bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of cancer omics data: a selective review of statistical techniques
Authors: Ma Chenjin , Wu Mengyun , Ma Shuangge
Published: December 2021

Cancer is an omics disease. The development in high-throughput profiling has fundamentally changed cancer research and clinical practice. Compared with clinical, demographic and environmental data, the analysis of omics data—which has higher dimensionality, weaker signals and more complex distributional properties—is much more challenging. Developments in the literature are often ‘scattered’, with individual studies focused on one or a few closely related methods. The goal of this review is to assist cancer researchers with limited statistical expertise in establishing the ‘overall framework’ of cancer omics data analysis. To facilitate understanding, we mainly focus on intuition, concepts and key steps, and refer readers to the original publications for mathematical details. This review broadly covers unsupervised and supervised analysis, as well as individual-gene-based, gene-set-based and gene-network-based analysis. We also briefly discuss ‘special topics’ including interaction analysis, multi-datasets analysis and multi-omics analysis.
DSGAT: predicting frequencies of drug side effects by graph attention networks
Authors: Xu Xianyu , Yue Ling , Li Bingchun , Liu Ying , Wang Yuan , Zhang Wenjuan , Wang Lin
Published: December 2021

A critical issue of drug risk–benefit evaluation is to determine the frequencies of drug side effects. Randomized controlled trail is the conventional method for obtaining the frequencies of side effects, while it is laborious and slow. Therefore, it is necessary to guide the trail by computational methods. Existing methods for predicting the frequencies of drug side effects focus on modeling drug–side effect interaction graph. The inherent disadvantage of these approaches is that their performance is closely linked to the density of interactions but which is highly sparse. More importantly, for a cold start drug that does not appear in the training data, such methods cannot learn the preference embedding of the drug because there is no link to the drug in the interaction graph. In this work, we propose a new method for predicting the frequencies of drug side effects, DSGAT, by using the drug molecular graph instead of the commonly used interaction graph. This leads to the ability to learn embeddings for cold start drugs with graph attention networks. The proposed novel loss function, i.e. weighted $\varepsilon$-insensitive loss function, could alleviate the sparsity problem. Experimental results on one benchmark dataset demonstrate that DSGAT yields significant improvement for cold start drugs and outperforms the state-of-the-art performance in the warm start scenario. Source code and datasets are available at https://github.com/xxy45/DSGAT.
Comparing transmembrane protein structures with ATOLL
Authors: Jacquemard Célien , Bret Guillaume , Grutter Thomas , Kellenberger Esther
Published: December 2021

The 3D structure of transmembrane helices plays a key role in the function of membrane proteins. While visual inspection can usually discern the distinctive features of a helix bundle, simply translating them into a 2D diagram can be difficult. ATOLL (Aligned Transmembrane dOmains Layout fLattening) projects the helix bundle onto the lipid bilayer plane, thereby facilitating the comparison of different structures of the same membrane protein or structures of different membrane proteins.

Availability and implementation

ATOLL is a program written in Python3. The source code is freely available on the web at https://github.com/LIT-CCM-lab/ATOLL. ATOLL is implemented into a web server (https://atoll.drugdesign.unistra.fr/).

Supplementary information

Supplementary data are available at Bioinformatics online.
Silencing of amygdala circuits during sepsis prevents the development of anxiety-related behaviours
Authors: Bourhy Lena , Mazeraud Aurélien , Costa Luis H. A. , Levy Jarod , Rei Damien , Hecquet Estéban , Gabanyi Ilana , Bozza Fernando A. , Chrétien Fabrice , Lledo Pierre-Marie , Sharshar Tarek , Lepousez Gabriel
Published: December 2021

Sepsis is a life-threatening condition induced by a deregulated host response to severe infection. Post-sepsis syndrome includes long-term psychiatric disorders, such as persistent anxiety and post-traumatic stress disorder, whose neurobiological mechanisms remain unknown.

Using a reference mouse model of sepsis, we showed that mice that recovered from sepsis further developed anxiety-related behaviours associated with an exaggerated fear memory. In the brain, sepsis induced an acute pathological activation of a specific neuronal population of the central nucleus of the amygdala, which projects to the ventral bed nucleus of the stria terminalis. Using viral-genetic circuit tracing and in vivo calcium imaging, we observed that sepsis induced persistent changes in the connectivity matrix and in the responsiveness of these central amygdala neurons projecting to the ventral bed nucleus of the stria terminalis. The transient and targeted silencing of this subpopulation only during the acute phase of sepsis with a viral pharmacogenetic approach, or with the anti-epileptic and neuroprotective drug levetiracetam, prevented the subsequent development of anxiety-related behaviours.

Specific inhibition of brain anxiety and fear circuits during the sepsis acute phase constitutes a preventive approach to preclude the post-infection psychiatric outcomes.
Normative intracranial EEG maps epileptogenic tissues in focal epilepsy
Authors: Bernabei John M , Sinha Nishant , Arnold T Campbell , Conrad Erin , Ong Ian , Pattnaik Akash R , Stein Joel M , Shinohara Russell T , Lucas Timothy H , Bassett Dani S , Davis Kathryn A , Litt Brian
Published: December 2021

Planning surgery for patients with medically refractory epilepsy often requires recording seizures using intracranial EEG. Quantitative measures derived from interictal intracranial EEG yield potentially appealing biomarkers to guide these surgical procedures; however, their utility is limited by the sparsity of electrode implantation as well as the normal confounds of spatiotemporally varying neural activity and connectivity. We propose that comparing intracranial EEG recordings to a normative atlas of intracranial EEG activity and connectivity can reliably map abnormal regions, identify targets for invasive treatment and increase our understanding of human epilepsy.

Merging data from the Penn Epilepsy Center and a public database from the Montreal Neurological Institute, we aggregated interictal intracranial EEG retrospectively across 166 subjects comprising >5000 channels. For each channel, we calculated the normalized spectral power and coherence in each canonical frequency band. We constructed an intracranial EEG atlas by mapping the distribution of each feature across the brain and tested the atlas against data from novel patients by generating a z-score for each channel. We demonstrate that for seizure onset zones within the mesial temporal lobe, measures of connectivity abnormality provide greater distinguishing value than univariate measures of abnormal neural activity. We also find that patients with a longer diagnosis of epilepsy have greater abnormalities in connectivity. By integrating measures of both single-channel activity and inter-regional functional connectivity, we find a better accuracy in predicting the seizure onset zones versus normal brain (area under the curve = 0.77) compared with either group of features alone.

We propose that aggregating normative intracranial EEG data across epilepsy centres into a normative atlas provides a rigorous, quantitative method to map epileptic networks and guide invasive therapy. We publicly share our data, infrastructure and methods, and propose an international framework for leveraging big data in surgical planning for refractory epilepsy.
Site and land-use associations of soil bacteria and fungi define core and indicative taxa
Authors: Gschwend Florian , Hartmann Martin , Mayerhofer Johanna , Hug Anna-Sofia , Enkerli Jürg , Gubler Andreas , Meuli Reto G , Frey Beat , Widmer Franco
Published: December 2021

Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.
Gap-com: general model selection criterion for sparse undirected gene networks with nontrivial community structure
Authors: Kuismin Markku , Dodangeh Fatemeh , Sillanpää Mikko J
Published: December 2021

We introduce a new model selection criterion for sparse complex gene network modeling where gene co-expression relationships are estimated from data. This is a novel formulation of the gap statistic and it can be used for the optimal choice of a regularization parameter in graphical models. Our criterion favors gene network structure which differs from a trivial gene interaction structure obtained totally at random. We call the criterion the gap-com statistic (gap community statistic). The idea of the gap-com statistic is to examine the difference between the observed and the expected counts of communities (clusters) where the expected counts are evaluated using either data permutations or reference graph (the Erdős-Rényi graph) resampling. The latter represents a trivial gene network structure determined by chance. We put emphasis on complex network inference because the structure of gene networks is usually nontrivial. For example, some of the genes can be clustered together or some genes can be hub genes. We evaluate the performance of the gap-com statistic in graphical model selection and compare its performance to some existing methods using simulated and real biological data examples.
Database of glutamate-gated chloride (GluCl) subunits across 125 nematode species: patterns of gene accretion and sequence diversification
Authors: O’Halloran Damien M
Published: December 2021

Glutamate-gated chloride channels belong to the Cys-loop receptor superfamily. Glutamate-gated chloride channels are activated by glutamate and form substrates for the antiparasitic drugs from the avermectin family. Glutamate-gated chloride channels are pentameric, and each subunit contains an N-terminal extracellular domain that binds glutamate and 4 helical transmembrane domains, which contain binding sites for avermectin drugs. In order to provide more insight into phylum-wide patterns of glutamate-gated chloride subunit gene expansion and sequence diversity across nematodes, we have developed a database of predicted glutamate-gated chloride subunit genes from 125 nematode species. Our analysis into this dataset described assorted patterns of species-specific glutamate-gated chloride gene counts across different nematodes as well as sequence diversity in key residues thought to be involved in avermectin binding.
Triple Linking Numbers and Heegaard Floer Homology
Authors: Gorsky Eugene , Lidman Tye , Liu Beibei , Moore Allison H
Published: December 2021

We establish some new relationships between Milnor invariants and Heegaard Floer homology. This includes a formula for the Milnor triple linking number from the link Floer complex, detection results for the Whitehead link and Borromean rings, and a structural property of the $d$-invariants of surgeries on certain algebraically split links.
Evolution and emergence: higher order information structure in protein interactomes across the tree of life
Authors: Klein Brennan , Hoel Erik , Swain Anshuman , Griebenow Ross , Levin Michael
Published: December 2021

The internal workings of biological systems are notoriously difficult to understand. Due to the prevalence of noise and degeneracy in evolved systems, in many cases the workings of everything from gene regulatory networks to protein–protein interactome networks remain black boxes. One consequence of this black-box nature is that it is unclear at which scale to analyze biological systems to best understand their function. We analyzed the protein interactomes of over 1800 species, containing in total 8 782 166 protein–protein interactions, at different scales. We show the emergence of higher order ‘macroscales’ in these interactomes and that these biological macroscales are associated with lower noise and degeneracy and therefore lower uncertainty. Moreover, the nodes in the interactomes that make up the macroscale are more resilient compared with nodes that do not participate in the macroscale. These effects are more pronounced in interactomes of eukaryota, as compared with prokaryota; these results hold even after sensitivity tests where we recalculate the emergent macroscales under network simulations where we add different edge weights to the interactomes. This points to plausible evolutionary adaptation for macroscales: biological networks evolve informative macroscales to gain benefits of both being uncertain at lower scales to boost their resilience, and also being ‘certain’ at higher scales to increase their effectiveness at information transmission. Our work explains some of the difficulty in understanding the workings of biological networks, since they are often most informative at a hidden higher scale, and demonstrates the tools to make these informative higher scales explicit.
Rifabutin versus rifampicin bactericidal and antibiofilm activities against clinical strains of Staphylococcus spp. isolated from bone and joint infections
Authors: Thill Pauline , Robineau Olivier , Roosen Gabrielle , Patoz Pierre , Gachet Benoit , Lafon-Desmurs Barthélémy , Tetart Macha , Nadji Safia , Senneville Eric , Blondiaux Nicolas
Published: December 2021

Background

Staphylococci account for approximately 60% of periprosthetic joint infections (PJIs). Rifampicin (RMP) combination therapy is generally considered to be the treatment of choice for staphylococcal PJIs but carries an important risk of adverse events and drug–drug interactions. Rifabutin (RFB) shares many of the properties of rifampicin but causes fewer adverse events.

Objectives

To compare the minimal inhibitory concentration (MIC), the minimum bactericidal concentrations (MBC), and the minimum biofilm eradication concentrations (MBEC) of rifabutin and rifampicin for staphylococcal clinical strains isolated from PJIs.

Methods

132 clinical strains of rifampicin-susceptible staphylococci [51 Staphylococcus aureus (SA), 48 Staphylococcus epidermidis (SE) and 33 other coagulase-negative staphylococci (CoNS)] were studied. The MBC and the MBEC were determined using the MBEC® Assay for rifabutin and rifampicin and were compared.

Results

When compared with the rifampicin MIC median value, the rifabutin MIC median value was significantly higher for SA (P < 0.05), but there was no statistically significant difference for SE (P = 0.25) and CoNS (P = 0.29). The rifabutin MBC median value was significantly higher than that of rifampicin for SA (P = 0.003) and was lower for SE (P = 0.003) and CoNS (P = 0.03). Rifabutin MBEC median value was statistically lower than that of rifampicin for all strains tested.

Conclusions

Using the determination of MBEC values, our study suggests that rifabutin is more effective than rifampicin against clinical strains of Staphylococcus spp. obtained from PJIs. Using MBECs instead of MICs seems to be of interest when considering biofilms. In vivo higher efficacy of rifabutin when compared with rifampicin needs to be confirmed.
Effect of Quorum Sensing Inducers and Inhibitors on Cytoplasmic Incompatibility Induced byWolbachia(Rickettsiales: Anaplasmataceae) in American Serpentine Leafminer (Diptera: Agromyzidae): Potential Tool for the Incompatible Insect Technique
Authors: Hidayanti Ardhiani Kurnia , Gazali Achmad , Tagami Yohsuke
Published: December 2021

Agricultural crops around the world are attacked by approximately 3,000–10,000 species of pest insect. There is increasing interest in resolving this problem using environmentally friendly approaches. Wolbachia (Hertig), an insect endosymbiont, can modulate host reproduction and offspring sex through cytoplasmic incompatibility (CI). The incompatible insect technique (IIT) based on CI-Wolbachia is a promising biological control method. Previous studies have reported an association between CI and Wolbachia density, which may involve a quorum sensing (QS) mechanism. In this study, we investigated the effect of manipulating QS in Wolbachia using several chemicals including 3O-C12-HSL; C2HSL; spermidine (QS inducers), 4-phenylbutanoyl; and 4-NPO (QS inhibitors) on American serpentine leafminer (Liriomyza trifolii [Burgess]), an agricultural pest. The results showed that inducing QS with 3O-C12-HSL decreased the proportion of hatched eggs and increased Wolbachia density, whereas QS inhibition with 4-phenylbutanoyl had the opposite effects. Thus, manipulating QS in Wolbachia can alter cell density and the proportion of hatched eggs in the host L. trifolii, thereby reducing the number of insect progeny. These findings provide evidence supporting the potential efficacy of the IIT based on CI-Wolbachia for the environmentally friendly control of insect pest populations.
Spectral analysis of cool white dwarfs accreting from planetary systems: from the ultraviolet to the optical
Authors: Hollands M A , Tremblay P-E , Gänsicke B T , Koester D
Published: December 2021

The accretion of planetary debris into the atmospheres of white dwarfs leads to the presence of metal lines in their spectra. Cool metal-rich white dwarfs, which left the main sequence many Gyr ago, allow the study of the remnants of the oldest planetary systems. Despite their low effective temperatures (Teff), a non-negligible amount of their flux is emitted in the near-ultraviolet (NUV), where many overlapping metal lines can potentially be detected. We have observed three metal-rich cool white dwarfs with the Space Telescope Imaging Spectrograph (STIS) onboard the Hubble Space Telescope, and compare the results determined from the NUV data with those previously derived from the analysis of optical spectroscopy. For two of the white dwarfs, SDSS J1038−0036 and SDSS J1535+1247, we find reasonable agreement with our previous analysis and the new combined fit of optical and NUV data. For the third object, SDSS J0956+5912, including the STIS data leads to a 10 per cent lower Teff, though we do not identify a convincing explanation for this discrepancy. The unusual abundances found for SDSS J0956+5912 suggest that the accreted parent body was composed largely of water ice and magnesium silicates, and with a mass of up to ≃ 2 × 1025 g. Furthermore, SDSS J0956+5912 shows likely traces of atomic carbon in the NUV. While molecular carbon is not observed in the optical, we demonstrate that the large quantity of metals accreted by SDSS J0956+5912 can suppress the C2 molecular bands, indicating that planetary accretion can convert DQ stars into DZs (and not DQZs/DZQs).
Spectral and polarization properties of reflected X-ray emission from black hole accretion discs
Authors: Podgorný J , Dovčiak M , Marin F , Goosmann R , Różańska A
Published: December 2021

X-ray polarimetric missions planned for this decade will significantly enhance our knowledge of compact accreting sources. Observations of the X-ray polarization signal from active galactic nuclei (AGNs) or X-ray binary systems (XRBs) will bring new means to study inner accretion flow in these objects that, together with currently used spectroscopic and timing techniques, will help us to determine better their properties, such as their inclination, orientation, shape, and size of their corona as well as the black hole spin. In this work, we present a yet missing piece in the global polarization models of black hole accretion discs. We compute the reflected X-ray emission from the disc in a local co-moving frame using (1) the radiative transfer code titan to obtain the ionization structure of the disc and (2) the Monte Carlo code stokes that incorporates the physics of absorption, re-emission, and Compton scattering to produce a complete spectropolarimetric output. We present the final Stokes parameters I, Q, and U for a set of photon-indices of the incident primary power-law radiation, the disc ionization parameters, incident and emission angles, for three independent polarization states of the incident coronal X-ray photons with a sufficient resolution in energy to allow for sharp discussion of spectral and polarization properties. We show that the spectral component matches well literature predictions. The polarization degree and angle are in agreement with analytical approximations previously appearing in reflection models and we demonstrate that the polarized reflected X-ray emission can be, locally, quite large in the $2{\!-\!}12\,$ keV band.
Orbital precession of the S2 star in Scalar–Tensor–Vector Gravity
Authors: Della Monica Riccardo , de Martino Ivan , de Laurentis Mariafelicia
Published: December 2021

We have obtained the first constraint of the parameter space of Scalar–Tensor–Vector Gravity using the motion of the S2-star around the supermassive black hole at the centre of the Milky Way, and we did not find any serious tension with General Relativity. We used the Schwarzschild-like metric of Scalar–Tensor–Vector Gravity to predict the orbital motion of S2-star, and to compare it with the publicly available astrometric data, which include 145 measurements of the positions, 44 measurements of the radial velocities of S2-star along its orbit, and only the inferred rate of precession, as the latest GRAVITY data are not yet public. We employed a Markov chain Monte Carlo algorithm to explore the parameter space, and constrained the only one additional parameter of Scalar–Tensor–Vector Gravity to α ≲ 0.662 at 99.7 ${{\ \rm per\ cent}}$ confidence level, where α = 0 reduces this modified theory of gravity to General Relativity.
Radio emission from outflow–cloud interaction and its constraint on tidal disruption event outflow
Authors: Mou Guobin , Wang Tinggui , Wang Wei , Yang Jingjing
Published: December 2021

Tidal disruption event (TDE) can launch an ultrafast outflow. If the black hole is surrounded by large amounts of clouds, outflow–cloud interaction will generate bow shocks, accelerate electrons, and produce radio emission. Here, we investigate the interaction between a non-relativistic outflow and clouds in active galaxies, which is manifested as outflow–BLR (broad-line region) interaction, and can be extended to outflow–torus interaction. This process can generate considerable radio emission, which may account for the radio flares appearing a few months later after TDE outbursts. Benefitting from efficient energy conversion from outflow to shocks and the strong magnetic field, outflow–cloud interaction may play a non-negligible, or even dominating role in generating radio flares in a cloudy circumnuclear environment if the CNM density is no more than 100 times the Sgr A*-like one. In this case, the evolution of radio spectra can be used to directly constrain the properties of outflows.
Persistence, Magnitude, and Patterns of Postacute Symptoms and Quality of Life Following Onset of SARS-CoV-2 Infection: Cohort Description and Approaches for Measurement
Authors: Peluso Michael J , Kelly J Daniel , Lu Scott , Goldberg Sarah A , Davidson Michelle C , Mathur Sujata , Durstenfeld Matthew S , Spinelli Matthew A , Hoh Rebecca , Tai Viva , Fehrman Emily A , Torres Leonel , Hernandez Yanel , Williams Meghann C , Arreguin Mireya I , Ngo Lynn H , Deswal Monika , Munter Sadie E , Martinez Enrique O , Anglin Khamal A , Romero Mariela D , Tavs Jacqueline , Rugart Paulina R , Chen Jessica Y , Sans Hannah M , Murray Victoria W , Ellis Payton K , Donohue Kevin C , Massachi Jonathan A , Weiss Jacob O , Mehdi Irum , Pineda-Ramirez Jesus , Tang Alex F , Wenger Megan A , Assenzio Melissa T , Yuan Yan , Krone Melissa R , Rutishauser Rachel L , Rodriguez-Barraquer Isabel , Greenhouse Bryan , Sauceda John A , Gandhi Monica , Scheffler Aaron Wolfe , Hsue Priscilla Y , Henrich Timothy J , Deeks Steven G , Martin Jeffrey N
Published: December 2021

Background

There is mounting evidence for the presence of postacute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (PASC), but there is limited information on the spectrum, magnitude, duration, and patterns of these sequelae as well as their influence on quality of life.

Methods

We assembled a cohort of adults with a documented history of SARS-CoV-2 RNA positivity at ≥2 weeks past onset of coronavirus disease 2019 (COVID-19) symptoms or, if asymptomatic, first positive test. At 4-month intervals, we queried physical and mental health symptoms and quality of life.

Results

Of the first 179 participants enrolled, 10 were asymptomatic during the acute phase of SARS-CoV-2 infection, 125 were symptomatic but not hospitalized, and 44 were symptomatic and hospitalized. During the postacute phase, fatigue, shortness of breath, concentration problems, headaches, trouble sleeping, and anosmia/dysgeusia were most common through 8 months of observation. Symptoms were typically at least somewhat bothersome and sometimes exhibited a waxing-and-waning course. Some participants experienced symptoms of depression, anxiety, and post-traumatic stress, as well as difficulties with performance of usual activities. The median visual analogue scale rating of general health was lower at 4 and 8 months compared with pre-COVID-19. Two clusters of symptom domains were identified.

Conclusions

Many participants report bothersome symptoms following onset of COVID-19 with variable patterns of persistence and impact on quality of life. The substantial variability suggests the existence of multiple subphenotypes of PASC. A rigorous approach to the prospective measurement of symptoms and functional manifestations sets the stage for the next phase of research focusing on the pathophysiologic causes of the various subgroups of PASC.
Conclusion
Authors: Aronczyk Melissa , Espinoza Maria I.
Published: December 2021

The conclusion, We’re Supposed to Be Engaging, acknowledges that public relations creates, shapes and promotes a politics that is embedded in our major institutions, our common practices of mediated debate, and the way we collectively think about what “the public” is and what it ought to do. This conception of democratic politics is so deeply engrained in our habits of action that even when we fight for better representation of those voices that are continually left unheard or denied participation or the right to engage, we retain its premises instead of attempting to challenge it at its base. Rather than turn to publicity to inform, engage, and mobilize, we call for a return to the authority of scientific models of inquiry in the fields of culture and politics.
Abraham von Franckenberg and the Ancient Wisdom of Rebirth
Authors: Zuber Mike A.
Published: December 2021

This chapter shows how the Silesian nobleman Abraham von Franckenberg linked Jacob Boehme’s spiritual alchemy to the idea of ancient wisdom, as exemplified by the gnostic church father Valentinus. Franckenberg himself experienced a crisis of faith in 1617 and discovered the heterodox devotional literature of his day upon his religious awakening. In the early 1620s, he read many of Boehme’s works in manuscript and met with their author in person repeatedly. Soon after Boehme’s death, Franckenberg composed an epistolary treatise that defended Valentinus against his detractors and presented him as a model Christian who had experienced rebirth. Much like Boehme, Franckenberg described this as spiritual alchemy. In later writings, he frequently alluded to concepts of his spiritual alchemy yet never again presented it as fully as in his early Theophrastia Valentiniana.
Collaboration, Counterfeit, and Calumny in Amsterdam
Authors: Zuber Mike A.
Published: December 2021

This chapter proves that Friedrich Breckling considerably adulterated a text originally composed in the late sixteenth century and embedded aspects of spiritual alchemy within it. Accusations raised among religious dissenters, notably by prophet and poet Quirinus Kuhlmann, and within the republic of letters at large led some of those who owned exemplars of the resulting book, Bartholomaeus Sclei’s Theosophische-Schrifften of 1686, to annotate their copies with information on Breckling’s interventions. Based on three such copies and other sources, several other collaborators and heavily edited passages can be identified. Yet there is reason to believe that even such annotated exemplars considerably underestimated Breckling’s contribution. In particular, the book’s index draws attention to several passages in which spiritual alchemy figures prominently and its bodily consequences are discussed.
The Company State at War
Authors: Sehgal Manu
Published: December 2021

This chapter brings together the distinct constituents of the early colonial order that had been created over the preceding three decades to execute conquest. The final conflict with the Marathas (1803–5) required much more than troops and an unprecedented commitment of financial resources. Disputes between civilian administrators and military officers, between legally subordinate civilian administrations and a politically ambitious Bengal council, and, between military forces mobilized across the shifting boundaries of the Company’s territorial expanse and civil administrators in the locales of western India—all received a more unequivocal response in the Second Anglo-Maratha War. Experiments that had been haltingly devised in response to deep structural problems that routinely surfaced during preceding periods of intensified military conflict were radically addressed. Legal innovations like delegating sweeping unqualified powers to military commanders were combined with the deployment of a politically effective ideology of Francophobia to set the stage for what became the most ambitious political project of conquest crafted in the long eighteenth century—the war against the Marathas.
Reassembling Provincial North India
Authors: Kumar Akshaya
Published: December 2021

This chapter weaves together historical geography and political ethnography, rendering provincial north India within an analytical reassembly. Drawing upon Chris Bayly’s Rulers, Townsmen and Bazaars (2012), along with other historians of South Asia, the chapter situates the north Indian province between empire and nation, contrasting the fluvial regime of colonial and postcolonial governments. It thus arrives at the question of flood-control embankments – and their frequent breaches – as an administrative allegory for the state in mid-Ganga plains of north India. It draws our focus to the role of embankments, as artefacts of administrative and engineering ‘solutions’ to a problem they only aggravated, established the character of state-society relations in the region, and forced a relentless wave of distress migration among the landless or small-landholding castes. The chapter argues that provincial India is dumped in a gulf and bypassed via the infrastructures of global modernity amplifying spatial, economic and infrastructural slippages, which underline the precarities of provincial life.
Training Birth Attendants in India
Authors: Petitet Pascale Hancart
Published: December 2021

This chapter documents the local and global processes of construction, legitimization and delegitimization, and the political uses of the knowledge of traditional birth attendants—TBAs. Based on four years’ ethnographical investigation in Tamil Nadu, this chapter discusses the issue from various points of view. It looks at the debates of actors involved in the national and international public health agendas, Indian movements promoting ‘Natural Childbirth’, and movements in favour of the preservation of traditional systems of medicine. TBAs are variously perceived as wicked mothers whose archaic practices must be controlled, the archetypal ambassadors of traditional knowledge, or as relevant actors bringing together ideal elements of any development activity—locality, community, and low cost. This careful reading of the contemporary social representations of TBAs and of their role reconfigurations offers a lens to examine authoritative knowledge’s social forms, practices, and paradoxes.
Loyalty
Authors: Pentiuc Eugen J.
Published: December 2021

This chapter analyzes the Scriptures in several hymns prescribed for Holy Tuesday, whose theme is faithfulness (loyalty), as shown by the three Jewish youths thrown by Nebuchadnezzar into a fiery furnace but saved by divine intervention, of an angel/son of God (Dan 3). The Theodotion version, which replaces the Septuagint of Daniel in Eastern Orthodox tradition, underscores the three youths’ unconditioned faithfulness (Dan 3:17–18), compared to the seven Maccabee brothers’ martyrdom (2 Macc 7). Thus, the three youths prefigure Christ’s perfect faithfulness tested through suffering up to the cross. Moreover, the lection Job 1:13–22 prescribed for this day points to Job as another type of the faithful Christ. The lection Matt 25:1–13 (parable of the ten bridesmaids) reminds one again of watchfulness, this time as prerequisite to faithfulness. The hymnographers interconnect the fiery furnace episode with the burning bush story (Exod 3).
Key Features and Hermeneutical Procedures
Authors: Pentiuc Eugen J.
Published: December 2021

This chapter makes use of all the data gathered over the six previous chapters by lexical-biblical-theological analyses of selected hymns. The final chapter is a compilation of key features and hermeneutical procedures of the “liturgical exegesis,” prefaced by a discussion on “liturgized Bible” and several Bible collections used by liturgists (Prophetologion, lectionaries, Psalter, etc.). For a better understanding of the notion of liturgized Bible and its correlative, liturgical exegesis, the chapter proposes an analogy between liturgical exegesis and the early-twentieth-century art style of cubism. Among the key features of liturgical exegesis are aural (hymnography) and visual (iconography) media, integration, collaboration, and actualization. Among hermeneutical procedures are hermeneutical pointers, intertextualities, and typologies. The typologies used by Byzantine hymnographers may be chiastic, reciprocal, embedded, converted, and meta-typologies. The chapter concludes with a list of dissimilarities between patristic biblical commentaries and liturgical exegesis.
Discourse and Discipline
Authors: Tribe Keith
Published: December 2021

This chapter advances the claim that to understand the development of economic knowledge from the mid-nineteenth to the mid-twentieth century, one needs to understand the new location that this knowledge found: the modern university. Broad questions of ‘education and economy’ in industrialising societies are raised and placed in an international context. Following on from this, existing work on the ‘institutionalisation’ of economics is reviewed, emphasising the need for detailed knowledge of institutional structures—what was taught, how it was taught, the sources of student demand, and the attitude of employers—if we are to adequately capture the dynamics of an emerging discipline.
The Moral Sciences Tripos and Cambridge Political Economy
Authors: Tribe Keith
Published: December 2021

The Cambridge Economics Tripos (an honours degree) was created in 1903 by detaching the teaching of economics in Cambridge from the Moral Sciences Tripos, a broad degree including logic, psychology, and politics and ethics. To understand why Alfred Marshall sought to detach the teaching of economics in this way we need to understand both the nature of this undergraduate programme of study, as well as the model that he sought to emulate: the Mathematical Tripos. This had been until mid-century the primary Cambridge qualification, and rather than a training in mathematics per se, its examination sought to foster a particular intellectual discipline. Students were trained in groups, usually by non-college private ‘coaches’, who drilled students in techniques with whose aid they might solve the questions put to them during several days of examinations. Good students became adept at the speedy selection of the appropriate technique and its application to a given problem. By contrast, the Moral Sciences Tripos was organised around the interpretation of set (canonical) books, and so did not foster this problem-solving approach.
Higher Commercial Education in Great Britain and Ireland
Authors: Tribe Keith
Published: December 2021

Intermediate-level adult and commercial education was well established in Manchester and Liverpool by the last third of the nineteenth century, but the first dedicated Faculty of Commerce was founded in Birmingham in 1902, headed by William Ashley. There was, however, little local support for the initiative, which was moreover aimed at school-leavers, and the Faculty of Commerce created in Manchester shortly afterwards had much greater early success. The teaching of commerce in British and Irish universities was established by the 1920s, but there was a general failure to establish a curriculum and develop supporting texts and journals. By the later 1940s these early foundations were increasingly teaching economics, indicating the way in which commercial education in Britain was mainly a vehicle for the development of the teaching of economics.
Agnes de Mille on Broadway: 1943–1945
Authors: Gennaro Liza
Published: December 2021

Examination of Agnes de Mille as a radical dance maker in her choreographic trifecta—Oklahoma! (1943), One Touch of Venus (1943), and Bloomer Girl (1944)—reveals an ideological shift in the production of dance on Broadway and the development of a paradigm for making dances in the musical theater. This chapter further explores de Mille’s ability to employ dance as a medium for presenting social commentary, developing character, and creating a space for female spectatorship. Her artistic project required dancers who were not merely technicians but rather actor-dancers capable of embodying character and expressing legible story through dance. Displacing the stable of Broadway chorus men and women, de Mille introduced the actor-dancer to the commercial stage, thereby developing some of the greatest dance talents of the twentieth century, including Joan McCracken, Bambi Linn, Sono Osato, and James Mitchell. Selected dances from One Touch of Venus (1943), Bloomer Girl (1944), and Carousel (1945) are analyzed.
Broadway Dance
Authors: Gennaro Liza
Published: December 2021

Acknowledging the 1980s HIV/AIDS crisis and the deaths of hundreds of would-be choreographers, this chapter explores the trauma experienced by the dance and theater communities as a defining moment in the history of Broadway dance. I examine the advent of Broadway outsiders, post-modernist Bill T. Jones (Spring Awakening [2006]) and physical theatre practitioner, Steven Hoggett (American Idiot [2010] [2012], Once [2012], The Last Ship [2014]) onto Broadway and assess the diminishment of systems created by de Mille and Robbins. I also analyze Broadway insiders Savion Glover (Bring In ‘Da Noise, Bring in ‘Da Funk [1996], Shuffle Along, The Making of the Musical Sensation of 1921 And All That Followed [2016]), Andy Blankenbuehler (In the Heights [2008], Hamilton [2015]), Sergio Trujillo (Memphis [2009], Hands on a Hardbody [2013]), and Lorin Latarro (Waitress [2016]). I investigate how these four negotiate the systems of Robbins and Fosse while at the same time absorbing the influx of ideas coming from physical theatre Finally, the chapter looks at contemporary dance choreographer Camille Brown, who possesses an exceptional ability to discover fresh interpretations of time-worn dance vocabularies and to tell stories with invented movement. I contend that Brown is the latest choreographer using Broadway as a vehicle for inventive dance and setting a new standard of dance excellence and innovation in musical theater.
Corn Politics
Authors: Hale-Dorrell Aaron T.
Published: December 2021

Industrial farming proved effective in diverse social, economic, and environmental conditions, but in the Soviet Union it suffered from impediments imposed by the country’s political and economic formations. Khrushchev’s considerable power ensured that the Communist Party and government formally adopted his policies. This required subordinates to appear to act accordingly by planting corn, but many complied only outwardly while quietly pursuing alternative goals. Fulfilling plans to plant a set number of hectares of corn, they did little to ensure that these plantings produced an economically viable harvest. Harvests, productivity, and measures of production cost fell far short of Khrushchev’s high expectations, a failure for which he deserves some blame, rather than all of it. In truth, he unsuccessfully fought constant battles with opponents whose foot-dragging and dissembling are signs of systemic failings larger than any one leader or program.
Better Living through Corn
Authors: Hale-Dorrell Aaron T.
Published: December 2021

The almost endless propaganda surrounding corn during Khrushchev’s crusade had two related phases. The journals, newspapers, radio, pamphlets, posters, and films comprising the Soviet Union’s mass media sought to convince the farmworkers, specialists, students, and other citizens doing the actual labor of growing corn that the crop was worthy of heroic efforts. Concurrently, this propaganda machine touted corn as a harbinger of prosperity and abundance to urban audiences who rarely encountered agricultural production. Using text and images to persuade audiences that “the queen of the fields” was in fact a “miracle-worker,” the mass-media blitz raised expectations that full store shelves were just around the corner. When broken, these promises provoked bitter reaction evidenced by the jokes that citizens told and the derision they heaped on its advocate by calling him a kukuruznik, or “corn-man.”
American Technology, Soviet Practice
Authors: Hale-Dorrell Aaron T.
Published: December 2021

Khrushchev’s adoption of industrial corngrowing depended on the industrial enterprises that manufactured machines, processed seeds, and supplied chemicals, all under the control of the bureaucracies in charge of the economy. Vital to any policy’s success, they constrained initiatives by implementing them unsystematically. A study of programs to manufacture farm machinery and produce high-yielding hybrid seeds—each derived from American know-how—reveals these workings of the state-run economy. The latter program, moreover, challenged Trofim Lysenko, whose pseudoscientific dogmas rejected principles of classical genetics required to produce the seeds. Addressing Khrushchev, agricultural experts argued against Lysenko by showing that the American seeds produced yields 30 percent higher than those of conventional seeds. Khrushchev hoped to quickly move these technologies from test station to farm, but his initiatives faltered. Facing reforms designed to make them more responsive, the bureaucracies dragged their feet and eventually coalesced into an interest group supporting Khrushchev’s ouster in 1964.
A Brain Listening to Itself
Authors: Bernini Marco
Published: December 2021

The ubiquitous presence of ambiguous voices in Beckett’s work remains an enduring mystery. The narrative work is no exception, to the point that Beckett’s fiction after Murphy (1938) can be read as, to quote The Unnamable (1953), “entirely a matter of voices; no other metaphor is appropriate” (319). Given the alien qualities of these voices, their intrusive independent agency, and their sometimes tormenting phenomenology, two frameworks of interpretation have so far prevailed. On the one hand, there are narratologists such as Brian Richardson (2006) who have proposed an “unnatural” reading of these voices, by arguing that these alien, multiple, sourceless voices cannot be traced back or ascribed to any actual experience within the human domain; that they cannot be “naturalized” (Culler 1975; 2018; see also Fludernik 1996) by the reader. On the other hand, there is a long-standing “pathological” framework, which sees voices in Beckett’s work as a fictional rendering of a wide range of experiences associated with mental illnesses, mostly of auditory-verbal hallucinations (AVHs) typical of schizophrenia. This chapter suggests that an alternative, natural, and non-pathological experience is the target of Beckett’s fictional cognitive models having voices as core modeling elements. By drawing on contemporary cognitive research on inner speech (roughly speaking, the activity of silently talking to, with and within oneself), it is advocated that voices in Beckett’s models target the working of inner speech, only defamiliarized or, as we shall see, “detuned” as a modeling alteration to explore its functioning within human cognition.
Synesthetic Innerscapes
Authors: Bernini Marco
Published: December 2021

When we speak of an “inner world,” we are trying to capture something that is to some extent more than metaphorical. We allude to the phenomenologically rich (and worldlike) sensation of being situated in the perspectival unfolding of spatiotemporal relations with inner sounds, images, past or imagined experiential settings. On the other hand, our inner experience has an elusive, underdetermined, and vaporous quality (Hurlburt and Schwitzgebel 2007). How can we build on the similarities between outer and inner worlds so that the latter can be enactively navigated as the former? This chapter argues that narrative, as a mean of extended introspection (see chapter 1.3), can have a role in stabilizing perceptual elements in inner experience into a worldlike ecology. The scope of this chapter is to provide a theory of Beckett’s narrative terraforming engineering, which transforms the mind into a perceptual, embodied, multisensory ecology or what the author terms an enactive innerscape. Once transformed into a world, however, Beckett’s mental kingdom acquires its own natural laws, such as the cross-sensory synaesthetic activation of sounds and voices. A reading of Beckett’s innerscapes as the result of introspective modeling terraforming might cast some additional light on this perceptual principle. The chapter begins by introducing the scientific debate about the use of spatial or geographical mind metaphors: on their possibilities or limitations in capturing the nature of mind and inner experience.