bluuebunny/crossref_metadata_2025 huggingface dataset:
Agenda for Mobilization: The Agrarian Question and Popular Mobilization in Contemporary Mexico
Authors: Foley Michael W.
Published: October 2022

Mexican politics has long been regarded as a closed system, with policy-making dominated by the reigning president and his circle and presidential succession (with all its possibilities for change of course) managed by an only slightly larger “Revolutionary Family” of top figures in the Partido Revolucionario Institucional (PRI). So intertwined are the Mexican state and the dominant party that scholars and opposition leaders alike have begun to speak of the “PRI state.” E. E. Schattschneider observed that in the U.S. system, 90 percent of the population never has access to the “pressure system” that directs policy choice. The percentage of the excluded is undoubtedly even larger in Mexico because the system is more decidedly “closed.” Yet in both countries, policy innovation is not uncommon. Marked changes of course have occurred at times, and opposition forces external to the system have occasionally managed to block presidential decisions and force reevaluation and sometimes painful adjustments. This article will examine the “agrarian question” in Mexico and will argue that its persistence and the ways in which it has been framed have constrained policymakers while encouraging and sustaining the development of an independent peasant movement during the 1970s and 1980s.
Socioeconomic Differentiation among Small Cultivators on Paraguay's Eastern Frontier
Authors: Nagel Beverly Y.
Published: October 2022

Until the 1970s, Paraguay's eastern frontier was known primarily for its vast virgin forests and its domination by semifeudal enterprises engaged in extracting yerba maté and timber. After the 1970s, however, the extension of transportation networks, construction of the massive binational Itaipú hydroelectric works, and the release of state lands for private purchase paved the way for large-scale in-migration, settlement, and transformation of the region into a zone for commercial agriculture. In less than two decades, the rapid expansion of soybean production into this area has catapulted Paraguay into the ranks of the world's major exporters of soybeans.
Parish Registers in Jacaltenango, Guatemala
Authors: Lovell W. George
Published: October 2022

Jacaltenango is a forlorn, unkempt-looking town lying in the tierra templada toward the western edge of the Cuchumatán highlands of Guatemala. It is perhaps best known to the academic world as a stop on the route taken by Frans Blom and Oliver La Farge (1926, 1927) in their pioneering reconnaissance of Mesoamerica earlier this century, a place to which the latter returned with Douglas Byers to document an intriguing array of Maya cultural survivals (La Farge and Byers 1931). More recently, one of its native sons has given local lore and storytelling eloquent written form, as well as documenting the town's painful experience during counterinsurgency operations in the early 1980s (Montejo 1984, 1987).
Populism: Authoritarian and Democratic
Authors: Dix Robert H.
Published: October 2022

Populism is one of those terms (democracy is another) that is frequently employed in the study of politics and varies in meaning from context to context and from author to author. Thus the term has been invoked in studies of such agrarian-based movements as nineteenth-century agrarian unrest in the United States and the narodniki of prerevolutionary Russia as well as being applied to the largely urban-based populism of Latin America. Moreover, most of those who have sought to characterize the populist parties in Latin America have done so in broad terms that encompass any party or political movement that has both a mass base and a cross-class composition. Torcuato DiTella's well-known definition characterized populism (in Latin America or elsewhere) as “a political movement which enjoys the support of the mass of the working class and/or the peasantry, but which does not result from the autonomous organizational power of either of these two sectors. It is also supported by non-working class sectors upholding an anti-status quo ideology.” Other Latin American students of populism such as Francisco Weffort and Ernesto Laclau, along with most others who have studied the phenomenon, have similarly broad conceptions of it.
Inquiries Into the Cristero Insurrection Against the Mexican Revolution
Authors: Jrade Ramón
Published: October 2022

Interest in the Cristero insurrection against the Mexican Revolution has continued unabated since the 1960s. Until now all the major published studies have viewed the rebellion as the climactic outcome of the long-standing conflict between church and state in Mexico. By adopting this perspective, these works have deepened knowledge of church-state relations and sharply delineated the composition and development of Catholic and revolutionary factions. At the same time, these studies have offered a wide range of interpretations of the Cristero movement, interpretations that are incompatible with one another.
Latin America's Jews: A Review of Sources
Authors: Elkin Judith Laikin
Published: October 2022

For the period since independence, Jews do not appear in Latin American history as it is written today. That there are Jews in Latin America we know. But what role have they played in their nations' histories? How have they balanced their inherited tradition with the cultures of the Luso-Hispanic world? What has been the quality of their lives as Jews and as immigrants, nonconformists in societies that exact conformity as the price of acceptance? Most important from the perspective of Latin Americanists, how have Jews been perceived by the majority societies, and what do these perceptions reveal about the nature of these societies?
Mixed Blessings: Disruption and Organization among Peasant Unions in Costa Rica
Authors: Anderson Leslie
Published: October 2022

One of the most urgent issues in contemporary Latin America is the popular struggle against rural poverty. Because Latin American states have failed to alleviate rural impoverishment, the poor have undertaken to solve their own problems. One fruitful way of improving their conditions has proved to be forming grass-roots peasant organizations outside state auspices. This approach, however, can bear fruit only under a democratic regime or in states that provide some political space in which peasants can act without being crushed.
Restoring the orangutan in a Whole- or Half-Earth context
Authors: Meijaard Erik , Sheil Douglas , Sherman Julie , Chua Liana , Ni'matullah Safwanah , Wilson Kerrie , Ancrenaz Marc , Liswanto Darmawan , Wich Serge A. , Goossens Benoit , Kühl Hjalmar S. , Voigt Maria , Rayadin Yaya , Kurniawan Yuyun , Trianto Agus , Priatna Dolly , Banes Graham L. , Massingham Emily , Payne John , Marshall Andrew J.
Published: October 2022

Various global-scale proposals exist to reduce the loss of biological diversity. These include the Half-Earth and Whole-Earth visions that respectively seek to set aside half the planet for wildlife conservation or to diversify conservation practices fundamentally and change the economic systems that determine environmental harm. Here we assess these visions in the specific context of Bornean orangutansPongo pygmaeusand their conservation. Using an expert-led process we explored three scenarios over a 10-year time frame: continuation of Current Conditions, a Half-Earth approach and a Whole-Earth approach. In addition, we examined a 100-year population recovery scenario assuming 0% offtake of Bornean orangutans. Current Conditions were predicted to result in a population c. 73% of its current size by 2032. Half-Earth was judged comparatively easy to achieve and predicted to result in an orangutan population of c. 87% of its current size by 2032. Whole-Earth was anticipated to lead to greater forest loss and ape killing, resulting in a prediction of c. 44% of the current orangutan population for 2032. Finally, under the recovery scenario, populations could be c. 148% of their current size by 2122. Although we acknowledge uncertainties in all of these predictions, we conclude that the Half-Earth and Whole-Earth visions operate along different timelines, with the implementation of Whole-Earth requiring too much time to benefit orangutans. None of the theorized proposals provided a complete solution, so drawing elements from each will be required. We provide recommendations for equitable outcomes.
Disjunctures in practice: ethnographic observations of orthopaedic ward practices in the care of older adults with hip fracture and presumed cognitive impairment
Authors: Cross Jane L. , Backhouse Tamara , Hammond Simon P. , Penhale Bridget , Scheibl Fiona , Lambert Nigel , Varley Anna , Fox Chris , Poland Fiona M.
Published: October 2022

Organisational priorities for health care focus on efficiency as the health and care needs of populations increase. But evidence suggests that excessive planning can be counterproductive, leading to resistance from staff and patients, particularly those living with cognitive impairment. The current paper adds to this debate reporting an Institutional Ethnography of staff delivering care for older patients with cognitive impairment on acute orthopaedic wards in three National Health Service hospitals in the United Kingdom. A key problematic identified in this study is the point of disjuncture seen between the actualities of staff experience and intentions of protocols and policies. We identified three forms of disjuncture typified as: ‘disruptions’, where sequenced care was interrupted by patient events; ‘discontinuities’, where divisions in professional culture, space or time interrupted sequenced tasks; and ‘dispersions’, where displaced objects or people interrupted sequenced care flow. Arguably disruption is an integral characteristic of care work; it follows that to enable staff to flourish, organisations need to confer staff the autonomy to address systemic disruptions rather than attempt to eradicate them. Ultimately, organisational representations of ‘good practice’ as readily joined up, impose a care standard ‘stereotype’ that obscures rather than clarifies the interactional problems encountered by staff.
The combinator M and the Mockingbird lattice
Authors: Giraudo Samuele
Published: October 2022

We study combinatorial and order theoretic structures arising from the fragment of combinatory logic spanned by the basic combinator
${{\mathbf{M}}}$
. This basic combinator, named as the Mockingbird by Smullyan, is defined by the rewrite rule
${{\mathbf{M}}} \mathsf{x}_1 \to \mathsf{x}_1 \mathsf{x}_1$
. We prove that the reflexive and transitive closure of this rewrite relation is a partial order on terms on
${{\mathbf{M}}}$
and that all connected components of its rewrite graph are Hasse diagram of lattices. This last result is based on the introduction of new lattices on duplicative forests, which are sorts of treelike structures. These lattices are not graded, not self-dual, and not semi-distributive. We present some enumerative properties of these lattices like the enumeration of their elements, of the edges of their Hasse diagrams, and of their intervals. These results are derived from formal power series on terms and on duplicative forests endowed with particular operations.
MRI evaluation of right heart functions in children with mild cystic fibrosis
Authors: Temur Hafize Otcu , Alkan Alpay , Yozgat Can Yilmaz , Cakir Erkan , Yazan Hakan , Yabul Fatma Celik , Cesme Dilek Hacer , Yozgat Yilmaz
Published: October 2022

Background:

This study aimed to assess the ventricular anatomy, function of the right ventricle, and the haemodynamic findings of pulmonary artery in children with cystic fibrosis using cardiac MRI.

Patients:

This prospective study consisted of 32 children with mild cystic fibrosis and 30 age-matched healthy control participants.

Methods:

Cardiac MRI was used to assess right ventricular volumes, anatomy, and function and to assessment of haemodynamic findings of pulmonary artery in the control and study groups. Haemodynamic findings of pulmonary arteries were determined using pulmonary arteries peak velocity (cm/s), and pulmonary arteries time-to-peak velocity (ms) and pulmonary artery systolic pressure. All data of children with mild cystic fibrosis were compared with those of 30 age-matched healthy control group participants.

Results:

Our patients and their age-matched controls were aged from 6 to 17 years and from 7 to 15 years, respectively. We found that ejection fraction (%), cardiac output (L/ml), cardiac output (L/ml/m2), and systolic volume (ml/m2) were significantly lower in children with cystic fibrosis (p < 0.01). Right ventricular anterior wall thickness (mm) was significantly higher in children with cystic fibrosis (p = 0.01). No significant difference was observed between the haemodynamic parameters of pulmonary artery in the patient group.

Conclusion:

In our study, cardiac MRI was used to investigate whether the right ventricle was affected functionally and anatomically in children with mild cystic fibrosis. We detected a significant decrease in right ventricular systolic functions and notable alterations in the right ventricular geometry of children with mild cystic fibrosis. These alterations usually manifest themselves as hypertrophy of the right ventricle. Our study’s results demonstrate no relationship between the development of pulmonary hypertension in mild cystic fibrosis children.
RapidPlan models for prostate radiotherapy treatment planning with 10-MV photon beams
Authors: Pupillo Francesco , Piliero Maria Antonietta , Casiraghi Margherita , Bellesi Luca , Presilla Stefano
Published: October 2022

Introduction:

The RapidPlan is a radiotherapy planning tool that uses a dataset of approved plans to predict the dose distribution and automatically generates the dose–volume constraints for optimisation of the new plan. This study compares three strategies of model building for the treatment of prostate cancer with the 10-MV photon beam.

Methods:

Three models for prostate treatment were compared: Model 6X, Model10X and Model6Xrefined. Model6X is already used in our department and was trained on treatment plans based on the 6-MV photon beam. Model10X was trained on treatment plans based on the 10-MV photon beam and manually optimised by an experienced medical physicist. Finally, Model6Xrefined was trained on plans automatically created by the Model6X, but using the 10-MV photon beam. The three models were used to generate 25 new plans with the 10-MV photon beam.

Results:

Model10X generated plans with 2 Gy lower mean dose to bladder-PTV and rectum-PTV volumes and 8% lower V15Gy at bladder and rectum volumes, although the number of monitor units increased by 170 on average.

Conclusions:

The model trained on manually optimised plans generated plans with higher normal tissue sparing. However, model building is a time-consuming process, so a cost–benefit balance should be performed.
THE LOGIC OF HYPERLOGIC. PART B: EXTENSIONS AND RESTRICTIONS
Authors: KOCUREK ALEXANDER W.
Published: October 2022

This is the second part of a two-part series on the logic of hyperlogic, a formal system for regimenting metalogical claims in the object language (even within embedded environments). Part A provided a minimal logic for hyperlogic that is sound and complete over the class of all models. In this part, we extend these completeness results to stronger logics that are sound and complete over restricted classes of models. We also investigate the logic of hyperlogic when the language is enriched with hyperintensional operators such as counterfactual conditionals and belief operators.
Design of multi-band and high radiation intensity piezoelectric antenna based on external circuit
Authors: Zhang Yong , Yan Zhongming , Dong Biao , Wang Yu , Zhou Hongcheng
Published: October 2022

This paper presents a novel method to improve the working bandwidth and radiation intensity of piezoelectric antenna by using external circuit. This method makes the piezoelectric antenna combined with roles of high radiation intensity and multiple resonant frequencies without changing the structural size of the piezoelectric antenna. The experimental results show that, compared with the original piezoelectric antenna, the tuning range of the resonant frequency of the piezoelectric antenna caused by the series capacitance and inductance is +13.6 and −24%, respectively. The series inductance will produce new resonance frequency, which provides a new method for the multi-band operation of the piezoelectric antenna. The LLC (series and parallel circuit) composite circuit can increase the number of resonant frequencies of the piezoelectric antenna from 1 to 3, and the S11 at the resonant frequencies are all lower than −10 dB, and the radiated magnetic field of the piezoelectric antenna is increased by 42.3% at least. This method makes the piezoelectric antenna have the dual functions of high radiation intensity and multi-band, which has great significance for broadening the application field of piezoelectric antenna.
Inhibition of Mps1 kinase enhances taxanes efficacy in castration resistant prostate cancer
Authors: Sarwar Sadia , Morozov Viacheslav M. , Purayil Hamsa , Daaka Yehia , Ishov Alexander M.
Published: October 2022

Androgen ablation therapy is the standard of care for newly diagnosed prostate cancer (PC) patients. PC that relapsed after hormonal therapy, referred to as castration-resistant PC (CRPC), often presents with metastasis (mCRPC) and is the major cause of disease lethality. The few available therapies for mCRPC include the Taxanes Docetaxel (DTX) and Cabazitaxel (CBZ). Alas, clinical success of Taxanes in mCRPC is limited by high intrinsic and acquired resistance. Therefore, it remains essential to develop rationally designed treatments for managing therapy-resistant mCRPC disease. The major effect of Taxanes on microtubule hyper-polymerization is a prolonged mitotic block due to activation of the Spindle Assembly Checkpoint (SAC). Taxane-sensitive cells eventually inactivate SAC and exit mitosis by mitotic catastrophe, resulting in genome instability and blockade of proliferation. Resistant cells remain in mitotic block, and, upon drug decay, resume mitosis and proliferation, underlying one resistance mechanism. In our study we explored the possibility of forced mitotic exit to elevate Taxane efficacy. Inactivation of the SAC component, mitotic checkpoint kinase Mps1/TTK with a small molecule inhibitor (Msp1i), potentiated efficacy of Taxanes treatment in both 2D cell culture and 3D prostasphere settings. Mechanistically, Mps1 inhibition forced mitotic catastrophe in cells blocked in mitosis by Taxanes. Androgen receptor (AR), the main driver of PC, is often mutated or truncated in mCRPC. Remarkably, Mps1i significantly potentiated CBZ cytotoxicity regardless of AR status, in both AR-WT and in AR-truncated CRPC cells. Overall, our data demonstrate that forced mitotic exit by Mps1 inhibition potentiates Taxanes efficacy. Given that several Mps1i’s are currently in different stages of clinical trials, our results point to Mps1 as a new therapeutic target to potentiate efficacy of Taxanes in mCRPC patients.
Manganese-driven CoQ deficiency
Authors: Diessl Jutta , Berndtsson Jens , Broeskamp Filomena , Habernig Lukas , Kohler Verena , Vazquez-Calvo Carmela , Nandy Arpita , Peselj Carlotta , Drobysheva Sofia , Pelosi Ludovic , Vögtle F.-Nora , Pierrel Fabien , Ott Martin , Büttner Sabrina
Published: October 2022

Overexposure to manganese disrupts cellular energy metabolism across species, but the molecular mechanism underlying manganese toxicity remains enigmatic. Here, we report that excess cellular manganese selectively disrupts coenzyme Q (CoQ) biosynthesis, resulting in failure of mitochondrial bioenergetics. While respiratory chain complexes remain intact, the lack of CoQ as lipophilic electron carrier precludes oxidative phosphorylation and leads to premature cell and organismal death. At a molecular level, manganese overload causes mismetallation and proteolytic degradation of Coq7, a diiron hydroxylase that catalyzes the penultimate step in CoQ biosynthesis. Coq7 overexpression or supplementation with a CoQ headgroup analog that bypasses Coq7 function fully corrects electron transport, thus restoring respiration and viability. We uncover a unique sensitivity of a diiron enzyme to mismetallation and define the molecular mechanism for manganese-induced bioenergetic failure that is conserved across species.
Spatially structured eco-evolutionary dynamics in a host-pathogen interaction render isolated populations vulnerable to disease
Authors: Höckerstedt Layla , Numminen Elina , Ashby Ben , Boots Mike , Norberg Anna , Laine Anna-Liisa
Published: October 2022

While the negative effects that pathogens have on their hosts are well-documented in humans and agricultural systems, direct evidence of pathogen-driven impacts in wild host populations is scarce and mixed. Here, to determine how the strength of pathogen-imposed selection depends on spatial structure, we analyze growth rates across approximately 4000 host populations of a perennial plant through time coupled with data on pathogen presence-absence. We find that infection decreases growth more in the isolated than well-connected host populations. Our inoculation study reveals isolated populations to be highly susceptible to disease while connected host populations support the highest levels of resistance diversity, regardless of their disease history. A spatial eco-evolutionary model predicts that non-linearity in the costs to resistance may be critical in determining this pattern. Overall, evolutionary feedbacks define the ecological impacts of disease in spatially structured systems with host gene flow being more important than disease history in determining the outcome.
Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches
Authors: Hill Jason , Lillie Mette , Pettersson Mats E. , Rubin Carl-Johan , Grant B. Rosemary , Grant Peter R. , Andersson Leif , Jern Patric
Published: October 2022

Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.
Measurements of metastable helium in Earth’s atmosphere by resonance lidar
Authors: Kaifler Bernd , Geach Christopher , Büdenbender Hans Christian , Mezger Andreas , Rapp Markus
Published: October 2022

Monitoring and predicting space weather activity is increasingly important given society’s growing reliance on space-based infrastructure but is hampered by a lack of observational data. Airglow at 1083 nm from metastable helium He(23S) in the thermosphere has long been a target for remote-sensing instruments seeking to fill that gap; however, passive measurements of He(23S) fluorescence are limited by low brightness, and interpretation of these observations is complicated by the > 500 km depth of the He(23S) layer. Here, we demonstrate a lidar instrument that is able to stimulate and detect He(23S) fluorescence, and we present measured profiles of He(23S) density. These measurements provide crucial validation to space weather models, support predictions of peak number density ( ~ 1 cm−3) and the dependence of density on altitude, solar zenith angle, and season, and extend by a factor of 4 the maximum probed altitude range by an atmospheric profiling lidar. These measurements open the door for the development of more sophisticated lidars: by applying well-established spectroscopic lidar techniques, one can measure the Doppler shift and broadening of the He(23S) line, thereby retrieving profiles of neutral wind speed and temperature, opening a window for studying space weather phenomena.
A predictive computational platform for optimizing the design of bioartificial pancreas devices
Authors: Ernst Alexander U. , Wang Long-Hai , Worland Scott C. , Marfil-Garza Braulio A. , Wang Xi , Liu Wanjun , Chiu Alan , Kin Tatsuya , O’Gorman Doug , Steinschneider Scott , Datta Ashim K. , Papas Klearchos K. , James Shapiro A. M. , Ma Minglin
Published: October 2022

The delivery of encapsulated islets or stem cell-derived insulin-producing cells (i.e., bioartificial pancreas devices) may achieve a functional cure for type 1 diabetes, but their efficacy is limited by mass transport constraints. Modeling such constraints is thus desirable, but previous efforts invoke simplifications which limit the utility of their insights. Herein, we present a computational platform for investigating the therapeutic capacity of generic and user-programmable bioartificial pancreas devices, which accounts for highly influential stochastic properties including the size distribution and random localization of the cells. We first apply the platform in a study which finds that endogenous islet size distribution variance significantly influences device potency. Then we pursue optimizations, determining ideal device structures and estimates of the curative cell dose. Finally, we propose a new, device-specific islet equivalence conversion table, and develop a surrogate machine learning model, hosted on a web application, to rapidly produce these coefficients for user-defined devices.
TGF-β-dependent lymphoid tissue residency of stem-like T cells limits response to tumor vaccine
Authors: Li Guo , Srinivasan Saranya , Wang Liwen , Ma Chaoyu , Guo Kai , Xiao Wenhao , Liao Wei , Mishra Shruti , Zhang Xin , Qiu Yuanzheng , Lu Qianjin , Liu Yong , Zhang Nu
Published: October 2022

TGF-β signaling is necessary for CD8+T cell differentiation into tissue resident memory T cells (TRM). Although higher frequency of CD8+TRMcells in the tumor microenvironment is associated with better prognosis, TGF-β−blockade typically improves rather than worsens outcomes. Here we show that in a mouse melanoma model, in the tumor-draining lymph nodes (TDLN) rather than in the tumors themselves, stem-like CD8+T cells differentiate into TRMs in a TGF-β and tumor antigen dependent manner. Following vaccination against a melanoma-specific epitope, most tumour-specific CD8+T cells are maintained in a stem-like state, but a proportion of cells lost TRMstatus and differentiate into CX3CR1+effector CD8+T cells in the TDLN, which are subsequently migrating into the tumours. Disruption of TGF-β signaling changes the dynamics of these developmental processes, with the net result of improving effector CD8+T cell migration into the tumours. In summary, TDLN stem-like T cells transiently switch from a TGF-β-dependent TRMdifferentiation program to an anti-tumor migratory effector development upon vaccination, which transition can be facilitated by targeted TGF-β blockade.
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Authors: Gounot Jean-Sebastien , Chia Minghao , Bertrand Denis , Saw Woei-Yuh , Ravikrishnan Aarthi , Low Adrian , Ding Yichen , Ng Amanda Hui Qi , Tan Linda Wei Lin , Teo Yik-Ying , Seedorf Henning , Nagarajan Niranjan
Published: October 2022

Despite extensive efforts to address it, the vastness of uncharacterized ‘dark matter’ microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36–88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
Optineurin links Hace1-dependent Rac ubiquitylation to integrin-mediated mechanotransduction to control bacterial invasion and cell division
Authors: Petracchini Serena , Hamaoui Daniel , Doye Anne , Asnacios Atef , Fage Florian , Vitiello Elisa , Balland Martial , Janel Sebastien , Lafont Frank , Gupta Mukund , Ladoux Benoit , Gilleron Jerôme , Maia Teresa M. , Impens Francis , Gagnoux-Palacios Laurent , Daugaard Mads , Sorensen Poul H. , Lemichez Emmanuel , Mettouchi Amel
Published: October 2022

Extracellular matrix (ECM) elasticity is perceived by cells via focal adhesion structures, which transduce mechanical cues into chemical signalling to conform cell behavior. Although the contribution of ECM compliance to the control of cell migration or division is extensively studied, little is reported regarding infectious processes. We study this phenomenon with the extraintestinal Escherichia coli pathogen UTI89. We show that UTI89 takes advantage, via its CNF1 toxin, of integrin mechanoactivation to trigger its invasion into cells. We identify the HACE1 E3 ligase-interacting protein Optineurin (OPTN) as a protein regulated by ECM stiffness. Functional analysis establishes a role of OPTN in bacterial invasion and integrin mechanical coupling and for stimulation of HACE1 E3 ligase activity towards the Rac1 GTPase. Consistent with a role of OPTN in cell mechanics, OPTN knockdown cells display defective integrin-mediated traction force buildup, associated with limited cellular invasion by UTI89. Nevertheless, OPTN knockdown cells display strong mechanochemical adhesion signalling, enhanced Rac1 activation and increased cyclin D1 translation, together with enhanced cell proliferation independent of ECM stiffness. Together, our data ascribe a new function to OPTN in mechanobiology.
Stable isotopes of C and N differ in their ability to reconstruct diets of cattle fed C3–C4 forage diets
Authors: Jaramillo David M. , Dubeux Jose C. B. , Ruiz-Moreno Martin , DiLorenzo Nicolas , Vendramini Joao M. B. , Sollenberger Lynn , Mackowiak Cheryl , Queiroz Luana M. D. , Abreu Daciele S. , Garcia Liza , Santos Erick R. S. , Kieke Burney A.
Published: October 2022

Stable isotopes are useful for estimating livestock diet selection. The objective was to compare δ13C and δ15N to estimate diet proportion of C3–C4 forages when steers (Bos spp.) were fed quantities of rhizoma peanut (Arachisglabrata; RP; C3) and bahiagrass (Paspalumnotatum; C4).Treatments were proportions of RP with bahiagrass hay: 100% bahiagrass (0%RP); 25% RP + 75% bahiagrass (25%RP); 50% RP + 50% bahiagrass (50%RP); 75% RP + 25% bahiagrass (75%RP); and 100% RP (100% RP). Feces, plasma, red blood cell (RBC), and hair were collected at 8-days intervals, for 32 days. Two-pool mixing model was utilized to back-calculate the proportion of RP based on the sample and forage δ13C or δ15N. Feces showed changes using δ13C by 8 days, and adj. R2 between predicted and observed RP proportion was 0.81 by 8 days. Plasma, hair, and RBC required beyond 32-days to reach equilibrium, therefore were not useful predictors of diet composition during the study. Diets were best represented using fecal δ13C at both 8-days and 32-days. By 32-days, fecal δ15N showed promise (R2 = 0.71) for predicting diet composition in C3–C4 diets. Further studies are warranted to further corroborate fecal δ15N as a predictor of diet composition in cattle.
Heat Wave Resilient Systems Architecture for Underwater Data Centers
Authors: Periola A. A. , Alonge A. A. , Ogudo K. A.
Published: October 2022

The need to design computing platforms with low water footprint and enhanced energy efficiency makes non-terrestrial computing platforms attractive. Large scale computing platforms in non-terrestrial environments are increasingly receiving attention. In this regard, underwater data centers (UDCs) are considered to have operational benefits due to their low cooling cost. Underwater data centers experience challenges due to marine heat waves. The occurrence of marine heat waves limits the amount of ocean water available for UDC cooling. This paper proposes a mechanism to detect marine heat waves, and ensure continued UDC functioning. The proposed mechanism utilizes reservoirs to store water and ensure continued functioning of underwater data center. In addition, the proposed research presents the reservoir as a service (RaaS) for ensuring UDC cooling. Furthermore, the presented research also describes modular form factor approach for UDC development. This is being done with the aim of enhancing UDC adoption and use in capital constrained contexts. The underwater data center operational duration is investigated. Evaluation shows that the proposed solution enhances the operational duration by an average of (5.5–12.3) % and (5.2–11.5) % given that marine heat waves span 10 epochs and 15 epochs during an operational phase, respectively.
Towards bright gamma-ray flash generation from tailored target irradiated by multi-petawatt laser
Authors: Hadjisolomou Prokopis , Jeong Tae Moon , Bulanov Sergei V.
Published: October 2022

One of the remarkable phenomena in the laser-matter interaction is the extremely efficient energy transfer to $$\gamma $$
γ
-photons, that appears as a collimated $$\gamma $$
γ
-ray beam. For interactions of realistic laser pulses with matter, existence of an amplified spontaneous emission pedestal plays a crucial role, since it hits the target prior to the main pulse arrival, leading to a cloud of preplasma and drilling a narrow channel inside the target. These effects significantly alter the process of $$\gamma $$
γ
-photon generation. Here, we study this process by importing the outcome of magnetohydrodynamic simulations of the pedestal-target interaction into particle-in-cell simulations for describing the $$\gamma $$
γ
-photon generation. It is seen that target tailoring prior the laser-target interaction plays an important positive role, enhancing the efficiency of laser pulse coupling with the target, and generating high energy electron-positron pairs. It is expected that such a $$\gamma $$
γ
-photon source will be actively used in various applications in nuclear photonics, material science and astrophysical processes modelling.
Gravity and magnetic anomalies of earthquake-prone areas in the southwestern Ulleung basin margin, East Sea (Sea of Japan)
Authors: Kim Chang Hwan , Kim Kwang-Hee , Choi Soon Young , Kim Won Hyuck , Choi Hyun Ok , Park Chan Hong
Published: October 2022

Submarine earthquakes have increased in the southwestern Ulleung Basin adjacent to the Korean Peninsula. This study analyzed the gravitational and magnetic properties of the three earthquake-prone areas (Hupo Bank and offshore regions near Pohang and Ulsan) in the basin. The basin was affected by tensile and compressive stresses during the formation of the East Sea. The southern Hupo Bank and the Pohang offshore exhibited high gravity anomalies and strong magnetic anomalies. Hupo Bank was separated from the peninsula and earthquakes in this region have been influenced by crustal fractures that facilitated igneous activities during the formation of the basin. Dense volcanic rocks and seaward dipping reflectors along the Pohang coast and continental slope suggest magmatic activities during the formation of the East Sea. Comparatively, the Ulsan offshore, with a thick sedimentary layer, exhibited a slightly higher gravity anomaly than the surrounding area, but no significant differences in the magnetic anomaly. Sequential tensile and compressive stresses related to the creation of the basin produced complex tectonic structures in this region. The magnetic tilt derivative results suggest that earthquakes were located near magnetic source boundaries. The results show that it is important to monitor earthquake-prone areas with gravity and magnetic anomalies.
Exposure to air pollution and its effect on ischemic strokes (EP-PARTICLES study)
Authors: Kuźma Łukasz , Roszkowska Sylwia , Święczkowski Michał , Dąbrowski Emil Julian , Kurasz Anna , Wańha Wojciech , Bachórzewska-Gajewska Hanna , Dobrzycki Sławomir
Published: October 2022

It is well known that exceeded levels of particulate matter in the air and other air pollutants harmfully affect the cardiovascular system. Empirical analyses of the effects of these factors on stroke incidence and mortality are still limited. The main objective of our analyses was to determine the association between short-term exposure to air pollutants and stroke incidence in non-industrial areas, more specifically in north-eastern Poland. To achieve this aim, we used data from the National Health Fund on patients hospitalized for stroke between 2011 and 2020 in the largest city of the region described as the Green Lungs of Poland. The pollution levels and atmospheric conditions data were obtained from the Provincial Inspectorate for Environmental Protection and the Institute of Meteorology and Water Management. Using daily data on hospitalizations, atmospheric conditions, and pollution, as well as ordered logistic regression models the hypotheses on the impact of weather and air pollution conditions on ischemic strokes were tested. The study group included 4838 patients, 45.6% of whom were male; the average patient age was approximately 74 years. The average concentrations of PM2.5 were 19.09 µg/m3, PM10 26.66 µg/m3 and CO 0.35 µg/m3. Analyses showed that an increase in PM2.5 and PM10 concentrations by 10 µg/m3 was associated with an increase in the incidence of stroke on the day of exposure (OR = 1.075, 95% CI 0.999–1.157, P = 0.053; OR = 1.056, 95% CI 1.004–1.110, P = 0.035) and the effect was even several times greater on the occurrence of a stroke event in general (PM2.5: OR = 1.120, 95% CI 1.013–1.237, P = 0.026; PM10: OR = 1.103, 95% CI 1.028–1.182, P = 0.006). Furthermore, a short-term (up to 3 days) effect of CO on stroke incidence was observed in the study area. An increase of 1 μg/m3 CO was associated with a lower incidence of stroke 2 days after the exposure (OR = 0.976, 95% CI 0.953–0.998, P = 0.037) and a higher incidence 3 days after the exposure (OR = 1.026, 95% CI 1.004–1.049, P = 0.022).
Immediate protein expression from exogenous mRNAs in embryonic brain
Authors: Naruse Masae , Saito Tetsuichiro
Published: October 2022

mRNA vaccines for SARS-CoV-2 have been widely used and saving millions of people in the world. How efficiently proteins are produced from exogenous mRNAs in the embryonic brain, however, is less known. Here we show that protein expression occurs highly efficiently in neural stem cells, in a very narrow time window after mRNA electroporation in the embryonic mouse brain, where plasmids have been successfully transfected. Protein expression is detected 1 h and 12 h after the electroporation of mRNAs and plasmids, respectively. The delivery of exogenous mRNAs may be useful for not only vaccines but also functional analysis in the brain.
Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core
Authors: Pacheco-García Juan Luis , Loginov Dmitry S. , Naganathan Athi N. , Vankova Pavla , Cano-Muñoz Mario , Man Petr , Pey Angel L.
Published: October 2022

Phosphoglycerate kinase has been a model for the stability, folding cooperativity and catalysis of a two-domain protein. The human isoform 1 (hPGK1) is associated with cancer development and rare genetic diseases that affect several of its features. To investigate how mutations affect hPGK1 folding landscape and interaction networks, we have introduced mutations at a buried site in the N-terminal domain (F25 mutants) that either created cavities (F25L, F25V, F25A), enhanced conformational entropy (F25G) or introduced structural strain (F25W) and evaluated their effects using biophysical experimental and theoretical methods. All F25 mutants folded well, but showed reduced unfolding cooperativity, kinetic stability and altered activation energetics according to the results from thermal and chemical denaturation analyses. These alterations correlated well with the structural perturbation caused by mutations in the N-terminal domain and the destabilization caused in the interdomain interface as revealed by H/D exchange under native conditions. Importantly, experimental and theoretical analyses showed that these effects are significant even when the perturbation is mild and local. Our approach will be useful to establish the molecular basis of hPGK1 genotype–phenotype correlations due to phosphorylation events and single amino acid substitutions associated with disease.
Assessment of variability in the plasma 7k SomaScan proteomics assay
Authors: Candia Julián , Daya Gulzar N. , Tanaka Toshiko , Ferrucci Luigi , Walker Keenan A.
Published: October 2022

SomaScan is a high-throughput, aptamer-based proteomics assay designed for the simultaneous measurement of thousands of proteins with a broad range of endogenous concentrations. In its most current version, the 7k SomaScan assay v4.1 is capable of measuring 7288 human proteins. In this work, we present an extensive technical assessment of this platform based on a study of 2050 samples across 22 plates. Included in the study design were inter-plate technical duplicates from 102 human subjects, which allowed us to characterize different normalization procedures, evaluate assay variability by multiple analytical approaches, present signal-over-background metrics, and discuss potential specificity issues. By providing detailed performance assessments on this wide range of technical aspects, we aim for this work to serve as a valuable resource for the growing community of SomaScan users.
Combining NGN2 programming and dopaminergic patterning for a rapid and efficient generation of hiPSC-derived midbrain neurons
Authors: Sheta Razan , Teixeira Maxime , Idi Walid , Pierre Marion , de Rus Jacquet Aurelie , Emond Vincent , Zorca Cornelia E. , Vanderperre Benoît , Durcan Thomas M. , Fon Edward A. , Calon Frédéric , Chahine Mohamed , Oueslati Abid
Published: October 2022

The use of human derived induced pluripotent stem cells (hiPSCs) differentiated to dopaminergic (DA) neurons offers a valuable experimental model to decorticate the cellular and molecular mechanisms of Parkinson’s disease (PD) pathogenesis. However, the existing approaches present with several limitations, notably the lengthy time course of the protocols and the high variability in the yield of DA neurons. Here we report on the development of an improved approach that combines neurogenin-2 programming with the use of commercially available midbrain differentiation kits for a rapid, efficient, and reproducible directed differentiation of hiPSCs to mature and functional induced DA (iDA) neurons, with minimum contamination by other brain cell types. Gene expression analysis, associated with functional characterization examining neurotransmitter release and electrical recordings, support the functional identity of the iDA neurons to A9 midbrain neurons. iDA neurons showed selective vulnerability when exposed to 6-hydroxydopamine, thus providing a viable in vitro approach for modeling PD and for the screening of small molecules with neuroprotective proprieties.
Synthesis of powdered and beaded chitosan materials modified with ZnO for removing lead (II) ions
Authors: Ngamsurach Pimploy , Namwongsa Nitthawan , Praipipat Pornsawai
Published: October 2022

Lead contamination in wastewater may affect aquatic organisms, the environment, and human consumption because it is a highly toxic metal that caused human health effects. Thus, it is recommended to remove lead before releasing it into the environment. Powdered and beaded chitosan materials modified with ZnO were synthesized and investigated by various characterized techniques. Lead removal efficiencies of chitosan materials were studied by batch experiments, adsorption isotherms, and kinetics. Chitosan powder (CP), chitosan beads (CB), chitosan beads mixed ZnO (CZB), and chitosan beads coated ZnO (ZCB) were synthesized. CP represented a semi-crystalline structure while CB was an amorphous structure. CZB and ZCB were semi-crystalline structures with ZnO peaks. CP was a scaly-sheet and coarse surface while CB, CZB, and ZCB were sphere shapes with scaly-sheet surfaces. C, O, and N were the main chemical elements in chitosan materials, and Zn was detected in CZB and ZCB. O–H, N–H, and C–O were the main functional groups of chitosan materials. All chitosan materials had high lead removal efficiencies of more than 92%, and Freundlich and pseudo-second-order kinetic models well explained their adsorption patterns and mechanisms. Therefore, both adding metal oxide and changing material form are recommended for improving material efficiency, and ZCB was a good offer for further industrial applications.
Modification of SWCNTs with hybrid materials ZnO–Ag and ZnO–Au for enhancing bactericidal activity of phagocytic cells against Escherichia coli through NOX2 pathway
Authors: Al Rugaie Osamah , Jabir Majid S. , Mohammed Mustafa K. A. , Abbas Ruaa H. , Ahmed Duha S. , Sulaiman Ghassan M. , Mohammed Salman A. A. , Khan Riaz A. , Al-Regaiey Khalid A. , Alsharidah Mansour , Mohany Khalid M. , Mohammed Hamdoon A.
Published: October 2022

Zinc oxide-silver (ZnO–Ag), and zinc oxide-gold (ZnO–Au) nano-composites were prepared through wet chemical process and laced into single-walled carbon nanotubes (SWCNTs) to yield ZnO–Ag-SWCNTs, and ZnO–Au-SWCNTs hybrids. These nano-composite-laced SWCNTs hybrids were characterized using Raman spectroscopic, X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM) analyses. The hybrids were evaluated for their effects on phagocytic cells and bactericidal activity against the gram-negative bacteria E. coli. Their phagocytic cell activities and intracellular killing actions were found to be significantly increased, as the ZnO–Ag-SWCNTs and ZnO–Au-SWCNTs nano-hybrids induced widespread clearance of Escherichia coli. An increase in the production of reactive oxygen species (ROS) also led to upregulated phagocytosis, which was determined mechanistically to involve the phagocyte NADPH oxidase (NOX2) pathway. The findings emphasized the roles of ZnO–Ag- and ZnO–Au-decorated SWCNTs in the prevention of bacterial infection by inhibiting biofilm formation, showing the potential to be utilized as catheter coatings in the clinic.