canada’s Response to Secondary Refugee Movements
Authors: Atak Idil , Abu Alrob Zainab , Ellis Claire
Published: October 2020

In 2019, Canada introduced legislative changes that made asylum seekers ineligible for protection if they have made a previous refugee claim in a country that Canada shares an information-sharing agreement with. Such agreements are currently in place with the US, Australia, the UK, and New Zealand. This article offers a critical assessment of the new ineligibility ground, arguing that the policy is designed to deter secondary refugee movements, particularly those across the Canada–US border which have considerably intensified since 2017. Based on the ‘first safe country’ rule, the new ineligibility ground enables Canada to exclude some asylum seekers from refugee protection without offering any alternative effective protection in Canada. This article demonstrates that the policy is inconsistent with Canada’s obligations under international refugee law.
Listening to the Alice Books
Authors: Vaclavik Kiera
Published: October 2020

Despite the ‘acoustic turn’ providing ‘a corrective to the visualist bias of much scholarship on modern and postmodern culture’, the Alice books and their author have been almost exclusively seen rather than heard by critics to date. Prompted by a collaboration with composer Paul Rissmann which resulted in a concert suite performed by the London Symphony Orchestra in 2015, in this article I undertake the first detailed exploration of the sonic dimension of these texts. This merits attention not only because of its very emphatic foregrounding within the frame narrative of Wonderland, but also because of authorial interests and preoccupations, and the quickly established and still enduring musical afterlife of the books. Although triggered in Wonderland by the pastoral and by the sounds of the natural world, a process of translation or transformation renders a very different sonic landscape within the narrative proper. The bucolic frames an often raucous modern core, with Carroll embedding not only catchy anodyne melodies but also the sounds of the everyday and of contemporary industry, transport, and material culture. Attending to the rich and varied soundscape of Carroll’s best-known works sheds new light on their widely examined images but also restores a key dimension of the texts, essential to their Victorian reception. The detailed exploration of the full range of sonic phenomena within the works, from music to noise, and spanning both sound and silence, opens up new relationships between Carroll and his Victorian contemporaries, as well as further reinforcing his status as a proto-modernist.
Predicted rates of merging neutron stars in galaxies
Authors: Molero Marta , Simonetti Paolo , Matteucci Francesca , della Valle Massimo
Published: October 2020

We compute rates of merging neutron stars (MNS) in different galaxies, as well as the cosmic MNS rate in different cosmological scenarios. Our aim is to provide predictions of kilonova rates for future observations both at low and high redshift. In the adopted galaxy models, the production of r-process elements either by MNS or core-collapse supernovae is taken into account. To compute the MNS rates, we adopt either a constant total time delay for merging (10 Myr) or a distribution function of such delays. We conclude (i) the observed present time MNS rate in our Galaxy is well reproduced either with a constant time delay or a distribution function ∝t−1. (ii) The [Eu/Fe] versus [Fe/H] relation can be well reproduced with only MNS, if the time delay is short and constant. If a distribution function of delays is adopted, core-collapse supernovae are also required. (iii) The present time cosmic MNS rate can be well reproduced in several cosmological scenarios. (iv) Spiral galaxies are the major contributors to the cosmic MNS at all redshifts in hierarchical scenarios. In the pure luminosity evolution scenario, the spirals are the major contributors locally, whereas at high redshift ellipticals dominate. (v) The predicted cosmic MNS rate well agrees with the cosmic rate of short gamma-ray bursts, if the distribution function of delays is adopted in a cosmological hierarchical scenario observationally derived. (vi) Future observations of kilonovae in ellipticals will allow us to disentangle among constant or a distribution of time delays and among different cosmological scenarios.
Prospects of probing dark energy with eLISA: Standard versus null diagnostics
Authors: Baral Pratyusava , Roy Soumendra Kishore , Pal Supratik
Published: October 2020

Gravitational waves from supermassive black hole binary mergers along with an electromagnetic counterpart have the potential to shed ‘light’ on the nature of dark energy in the intermediate redshift regime. Accurate measurement of dark energy parameters at intermediate redshift is extremely essential to improve our understanding of dark energy, and to possibly resolve a couple of tensions involving cosmological parameters. We present a Fisher matrix forecast analysis in the context of eLISA to predict the errors for three different cases: the non-interacting dark energy with constant and evolving equation of state (EoS), and the interacting dark sectors with a generalized parametrization. In all three cases, we perform the analysis for two separate formalisms, namely, the standard EoS formalism and the Om parametrization which is a model-independent null diagnostic for a wide range of fiducial values in both phantom and non-phantom regions, to make a comparative analysis between the prospects of these two diagnostics in eLISA. Our analysis reveals that it is wiser and more effective to probe the null diagnostic instead of the standard EoS parameters for any possible signature of dark energy at intermediate redshift measurements like eLISA.
Can complex T Tauri star light curves be modelled with star-spots?
Authors: Koen C
Published: October 2020

‘Transiting Exoplanet Survey Satellite’ photometry of 10 young stars with very complex periodic light curves is considered. Previous findings that these cannot be due to dark surface spots are re-evaluated by allowing arbitrarily shaped areas on the stellar surface to have sub-photospheric fluxes. This is done by approximating flux integrals by sums over surface elements. The unknown ratios of spot to photospheric fluxes are determined by lasso or ridge regression procedures. It is found that almost all light curves can be modelled very accurately in this way. The usual, if rarely stated, caveat applies – star-spot models presented in the paper are not unique.
Simulated predictions for H i at z = 3.35 with the Ooty Wide Field Array (OWFA) – II. Foreground avoidance
Authors: Chatterjee Suman , Bharadwaj Somnath , Marthi Visweshwar Ram
Published: October 2020

Considering the upcoming OWFA, we use simulations of the foregrounds and the z = 3.35 H i 21-cm intensity mapping signal to identify the (k⊥, k∥) modes where the expected 21-cm power spectrum P(k⊥, k∥) is substantially larger than the predicted foreground contribution. Only these uncontaminated k modes are used for measuring P(k⊥, k∥) in the “Foreground Avoidance” technique. Though the foregrounds are largely localized within a wedge. we find that the small leakage beyond the wedge surpasses the 21-cm signal across a significant part of the (k⊥, k∥) plane. The extent of foreground leakage is extremely sensitive to the frequency window function used to estimate P(k⊥, k∥). It is possible to reduce the leakage by making the window function narrower; however, this comes at the expense of losing a larger fraction of the 21-cm signal. It is necessary to balance these competing effects to identify an optimal window function. Considering a broad class of cosine window functions, we identify a six term window function as optimal for 21-cm power spectrum estimation with OWFA. Considering only the k modes where the expected 21-cm power spectrum exceeds the predicted foregrounds by a factor of 100 or larger, a $5\, \sigma$ detection of the binned power spectrum is possible in the k-ranges $0.18 \le k \le 0.3 \, {\rm Mpc}^{-1}$ and $0.18 \le k \le 0.8 \, {\rm Mpc}^{-1}$ with 1000–2000  and 104 h of observation, respectively.
Gamma-ray bursts: not so much deadlier than we thought
Authors: Thomas Brian C , Atri Dimitra , Melott Adrian L
Published: October 2020

We analyse the additional effect on planetary atmospheres of recently detected gamma-ray burst afterglow photons in the range up to 1 TeV. For an Earth-like atmosphere, we find that there is a small additional depletion in ozone versus that modeled for only prompt emission. We also find a small enhancement of muon flux at the planet surface. Overall, we conclude that the additional afterglow emission, even with TeV photons, does not result in a significantly larger impact over that found in past studies.
Stars and gas in the most metal-poor galaxies – I. COS and MUSE observations of SBS 0335−052E
Authors: Wofford Aida , Vidal-García Alba , Feltre Anna , Chevallard Jacopo , Charlot Stéphane , Stark Daniel P , Herenz Edmund C , Hayes Matthew
Published: October 2020

Among the nearest most metal-poor starburst-dwarf galaxies known, SBS 0335−052E is the most luminous in integrated nebular He ii λ4686 emission. This makes it a unique target to test spectral synthesis models and spectral interpretation tools of the kind that will be used to interpret future rest-frame UV observations of primeval galaxies. Previous attempts to reproduce its He ii λ4686 luminosity found that X-ray sources, shocks, and single Wolf–Rayet stars are not main contributors to the He ii-ionizing budget; and that only metal-free single rotating stars or binary stars with a top-heavy IMF and an unphysically low metallicity can reproduce it. We present new UV (COS) and optical (MUSE) spectra that integrate the light of four super star clusters in SBS 0335−052E. Nebular He ii, [C iii], C iii], C iv, and O iii] UV emission lines with equivalent widths between 1.7 and 5 Å and a C iv λλ1548, 1551 P-Cygni like profile are detected. Recent extremely metal-poor shock + precursor models and binary models fail to reproduce the observed optical emission-line ratios. We use different sets of UV and optical observables to test models of constant star formation with single non-rotating stars that account for very massive stars as blueshifted O v λ1371 absorption is present. Simultaneously fitting the fluxes of all high-ionization UV lines requires an unphysically low metallicity. Fitting the P-Cygni like + nebular components of C iv λλ1548, 1551 does not constrain the stellar metallicity and time since the beginning of star formation. We obtain 12+log(O/H)$\, = 7.45\pm 0.04$ and log(C/O)$\, = -0.45^{+0.03}_{-0.04}$ for the galaxy. Model testing would benefit from higher spatial resolution UV and optical spectroscopy of the galaxy.
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens
Authors: Gatt Yair E , Margalit Hanah
Published: October 2020

Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation
Authors: Meisig Johannes , Dreser Nadine , Kapitza Marion , Henry Margit , Rotshteyn Tamara , Rahnenführer Jörg , Hengstler Jan G , Sachinidis Agapios , Waldmann Tanja , Leist Marcel , Blüthgen Nils
Published: October 2020

Thousands of transcriptome data sets are available, but approaches for their use in dynamic cell response modelling are few, especially for processes affected simultaneously by two orthogonal influencing variables. We approached this problem for neuroepithelial development of human pluripotent stem cells (differentiation variable), in the presence or absence of valproic acid (signaling variable). Using few basic assumptions (sequential differentiation states of cells; discrete on/off states for individual genes in these states), and time-resolved transcriptome data, a comprehensive model of spontaneous and perturbed gene expression dynamics was developed. The model made reliable predictions (average correlation of 0.85 between predicted and subsequently tested expression values). Even regulations predicted to be non-monotonic were successfully validated by PCR in new sets of experiments. Transient patterns of gene regulation were identified from model predictions. They pointed towards activation of Wnt signaling as a candidate pathway leading to a redirection of differentiation away from neuroepithelial cells towards neural crest. Intervention experiments, using a Wnt/beta-catenin antagonist, led to a phenotypic rescue of this disturbed differentiation. Thus, our broadly applicable model allows the analysis of transcriptome changes in complex time/perturbation matrices.
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies
Authors: Yue Zongliang , Zhang Eric , Xu Clark , Khurana Sunny , Batra Nishant , Dang Son Do Hai , Cimino James J , Chen Jake Y
Published: October 2020

PAGER-CoV (http://discovery.informatics.uab.edu/PAGER-CoV/) is a new web-based database that can help biomedical researchers interpret coronavirus-related functional genomic study results in the context of curated knowledge of host viral infection, inflammatory response, organ damage, and tissue repair. The new database consists of 11 835 PAGs (Pathways, Annotated gene-lists, or Gene signatures) from 33 public data sources. Through the web user interface, users can search by a query gene or a query term and retrieve significantly matched PAGs with all the curated information. Users can navigate from a PAG of interest to other related PAGs through either shared PAG-to-PAG co-membership relationships or PAG-to-PAG regulatory relationships, totaling 19 996 993. Users can also retrieve enriched PAGs from an input list of COVID-19 functional study result genes, customize the search data sources, and export all results for subsequent offline data analysis. In a case study, we performed a gene set enrichment analysis (GSEA) of a COVID-19 RNA-seq data set from the Gene Expression Omnibus database. Compared with the results using the standard PAGER database, PAGER-CoV allows for more sensitive matching of known immune-related gene signatures. We expect PAGER-CoV to be invaluable for biomedical researchers to find molecular biology mechanisms and tailored therapeutics to treat COVID-19 patients.
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
Authors: Moretti Sébastien , Tran Van Du T , Mehl Florence , Ibberson Mark , Pagni Marco
Published: October 2020

MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).
Radiological assessment schedule for high-grade glioma patients during the surveillance period using parametric modeling
Authors: Ji So Young , Lee Jongjin , Lee Joo Ho , Lee Soon-Tae , Won Jae Kyung , Kim Jin Wook , Kim Yong Hwy , Kim Tae Min , Choi Seung Hong , Park Sung-Hye , Kim Yongdai , Park Chul-Kee
Published: October 2020

Background

An optimal radiological surveillance plan is crucial for high-grade glioma (HGG) patients, which is determined arbitrarily in daily clinical practice. We propose the radiological assessment schedule using a parametric model of standardized progression-free survival (PFS) curves.

Methods

A total of 277 HGG patients (178 glioblastoma [GBM] and 99 anaplastic astrocytoma [AA]) from a single institute who completed the standard treatment protocol were enrolled in this cohort study and retrospectively analyzed. The patients were stratified into each layered risk group by genetic signatures and residual mass or through recursive partitioning analysis. PFS curves were estimated using the piecewise exponential survival model. The criterion of a 10% progression rate among the remaining patients at each observation period was used to determine the optimal radiological assessment time point.

Results

The optimal follow-up intervals for MRI evaluations of isocitrate dehydrogenase (IDH) wild-type GBM was every 7.4 weeks until 120 weeks after the end of standard treatment, followed by a 22-week inflection period and every 27.6 weeks thereafter. For the IDH mutated GBM, scans every 13.2 weeks until 151 weeks are recommended. The optimal follow-up intervals were every 22.8 weeks for IDH wild-type AA, and 41.2 weeks for IDH mutated AA until 241 weeks. Tailored radiological assessment schedules were suggested for each layered risk group of the GBM and the AA patients.

Conclusions

The optimal schedule of radiological assessments for each layered risk group of patients with HGG could be determined from the parametric model of PFS.
Mexico City
Authors: Leal Martínez Alejandra María
Published: October 2020

Numerous urban scholars have been studying Mexico City—the capital of Mexico—since at least the 1970s, drawn to its remarkable growth during the second half of the 20th century and to its specific patterns of urbanization. The city is located at more than 7,000 feet above sea level in the southern section of a large, enclosed basin known as the Valley of Mexico. Its name officially designates what until recently was the Federal District, an area of 550 square miles divided into sixteen administrative jurisdictions and which, until 1997, lacked a democratically elected government. A 2016 reform transformed Mexico City into the country’s thirty-second state. In common usage, the name Mexico City also refers to the greater Mexico City Metropolitan Area, which as of 2010 also included fifty-nine adjacent municipalities in the State of Mexico and one in the State of Hidalgo, with a total extent of nearly 3,100 square miles. According to the 2010 census, Mexico City’s population is around nine million, while the greater Metropolitan Area has more than twenty million inhabitants. The city was founded in 1521 on the ruins of the Aztec capital on a small island in Lake Texcoco and gradually expanded onto the increasingly desiccated lakebed, which has created a particular set of environmental problems, such as constant flooding. Like other major Latin American cities, Mexico City—and later the Metropolitan Area—grew exponentially after the 1940s, as industrialization attracted massive migration. Its population jumped from three million in 1930 to around fifteen million in 1985. Mexico’s most important city, as well as its political, cultural, and economic center, Mexico City is a study in contrasts. It displays wealth and poverty extremes, world-class architecture next to marginal shantytowns, and a vibrant, cosmopolitan cultural life alongside high criminal rates and seemingly intractable environmental problems, which continue to attract the interest of a wide variety of urban scholars. This bibliography is selective rather than exhaustive. It privileges recent English- and Spanish-language scholarship, but also includes key texts that continue to inform the field, as well as recent urban historiography. It is divided into the main topics covered by urban scholars of Mexico City since the 1970s. These range from urban planning, urban politics, informality, poverty, and marginality, which were dominant themes until the 1980s, to urban protest and social movements, gentrification, and environmental, gender, and cultural studies, which have expanded the field more recently. The author wishes to thank Carlos Humberto Arroyo Batista for his research assistance in elaborating this bibliography.
Urban Sociology
Authors: Monti Daniel J.
Published: October 2020

Urban sociology is among the earliest and richest areas of sociological inquiry. It touches on topics and problems related to the way urban areas develop and the way people live in urban areas. While most of the attention of urban sociologists has been on more contemporary urban settings in Western societies, they’ve shown increasing interest in urban development and urban life in so-called developing countries and the Far East, especially India and China. By nature an interdisciplinary pursuit, five major academic fields contribute to urban sociology: anthropology, economics, history, political science, and social psychology. Specialists in these respective disciplines read and cite each other’s work and borrow from each other’s theoretical insights. One major profession, urban planning, is affiliated with urban sociology. It, too, has its own entry in Oxford Bibliographies in Geography: “Urban Planning and Geography.” Other Oxford Bibliographies touch on themes discussed here. Among them are “The Chicago School of Urban Sociology,” “Suburbanism,” “Gentrification,” “Residential Segregation,” “Community,” “Urban Economics,” “Social Movements in Cities,” and “Riots.” Given the rich disciplinary sources that feed into urban sociology, this area of inquiry probably can be best understood by the themes that allow researchers to connect the disparate kinds of studies they do. The several sections into which this essay is divided have works that reflect one or more of the following four themes: (1) Urban sociologists focus on either the physical development of urban places (i.e., urbanization) or the way of life or culture practiced there (i.e., urbanism). (2) The work of urban sociologists asks how urban places are built and laid out as cities and metropolitan areas. It also asks how urban settlements might be rebuilt or developed so they better serve or complement the way people live there. (3) Some sociologists look at smaller groups of urban dwellers or venues in urban areas such as neighborhoods (i.e., “micro” studies) and other kinds of “communities” such as those one might find in a suburb. Others look at much larger geographic landscapes such as metropolitan areas and urban regions (i.e., “macro” studies). (4) Urban sociologists can be optimistic about the prospects for urban places and people or, more frequently, pessimistic about how well they will fare. The resilience and effectiveness of people living in urban settings are more often subordinated to a view of them as part of a marginalized and less well-regarded group, surviving rather than accomplishing much in the places they live, work, and practice politics.
Smart Growth
Authors: Knaap Gerrit-Jan , Lewis Rebecca , Chakraborty Arnab , June-Friesen Katy
Published: October 2020

In market economies such as the United States and most western nations, land-use and development patterns are influenced by government regulations and investments in infrastructure but determined largely by market forces. Under these conditions, post–World War II development patterns—when the automobile became the dominant form of transportation—became highly dispersed, haphazard, and dominated by low-density development. Scholars and planners have pejoratively characterized this as urban sprawl, to which they attribute adverse social and environmental consequences, such as high rates of farm and forest land consumption, excessive driving and resultant air pollution, costly public infrastructure, and social segmentation. For many years, efforts to combat sprawl were called “growth control” or “growth management” and primarily focused on slowing the rate of urban growth. But in the 1990s in the United States, a new term and set of ideas entered the lexicon of planners, developers, and policy makers: smart growth. Proponents of smart growth aimed to change the focus from stopping or slowing growth to assuring that growth was “smarter” in location, intensity, and form. Although the precise meaning of the term remains ambiguous, the Smart Growth Network—a national alliance of more than thirty private sector, public sector, and nongovernmental organizations—continues to advance the following ten principles: (1) mix land uses; (2) taking advantage of compact building design; (3) creating a wide range of housing opportunities and choices; (4) creating walkable neighborhoods; (5) fostering distinctive, attractive communities with a strong sense of place; (6) preserving open space, farmland, natural beauty, and critical environmental areas; (7) strengthening and directing development toward existing communities; (8) providing a variety of transportation choices; (9) making development decisions predictable, fair, and cost-effective; and (10) encouraging community and stakeholder collaboration in development decisions. Over the past twenty years, scholars have undertaken considerable research to confirm or dispute the virtues of these principles and to understand how best to implement them. Recently, smart growth advocates have begun to address more contemporary challenges, such as climate change, social equity, public health, and more. Smart growth’s underlying principles are now also represented in the popular terminologies of “sustainable development” and “urban resilience” and in broader efforts such as the United Nations 2015 Sustainable Development Goals. This article, however limited in scope to the original set of smart growth principles, traces the history of the concept and presents research that explores the validity of the principles, the challenges of implementation, and the extent of success.
Postcolonial Urbanism
Authors: Ren Julie
Published: October 2020

Postcolonial urbanism encompasses a range of scholarship in urban studies that engages with postcolonial theory, postcoloniality as a historico-political status, and postcolonial criticism of urban theory. There is not a singular concept of postcolonialism. A rudimentary definition of postcolonialism as the study of the lasting effects of being a former colony confines it to a historical category, which dissonant voices have largely displaced. In place of a conceptual uniformity, postcolonial urbanism can rather be understood as a kind of intervention, in terms of both the places and issues at the core of its concern, as well as an intervention into the way that urban research and theory is being generated. Building on postcolonial thought from the 20th century that emerged from a period of decolonial and anticolonial political struggle and largely defined by key scholarship in the humanities, postcolonial urbanism translates these concepts and questions for urban space, urban research and urban theory. The analysis of power, representation, and identity is transmuted for a spatial analysis of urbanization, urban development, and urban life. This is particularly evident in the postcolonial scholarship on urban planning and architecture, which situates the built environment within a contextual postcoloniality or applies a postcolonial lens to analyzing the cultures of planning or architecture. Moreover, the critiques of discipline that postcolonial theory espouses are also adopted in postcolonial urbanism in the watershed of scholarship on issues around knowledge production in urban studies. These have spurred debates around the parochialism of urban theory, the nature of theory, and the comparative approaches that could possibly enrich theoretical developments. In parallel to these epistemological debates is a rich scholarship with a long tradition in area studies that continue to delve into the question of alternative urbanisms, seeing the postcolonial world as determined category of shared experience, which may help generate various forms of “Southern” urbanisms. The key question here is whether postcolonial urbanism serves more as a theoretical intervention into the way that urban theory is generated, or an empirical intervention into the sites and concerns of urban theory. The scholarship shows that these positions are not easily extricated from one another. Out of this lively debate has emerged an outpouring of influential conceptual developments particularly in theorizing urban everyday life around topics like informality, periphery, grey space, waste, and utopia.
Toronto
Authors: Taylor Zack
Published: October 2020

With a greater regional population of eight million residents, Toronto is one of the largest and fastest growing metropolitan areas in North America and Canada’s emergent global city. Toronto is both exceptional and typical in its continental context. Originally an indigenous peoples’ crossroads, a British military garrison and town were established at Toronto in the 1790s and a municipal government was incorporated in 1834. Its 19th- and early-20th-century history of railway and industrial development, and also European immigration, is similar to other cities of similar vintage. While geographically proximate to Midwestern “rustbelt” cities, Toronto evaded their postwar fate; indeed, the region’s growth profile and diversified manufacturing, services, and agricultural economy more closely resembles that of postwar boomtowns in the American New South and Southwest than formerly dynamic, but now struggling, Great Lakes cities. Once smaller and economically and culturally secondary to Montreal within Canada, greater Toronto is now the country’s largest metropolitan area, predominant economic engine, and English-speaking cultural center. Toronto is further distinguished from many American cities in having become a hyper-diverse attractor of immigrants since the 1980s. A predominately white and British city as recently as 1970 (indeed, author Wyndham Lewis characterized Toronto as a “mournful Scottish version of an American city” in 1940), more than half the population of both the central city and the broader region is now foreign born and nonwhite. Toronto is thus a globally significant crucial case in urban immigrant integration and social cohesion. Academic scholarship on Toronto lacks comprehensive coverage and an identifiable progression of schools of thought. Most works focus on illuminating specific historical events or social and economic phenomena rather than situating the city and its development in a broader context. Nonetheless, these works cumulate to illustrate Toronto’s contemporary and historical relevance to urban studies. This article generally excludes comparative works in which Toronto is one of several cases unless the treatment stands on its own. It also excludes works that focus primarily on provincial-level matters, although it should be acknowledged that the Province of Ontario plays a much greater role in the municipal sphere than do other Canadian provincial and American state governments.
Cairo
Authors: Prestel Joseph Ben
Published: October 2020

Much like the vibrant city on the Nile itself, scholarship on Cairo has seen many changes in recent years. The continued growth of the Egyptian capital, the transformation of its cityscape, as well as the political transitions of the last decade have contributed to shifting depictions of the city. Between the Egyptian revolution of 2011 and the rise of Abdel Fattah al-Sisi to the Egyptian presidency, a few years could fundamentally change authors’ perspectives. The magnitude of change is probably best reflected in the new capital that the Egyptian government is building approximately 40 kilometers east of Cairo. Scholars have described this project as an “anti-Cairo” and its conclusion is set to affect the city. Demographic developments add to the image of transformation. Since the publication of Janet Abu-Lughod’s groundbreaking study The City Victorious in 1971, Cairo’s number of inhabitants has grown from around seven million to between fifteen and twenty-five million. In tandem with demographic growth, the city has been expanding into neighboring governorates along the Nile. Real estate companies and the state have also continued to develop new satellite cities at a distance from previously urbanized land. The Egyptian capital now extends much further along the Nile and also reaches deeper into the desert west and east of the city than it did five decades ago. While mapping is a politically fraught issue, David Sims estimated in 2010 that the newly planned towns around Cairo alone extend over a combined area of 1,174 square kilometers (Sims 2010, p. 172). This shifting terrain sets limits to any attempt at a comprehensive overview of literature about Cairo. Instead, the present bibliography seeks to capture continuity and change in scholarly literature on the city. It contains older works, which still inspire thinking about Cairo, as well as studies that focus on the city’s recent transformation over the past ten years. The bibliography is split into eight parts: General Overviews; Urban Planning, Architecture, and the Cityscape; The State and Urban Politics; Economy and Inequality; History; Neighborhoods; Gender and Sexuality; and Religion. This division reflects some of the priorities of scholarship about the city; it illustrates under which headings scholars have thought about Cairo. Such priorities have themselves invited criticism. Several titles in the categories of history or gender and sexuality demonstrate how the focus of scholarship has changed over time. In some studies, the dividing line between research on Cairo and Egypt also tends to become blurred. The particular political, cultural, and economic centralization of the country contributes to publications that are largely based on observations in Cairo, but are framed in terms of analyses of the whole country. It is therefore important to highlight that the city’s centrality endows it with an especially prominent place in studies of Egypt at large.