bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuroqueer frontiers: Neurodiversity, gender, and the (a)social self
Authors: Barnett Jessica Penwell 
Published: May 2024

AbstractThis paper critically synthesizes leading edge scholarship on neurodiversity, arguing that sociology could expand its account for the relationship between self and society through attention to the (a)social practices of those constructed as neurologically disabled. Autistic scholar‐activism birthed the neurodiversity paradigm, which claims respect for neurological diversity and its social manifestations. Sexual and gender variation are among those. I review research on the confluence of neurological, sexual, and gender variance, pointing to opportunities for documenting the roles of social institutions in constructing and regulating divergent bodyminds, as well as new intersectional identities and social movements. Next, I synthesize nascent literature developing neuroqueer theory. “Neuroqueer” articulates the queer nature of neurodivergence and examines the entwinement of the two. Centering the epistemic authority of bodyminds problematized as lacking self‐control/intent, perspective‐taking, and reliance on the social symbolic, neuroqueer scholars forward (a)social ways of knowing, communicating, communing, and being human. Focusing on neuronormativity, interdependent with better‐recognized normativities (e.g., gender, ethnicity, etc.), neuroqueer theory offers fresh perspective on how dominant concepts and relations render some bodyminds problematic—legitimate objects of exclusion, marginalization, and “rehabilitation.” In doing so, it troubles sociological ideas about agency, sociality, communication, and what it means to be/have a (social) self.
A Novel Analysis of the Size Effect on Stress Intensity Factor for Center and Edge Cracks in Tension by the Net-Section Mechanics
Authors: Ravi Chandran K. S. 
Published: May 2024

Abstract
An unresolved question in fracture mechanics is whether the variations in the size or aspect-ratio of cracked plates or structures have a significant effect on the stress intensity factor (SIF) at the crack tip. Indeed, there are significant numerical data showing the effect of specimen aspect-ratio on SIF. There is also experimental evidence supporting the existence of the size effect on fatigue and fracture behavior. However, there is no analytical formula to capture such a size effect on the stress intensity factor for standard fracture mechanics crack configurations. In this study, a novel net-section-based approach is used to develop simple and approximate SIF expressions for center and edge cracks in tension plates of various aspect ratios. Expressions have been derived for both uniform stress as well as uniform displacement boundary conditions. Comparisons are made with the available numerical stress intensity factor data. A remarkable agreement of the net-section-based SIF expressions with the numerical data (complex potential, finite element, and variational approaches) is found. For the clamped-end condition, the net-section approach leads to Rice's limiting SIF for a semi-infinite crack in an infinitely wide strip, validating the analysis. Additionally, the SIF expressions developed here also highlight some discrepancies in numerical data. The study provides simple SIF expressions that can be readily used to analyze specimen size or aspect-ratio effects on critical values of stress intensity factors for cracks in materials and structures under tension loading.
Oxygenation of Earth’s atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion
Authors: Sumner Dawn Y. 
Published: May 2024

ABSTRACT

The oxygenation of Earth’s atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves
13
C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of
12
C into organic carbon and CH
4
. Extreme and variable
13
C enrichments in carbonates were caused by
13
C-depleted CH
4
loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH
4
loss slowed, dissolved inorganic carbon in shallow environments was no longer highly
13
C enriched. Thus, the loss of extreme
13
C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth’s atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.

IMPORTANCE
The oxygenation of Earth’s atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth’s surface chemistry through time.
Asking a question
Authors: Kolter Roberto 
Published: May 2024

ABSTRACT

While scientific research should be carried out objectively, the choices of questions asked and approaches taken are deeply personal and subjective. I urge individuals to pursue questions they love and to periodically scrutinize the reasons (the philosophies) that drive that love. As a case study, I scrutinize the “whys” behind some of the scientific questions I pursued during my career.
Involvement of ArlI, ArlJ, and CirA in archaeal type IV pilin-mediated motility regulation
Authors: Chatterjee Priyanka , Garcia Marco A. , Cote Jacob A. , Yun Kun , Legerme Georgio P. , Habib Rumi , Tripepi Manuela , Young Criston , Kulp Daniel , Dyall-Smith Mike , Pohlschroder Mecky 
Published: May 2024

ABSTRACT

Many prokaryotes use swimming motility to move toward favorable conditions and escape adverse surroundings. Regulatory mechanisms governing bacterial flagella-driven motility are well-established; however, little is yet known about the regulation underlying swimming motility propelled by the archaeal cell surface structure, the archaella. Previous research showed that the deletion of the adhesion pilins (PilA1-6), subunits of the type IV pili cell surface structure, renders the model archaeon
Haloferax volcanii
non-motile. In this study, we used ethyl methanesulfonate mutagenesis and a motility assay to identify motile suppressors of the ∆
pilA
[
1-6
] strain. Of the eight suppressors identified, six contain missense mutations in archaella biosynthesis genes,
arlI
and
arlJ. In trans
expression of
arlI
and
arlJ
mutant constructs in the respective multi-deletion strains ∆
pilA
[
1-6
]∆
arlI
and ∆
pilA
[
1-6
]∆
arlJ
confirmed their role in suppressing the ∆
pilA
[
1-6
] motility defect. Additionally, three suppressors harbor co-occurring disruptive missense and nonsense mutations in
cirA
, a gene encoding a proposed regulatory protein. A deletion of
cirA
resulted in hypermotility, while
cirA
expression
in trans
in wild-type cells led to decreased motility. Moreover, quantitative real-time PCR analysis revealed that in wild-type cells, higher expression levels of
arlI
,
arlJ
, and the archaellin gene
arlA1
were observed in motile early-log phase rod-shaped cells compared to non-motile mid-log phase disk-shaped cells. Conversely, ∆
cirA
cells, which form rods during both early- and mid-log phases, exhibited similar expression levels of
arl
genes in both growth phases. Our findings contribute to a deeper understanding of the mechanisms governing archaeal motility, highlighting the involvement of ArlI, ArlJ, and CirA in pilin-mediated motility regulation.

IMPORTANCE

Archaea are close relatives of eukaryotes and play crucial ecological roles. Certain behaviors, such as swimming motility, are thought to be important for archaeal environmental adaptation. Archaella, the archaeal motility appendages, are evolutionarily distinct from bacterial flagella, and the regulatory mechanisms driving archaeal motility are largely unknown. Previous research has linked the loss of type IV pili subunits to archaeal motility suppression. This study reveals three
Haloferax volcanii
proteins involved in pilin-mediated motility regulation, offering a deeper understanding of motility regulation in this understudied domain while also paving the way for uncovering novel mechanisms that govern archaeal motility. Understanding archaeal cellular processes will help elucidate the ecological roles of archaea as well as the evolution of these processes across domains.
Metagenome-assembled genomes from microbiomes fermenting dairy coproducts
Authors: Walters Kevin A. , Myers Kevin S. , Donohue Timothy J. , Noguera Daniel R. 
Published: May 2024

ABSTRACT

To advance knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from six anaerobic bioreactors that were fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. These metagenomes produced 122 metagenome-assembled genomes that represent 34 distinct taxa.
Integrative analyses on the ciliates
Colpoda
illuminate the life history evolution of soil microorganisms
Authors: Li Haichao , Wu Kun , Feng Yuan , Gao Chao , Wang Yaohai , Zhang Yuanyuan , Pan Jiao , Shen Xiaopeng , Zufall Rebecca A. , Zhang Yu , Zhang Weipeng , Sun Jin , Ye Zhiqiang , Li Weiyi , Lynch Michael , Long Hongan 
Published: May 2024

ABSTRACT

Microorganisms play a central role in sustaining soil ecosystems and agriculture, and these functions are usually associated with their complex life history. Yet, the regulation and evolution of life history have remained enigmatic and poorly understood, especially in protozoa, the third most abundant group of organisms in the soil. Here, we explore the life history of a cosmopolitan species—
Colpoda steinii
. Our analysis has yielded a high-quality macronuclear genome for
C. steinii
, with size of 155 Mbp and 37,123 protein-coding genes, as well as mean intron length of ~93 bp, longer than most other studied ciliates. Notably, we identify two possible whole-genome duplication events in
C. steinii
, which may account for its genome being about twice the size of
C. inflata’s
, another co-existing species. We further resolve the gene expression profiles in diverse life stages of
C. steinii
, which are also corroborated in
C. inflata
. During the resting cyst stage, genes associated with cell death and vacuole formation are upregulated, and translation-related genes are downregulated. While the translation-related genes are upregulated during the excystment of resting cysts. Reproductive cysts exhibit a significant reduction in cell adhesion. We also demonstrate that most genes expressed in specific life stages are under strong purifying selection. This study offers a deeper understanding of the life history evolution that underpins the extraordinary success and ecological functions of microorganisms in soil ecosystems.

IMPORTANCE

Colpoda
species, as a prominent group among the most widely distributed and abundant soil microorganisms, play a crucial role in sustaining soil ecosystems and promoting plant growth. This investigation reveals their exceptional macronuclear genomic features, including significantly large genome size, long introns, and numerous gene duplications. The gene expression profiles and the specific biological functions associated with the transitions between various life stages are also elucidated. The vast majority of genes linked to life stage transitions are subject to strong purifying selection, as inferred from multiple natural strains newly isolated and deeply sequenced. This substantiates the enduring and conservative nature of
Colpoda
’s life history, which has persisted throughout the extensive evolutionary history of these highly successful protozoa in soil. These findings shed light on the evolutionary dynamics of microbial eukaryotes in the ever-fluctuating soil environments. This integrative research represents a significant advancement in understanding the life histories of these understudied single-celled eukaryotes.
Left atrial appendage closure for patients with atrial fibrillation at high intracranial haemorrhagic risk
Authors: Abramovitz Fouks Avia , Yaghi Shadi , Gokcal Elif , Das Alvin S , Rotschild Ofer , Silverman Scott B , Singhal Aneesh B , Romero Jorge , Kapur Sunil , Greenberg Steven M , Gurol Mahmut Edip 
Published: May 2024

Background and objectivesAlthough left atrial appendage closure (LAAC) is performed in patients with non-valvular atrial fibrillation (NVAF) at increased risk of intracranial haemorrhage (ICH), outcome data are scarce. We assessed the detailed neurological indications for LAAC and outcomes after LAAC in high ICH risk patients.MethodsStudy population included consecutive patients with NVAF who underwent LAAC in a single hospital network between January 2015 and October 2021 because of prior ICH or the presence of high ICH risk imaging markers on brain MRI (cerebral microbleeds (CMBs)). Primary safety and efficacy outcome measures were the occurrence of ICH and thromboembolic events, respectively, after LAAC.ResultsAmong 146 patients with NVAF who underwent LAAC for high ICH risk, 122 had a history of ICH, while 24 presented with high ICH risk imaging markers only. Mean age was 75.7±7.61, 42 (28.8%) were women. Mean CHA2DS2-VASc score was 5.23±1.52. Of 122 patients with ICH history, 58 (47.5%) had intraparenchymal haemorrhage (IPH), 40 (32.8%) had traumatic ICH (T-ICH) and 18 (14.7%) had non-traumatic subdural haemorrhage. Of 85 patients with brain MRIs including necessary sequences, 43 (50.6%) were related to cerebral amyloid angiopathy and 37 (43.5%) to hypertensive microangiopathy. While 70% of patients were discharged on oral anticoagulants (OAC), 92% were not taking OAC at 1 year. Over 2.12 years mean follow-up, one patient had recurrent non-traumatic IPH (incidence rate (IR) 0.32 per 100 patient-years), five had T-ICH (IR 1.61 per 100 patient-years) and six had an ischaemic stroke (IR 1.94 per 100 patient-years).ConclusionsAmong patients with NVAF at high ICH risk, LAAC demonstrated a low risk of recurrent ICH or ischaemic stroke compared with previously published data. LAAC in high ICH risk populations should be considered in clinical practice per FDA approval and recent guidelines.
Water Cherenkov muon veto for the COSINUS experiment: design and simulation optimization
Authors: Angloher G. , Bharadwaj M. R. , Cababie M. , Dafinei I. , Di Marco N. , Einfalt L. , Ferroni F. , Fichtinger S. , Filipponi A. , Friedl M. , Fuss A. , Ge Z. , Heikinheimo M. , Hughes M. N. , Huitu K. , Kellermann M. , Maji R. , Mancuso M. , Pagnanini L. , Petricca F. , Pirro S. , Pröbst F. , Profeta G. , Puiu A. , Reindl F. , Schäeffner K. , Schieck J. , Schmiedmayer D. , Schreiner P. , Schwertner C. , Shera K. , Stahlberg M. , Stendhal A. , Stukel M. , Tresca C. , Wagner F. , Yue S. , Zema V. , Zhu Y. 
Published: May 2024

AbstractCOSINUS is a dark matter (DM) direct search experiment that uses sodium iodide (NaI) crystals as cryogenic calorimeters. Thanks to the low nuclear recoil energy threshold and event-by-event discrimination capability, COSINUS will address the long-standing DM claim made by the DAMA/LIBRA collaboration. The experiment is currently under construction at the Laboratori Nazionali del Gran Sasso, Italy, and employs a large cylindrical water tank as a passive shield to meet the required background rate. However, muon-induced neutrons can mimic a DM signal therefore requiring an active veto system, which is achieved by instrumenting the water tank with an array of photomultiplier tubes (PMTs). This study optimizes the number, arrangement, and trigger conditions of the PMTs as well as the size of an optically invisible region. The objective was to maximize the muon veto efficiency while minimizing the accidental trigger rate due to the ambient and instrumental background. The final configuration predicts a veto efficiency of 99.63 ± 0.16% and 44.4 ± 5.6% in the tagging of muon events and showers of secondary particles, respectively. The active veto will reduce the cosmogenic neutron background rate to 0.11 ± 0.02 cts$$\cdot $$
·
kg$$^{-1}\cdot $$

-
1

·

year$$^{-1},$$

-
1

,

corresponding to less than one background event in the region of interest for the whole COSINUS-1$$\pi $$
π
exposure of 1000 kg$$\cdot $$
·
days.
A SIMPLE PROBLEM FOR SIMULATING DEMOGRAPHIC NOISE IN BIOLOGICAL DIFFERENTIAL EQUATION MODELS: A DISCREPANCY EFFECT
Authors: MACRELLI ROBERTO , CARLETTI MARGHERITA , STABILE GIOVANNI 
Published: May 2024

Dynamical systems described by deterministic differential equations represent idealized situations where random implications are ignored. In the context of biomathematical modeling, the introduction of random noise must be distinguished between environmental (or extrinsic) noise and demographic (or intrinsic) noise. In this last context it is assumed that the variation over time is due to demographic variation of two or more interacting populations, and not to fluctuations in the environment. The modeling and simulation of demographic noise as a stochastic process affecting single units of the populations involved in the model are well known in the literature and they result in discrete stochastic systems. When the population sizes are large, these discrete stochastic processes converge to continuous stochastic processes, giving rise to stochastic differential equations. If noise is ignored, these stochastic differential equations turn to ordinary differential equations. The inverse process, i.e., inferring the effects of demographic noise on a natural system described by a set of ordinary differential equations, is an issue addressed in a recent paper by Carletti M, Banerjee M, A backward technique for demographic noise in biological ordinary differential equation models, Mathematics 7:1204, 2019. In this paper we show an example of how the technique to model and simulate demographic noise going backward from a deterministic continuous differential system to its underlying discrete stochastic process can provide a discrepancy effect, modifying the dynamics of the deterministic model.
Treating Type 2 Diabetes With Early, Intensive, Multimodal Pharmacotherapy: Real‐World Evidence From an International Collaborative Database
Authors: Anson Matthew , Malik Ayesha , Zhao Sizheng S. , Austin Philip , Ibarburu Gema H. , Jaffar Shabbar , Garrib Anupam , Cuthbertson Daniel J. , Alam Uazman 
Published: May 2024

Aims: We compared the glycaemic and cardiorenal effects of combination therapy involving metformin, pioglitazone, sodium‐glucose‐linked‐cotransporter‐2 inhibitor (SGLT2i), and glucagon‐like peptide‐1 receptor agonist (GLP‐1RA) versus a more conventional glucocentric treatment approach combining sulphonylureas (SU) and insulin from the point of type 2 diabetes (T2D) diagnosis.Methods: We performed a retrospective cohort study using the Global Collaborative Network in TriNetX. We included individuals prescribed metformin, pioglitazone, an SGLT2i, and a GLP‐1 RA for at least 1‐year duration, within 3 years of a T2D diagnosis, and compared with individuals prescribed insulin and a SU within the same temporal pattern. Individuals were followed up for 3 years.Results: We propensity score‐matched (PSM) for 26 variables. A total of 1762 individuals were included in the final analysis (n = 881 per cohort). At 3‐years, compared to the insulin/SU group, the metformin/pioglitazone/SGLT2i/GLP‐1 RA group had a lower risk of heart failure (HR 0.34, 95% CI 0.13–0.87, p = 0.018), acute coronary syndrome (HR 0.29, 95% CI 0.12–0.67, p = 0.002), stroke (HR 0.17, 95% CI 0.06–0.49, p < 0.001), chronic kidney disease (HR 0.50, 95% CI 0.25–0.99, p = 0.042), and hospitalisation (HR 0.59, 95% CI 0.46–0.77, p < 0.001).Conclusions: In this real‐world study, early, intensive polytherapy, targeting the distinct pathophysiological defects in T2D, is associated with significantly more favourable cardiorenal outcomes, compared to insulin and SU therapy.
Multifunctional Bispecific Nanovesicles Targeting SLAMF7 Trigger Potent Antitumor Immunity
Authors: Zhu Manman , Wu Yongjian , Zhu Tianchuan , Chen Jian , Chen Zhenxing , Ding Hanxi , Tan Siyi , He Jianzhong , Zeng Qi , Huang Xi 
Published: May 2024

Abstract
The effectiveness of immune checkpoint inhibitor (ICI) therapy is hindered by the ineffective infiltration and functioning of cytotoxic T cells and the immunosuppressive tumor microenvironment (TME). Signaling lymphocytic activation molecule family member 7 (SLAMF7) is a pivotal co-stimulatory receptor thought to simultaneously trigger NK-cell, T-cell, and macrophage antitumor cytotoxicity. However, the potential of this collaborative immune stimulation in antitumor immunity for solid tumors is underexplored due to the exclusive expression of SLAMF7 by hematopoietic cells. Here, we report the development and characterization of multifunctional bispecific nanovesicles (NVs) targeting SLAMF7 and glypican-3—a hepatocellular carcinoma (HCC)–specific tumor antigen. We found that by effectively “decorating” the surfaces of solid tumors with SLAMF7, these NVs directly induced potent and specific antitumor immunity and remodeled the immunosuppressive TME, sensitizing the tumors to programmed cell death protein 1 (PD1) blockade. Our findings highlight the potential of SLAMF7-targeted multifunctional bispecific NVs as an anticancer strategy with implications for designing next-generation targeted cancer therapies.
Educating Students for Climate Action: Distraction or Higher-Education Capital?
Authors: Reimers Fernando M. 
Published: May 2024

Abstract
This essay examines how universities are responding to demands to educate students for climate action. I argue for a whole-of-university approach, in which sustainability becomes part of the mission of the university, and translates into reimagined forms of education, research, outreach, and management of the university operations. This approach runs counter to the most common response of universities, incremental to new demands, and is likely to take place only in institutions with greater capacity for innovation. Strategy and knowledge are key resources to support such innovation, drawing on the comparative analysis of the global experience of higher education, as there are already high rates of institutional innovation globally in educating for climate action.