bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the impact of climate change on long-term and short-term variability of rainfall in Madhya Pradesh, Central India
Authors: Kumar Parvendra , Sharma Vikram , Jayal Tripti , Deswal Sanjay
Published: January 2024

The present study assesses trends in rainfall in Madhya Pradesh, Central India, over the long (1871–2016) as well as short (1987–2016) temporal scales. The region is home to disadvantageous groups of the population including vulnerable tribals who depend on rainfall-based agriculture and forest products. Therefore, any disruption in rainfall trends due to climate change needs to be documented for better planning. This study focuses on two meteorological subdivisions, East and West Madhya Pradesh, which receive a major portion of rainfall through the Bay of Bengal branch and the Arabian Sea branch of the Indian Summer Monsoon. The study is based on the rainfall series provided by the Indian Institute of Tropical Meteorology, Pune, India. This study used the Mann–Kendall test to detect a trend and Sen’s Slope to estimate the magnitude of change in rainfall. Statistically significant negative trends were detected in total annual (− 1.125 mm y − 1) and monsoon (− 1.242 mm y − 1) rainfall over long-term observation in East Madhya Pradesh only. However, during the last 30 years, no trends have been recorded in East Madhya Pradesh. In West Madhya Pradesh, rainfall has not recorded any trend for long- as well as short-term observation periods. The non-availability of a trend in rainfall during May and October at both meteorological subdivisions shows that there is no shift in the duration of the monsoon season over long as well as short temporal observations. The decreasing rainfall trends in Eastern Madhya Pradesh over the long-term observation seem to be caused by changing patterns of tropical cyclone frequency in the Bay of Bengal.
The Private as a Core Part of International Law: The School of Salamanca, Slavery, and Marriage (Sixteenth Century)
Authors: Martineau Anne-Charlotte
Published: January 2024

In “Gender and the Lost Private Side of International Law,” Karen Knop argued that “recuperating private international law as a lost side of international law can open up counter-disciplinary research on gender in the history of international law.”1 In this essay, I use Knop's argument to revisit our understanding of the sixteen century “School of Salamanca”2 and its importance for international legal history from a gender perspective. I focus on the practice of jurists and theologians associated with the School of Salamanca in assessing the validity of marriages of newly converted Indigenous peoples in Brazil (negros da terra), and later the validity of remarriages of Indigenous people and enslaved Africans (negros da Guiné) who had already been married in places from which they had been forcibly removed.3 To do this, these jurists and theologians engaged in private international law (or conflict of laws) reasoning. A key question involved determining what law governed each marriage—was it ius gentium, natural law, or canon law? Examining their arguments, I argue, offers an instance of Knop's insight that recuperating private international law allows us to redress the invisibility of women in the history of international law. In my case study, not only do we better understand “how power operates through international legal concepts and institutions”4 in the private sphere of the family in the colonies, but also, and crucially, how “private international law make[s] visible the effects of colonial . . . law on gender relations and national identity at home,”5 to borrow Knop's words.
Smith theory and cyclic base change functoriality
Authors: Feng Tony
Published: January 2024

Lafforgue and Genestier-Lafforgue have constructed the global and (semisimplified) local Langlands correspondences for arbitrary reductive groups over function fields. We establish various properties of these correspondences regarding functoriality for cyclic base change: For

$\mathbf {Z}/p\mathbf {Z}$

-extensions of global function fields, we prove the existence of base change for mod p automorphic forms on arbitrary reductive groups. For

$\mathbf {Z}/p\mathbf {Z}$

-extensions of local function fields, we construct a base change homomorphism for the mod p Bernstein center of any reductive group. We then use this to prove existence of local base change for mod p irreducible representation along

$\mathbf {Z}/p\mathbf {Z}$

-extensions, and that Tate cohomology realizes base change descent, verifying a function field version of a conjecture of Treumann-Venkatesh.

The proofs are based on equivariant localization arguments for the moduli spaces of shtukas. They also draw upon new tools from modular representation theory, including parity sheaves and Smith-Treumann theory. In particular, we use these to establish a categorification of the base change homomorphism for mod p spherical Hecke algebras, in a joint appendix with Gus Lonergan.
Intragroup communication in social dilemmas: An artefactual public good field experiment in small-scale communities
Authors: Hoenow Nils Christian , Pourviseh Adrian
Published: January 2024

Communication is well-known to increase cooperation rates in social dilemma situations, but the exact mechanisms behind this remain largely unclear. This study examines the impact of communication on public good provisioning in an artefactual field experiment conducted with 216 villagers from small, rural communities in northern Namibia. In line with previous experimental findings, we observe a strong increase in cooperation when face-to-face communication is allowed before decision-making. We additionally introduce a condition in which participants cannot discuss the dilemma but talk to their group members about an unrelated topic prior to learning about the public good game. It turns out that this condition already leads to higher cooperation rates, albeit not as high as in the condition in which discussions about the social dilemma are possible. The setting in small communities also allows investigating the effects of pre-existing social relationships between group members and their interaction with communication. We find that both types of communication are primarily effective among socially more distant group members, which suggests that communication and social ties work as substitutes in increasing cooperation. Further analyses rule out better comprehension of the game and increased mutual expectations of one’s group members’ contributions as drivers for the communication effect. Finally, we discuss the role of personal and injunctive norms to keep commitments made during discussions.
What can radar-based measures of subglacial hydrology tell us about basal shear stress? A case study at Thwaites Glacier, West Antarctica
Authors: Haris Rohaiz , Chu Winnie , Robel Alexander
Published: January 2024

Ice sheet models use observations to infer basal shear stress, but the variety of methods and datasets available has resulted in a wide range of estimates. Radar-based metrics such as reflectivity and specularity content have been used to characterize subglacial hydrologic conditions that are linked to spatial variations in basal shear stress. We explore whether radar metrics can be used to inform models about basal shear stress. At Thwaites Glacier, West Antarctica, we sample basal shear stress inversions across a wide range of ice sheet models to see how the basal shear stress distribution changes in regions of varying relative reflectivity and specularity content. Our results reveal three key findings: (1) Regions of high specularity content exhibit lower mean basal shear stresses (2) Wet and bumpy regions, as characterized by high relative reflectivity and low specularity content, exhibit higher mean basal shear stresses (3) Models disagree about what basal shear stress should be at the onset of rapid ice flow and high basal melt where relative reflectivity and specularity content are low.
SIR model with social gatherings
Authors: Cortez Roberto
Published: January 2024

We introduce an extension to Kermack and McKendrick’s classic susceptible–infected–recovered (SIR) model in epidemiology, whose underlying mechanism of infection consists of individuals attending randomly generated social gatherings. This gives rise to a system of ordinary differential equations (ODEs) where the force of the infection term depends non-linearly on the proportion of infected individuals. Some specific instances yield models already studied in the literature, to which the present work provides a probabilistic foundation. The basic reproduction number is seen to depend quadratically on the average size of the gatherings, which may be helpful in understanding how restrictions on social gatherings affect the spread of the disease. We rigorously justify our model by showing that the system of ODEs is the mean-field limit of the jump Markov process corresponding to the evolution of the disease in a finite population.
An unusual presentation: temporomandibular tissue herniation through congenital foramen of Huschke
Authors: Patel Sachin Tushar , Dusu Keli , Moharrum Tamir , Salem Mohammed
Published: January 2024

Background

The herniation of temporomandibular tissue through the foramen of Huschke into the external auditory canal is a rare clinical anomaly. This paper describes one such case and provides an overview of the relevant literature. This paper elaborates upon the aetiology, clinical assessment, management and associated complications.

Case report

A 54-year-old woman presented with a 3-month history of right ear pain and a polypoid lesion in her right ear canal. This lesion expanded during a Valsalva manoeuvre, and imaging demonstrated a defect in the antero-superior aspect of the canal with herniation of soft tissue. The patient was managed conservatively as the symptoms resided.

Conclusion

Ear canal lesions that protrude or change in size with a Valsalva manoeuvre could be due to a persistent foramen of Huschke. In symptomatic cases needing surgical intervention, a variety of materials may be used to close the defect. Titanium mesh, with or without cartilage overlay, appears to be the most popular choice.
The mythic narratives of Candomblé Nagô and what they imply about its Supreme Being
Authors: Porcher José Eduardo
Published: January 2024

In this article, I explore the mythic narratives of the Yoruba-derived tradition of Candomblé Nagô to discern the attributes of its Supreme Being. I introduce Candomblé, offering an overview of its central beliefs and practices, and then present theological perspectives on the Supreme Being in African Traditional Religion as a basis for comparison with the myths I will examine. I consider the primary creation myths of Candomblé, emphasizing references to the tradition's Supreme Being and, analysing these myths, I argue that Candomblé's Supreme Being, as depicted in these narratives, amounts to a limited god. This portrayal accounts for the absence of a problem of evil within the tradition. It suggests the moral ambivalence of Candomblé's Supreme Being and other high deities, as well as the world itself. This exploration sheds light on a lesser-explored tradition and its unique approach to philosophical dilemmas, distinct from the predominantly theistic framework of most philosophy of religion, and evinces that philosophizing through immersion in myths should involve appreciating the complexities and richness inherent in these forms of life, free from the imposition of external assumptions or biases.
A game of raids: Expanding on a game theoretical approach utilising the prisoner's dilemma and ethnography in situ
Authors: Jeffries Emily M. L. , Wright Sarah E. , Lew-Levy Sheina
Published: January 2024

In this commentary, we set out the specifics of how Glowacki's game theoretical framework for the evolution of peace could be incorporated within broader cultural evolutionary approaches. We outline a formal proposal for prisoner's dilemma games investigating raid-based conflict. We also centre an ethnographic lens to understand the norms surrounding war and peace in intergroup interactions in small-scale communities.
Experimental evidence suggests intergroup relations are, by default, neutral rather than aggressive
Authors: Imada Hirotaka , Mifune Nobuhiro
Published: January 2024

The target article offers a game-theoretical analysis of primitive intergroup aggression (i.e., raiding) and discusses difficulties in achieving peace. We argue the analysis does not capture the actual strategy space, missing out “do-nothing.” Experimental evidence robustly shows people prefer doing nothing against out-group members over cooperating with/attacking them. Thus, the target article overestimates the likelihood of intergroup aggression.
Peace in other primates
Authors: Grüning David J. , Krueger Joachim I.
Published: January 2024

We elaborate on Glowacki's claim that humans are more capable of establishing peace than other mammals. We present three aspects suggesting caution. First, the social capabilities of nonhuman primates should not be underestimated. Second, the effect of these capabilities on peace establishment is nonmonotonous. Third, defining peace by human-centered values introduces a fallacy.
Quantifying stakeholders’ preference for implantable medical devices in China: a discrete choice experiment
Authors: Wan Bin , Shen Jiaojie , Chen Jiali , Weng Linjia , Zhao Peng , Deng Yunfei , Zhang Lingli , Zhang Feiyi , Wang Yingpeng , Li Xin , Chang Feng , Ding Haixia , Lu Yun
Published: January 2024

Objectives

This study aims to gain insight into each attribute as presented in the value of implantable medical devices, quantify attributes’ strength and their relative importance, and identify the determinants of stakeholders’ preferences.

Methods

A mixed-methods design was used to identify attributes and levels reflecting stakeholders’ preference toward the value of implantable medical devices. This design combined literature reviewing, expert’s consultation, one-on-one interactions with stakeholders, and a pilot testing. Based on the design, six attributes and their levels were settled. Among 144 hypothetical profiles, 30 optimal choice sets were developed, and healthcare professionals (decision-makers, health technology assessment experts, hospital administrators, medical doctors) and patients as stakeholders in China were surveyed. A total of 134 respondents participated in the survey. Results were analyzed by mixed logit model and conditional logit model.

Results

The results of the mixed logit model showed that all the six attributes had a significant impact on respondents’ choices on implantable medical devices. Respondents were willing to pay the highest for medical devices that provided improvements in clinical safety, followed by increased clinical effectiveness, technology for treating severe diseases, improved implement capacity, and innovative technology (without substitutes).

Conclusions

The findings of DCE will improve the current evaluation on the value of implantable medical devices in China and provide decision-makers with the relative importance of the criteria in pricing and reimbursement decision-making of implantable medical devices.
Healthy Mistrust: Medical Black Box Algorithms, Epistemic Authority, and Preemptionism
Authors: Wolkenstein Andreas
Published: January 2024

In the ethics of algorithms, a specifically epistemological analysis is rarely undertaken in order to gain a critique (or a defense) of the handling of or trust in medical black box algorithms (BBAs). This article aims to begin to fill this research gap. Specifically, the thesis is examined according to which such algorithms are regarded as epistemic authorities (EAs) and that the results of a medical algorithm must completely replace other convictions that patients have (preemptionism). If this were true, it would be a reason to distrust medical BBAs. First, the author describes what EAs are and why BBAs can be considered EAs. Then, preemptionism will be outlined and criticized as an answer to the question of how to deal with an EA. The discussion leads to some requirements for dealing with a BBA as an EA.
Effective control of refractory pulmonary hypertension with iloprost inhalation in an infant with congenital absence of the right pulmonary artery: a case report
Authors: Hsiao Chu-Yuan , Lu Wen-Hsien
Published: January 2024

Unilateral absence of the pulmonary artery is a rare congenital cardiovascular anomaly that can lead to pulmonary hypertension and poor outcomes. We report the case of a 1-month-old infant with isolated unilateral absence of the pulmonary artery and severe pulmonary hypertension on the right and left sides, respectively. The patient was unresponsive to multiple medications for pulmonary hypertension, and surgical revascularisation was unfeasible. However, iloprost inhalation was effective.
Alice Meynell and the Politics of an Image: “The Climate of Smoke”
Authors: Armstrong Isobel
Published: January 2024

The collaboration of William Hyde and Alice Meynell in London Impressions (1898) led to Hyde's photogravure image, “Utilitarian London,” which is a direct critique of Turner's Rain, Steam and Speed (1844), and to a companion essay by Meynell, “The Climate of Smoke,” that is an ecological poetics exploring the deep harms of pollution.
Gender and Precarity across Time: Where Are the Writing Working Women?
Authors: Wånggren Lena
Published: January 2024

The end of the nineteenth century in Britain saw a range of “newnesses”; New Unionism signified a boom in trade unionism, while the New Woman figure symbolized women's struggle for independence. However, both as literary figures and as real-life writers, such New Women were largely middle class and educated. Where are the working women within the sphere of literary and cultural production, and how are they represented within the New Unionism? Against a dominant trade unionism that argued for a “family wage” and considered women's organizing as a threat, the Women's Trade Union League (1874), the National Federation of Women Workers (1906), the 1888 Match Girls strike, and writers and labor activists such as Annie Besant and Clementina Black noted women's roles within labor. Attempting to locate a working New Woman in the trade union movement, this paper is a reflective work-in-progress, an exploration rather than a finished argument. Written by a precariously employed woman trade unionist in the twenty-first century, struggling to find time to write, examining the works of precariously employed women workers one hundred years earlier, the essay poses questions about what happens to politically engaged scholarship in a time of increasingly precarious working conditions and knowledges.
The effects of health-related food taxes on the environmental impact of consumer food purchases: secondary analysis of data from a randomised controlled trial in a virtual supermarket
Authors: Eykelenboom Michelle , Mersch Derek , Grasso Alessandra C , Vellinga Reina E , Temme Elisabeth HM , Steenhuis Ingrid HM , Olthof Margreet R
Published: January 2024

Objective:

To measure the effects of health-related food taxes on the environmental impact of consumer food purchases in a virtual supermarket.

Design:

This is a secondary analysis of data from a randomised controlled trial in which participants were randomly assigned to a control condition with regular food prices (n 152), an experimental condition with a sugar-sweetened beverage (SSB) tax (n 131) or an experimental condition with a nutrient profiling tax based on Nutri-Score (n 112). Participants were instructed to undertake their typical weekly grocery shopping for their households. Primary outcome measures were three environmental impact indicators: greenhouse gas (GHG) emissions, land use and blue water use per household per week. Data were analysed using linear regression analyses.

Setting:

Three-dimensional virtual supermarket.

Participants:

Dutch adults (≥ 18 years) who were responsible for grocery shopping in their household (n 395).

Results:

GHG emissions (–7·6 kg CO2-eq; 95 % CI –12·7, –2·5) and land use (–3·9 m2/year; 95 % CI –7·7, –0·2) were lower for the food purchases of participants in the nutrient profiling tax condition than for those in the control condition. Blue water use was not affected by the nutrient profiling tax. Moreover, the SSB tax had no significant effect on any of the environmental impact indicators.

Conclusions:

A nutrient profiling tax based on Nutri-Score reduced the environmental impact of consumer food purchases. An SSB tax did not affect the environmental impact in this study.
Association of birthweight with diabetes, hypertension, and ischemic heart disease in young adulthood: a retrospective cohort study
Authors: Yoshida-Montezuma Yulika , Keown-Stoneman Charles D.G. , Birken Catherine S. , Maguire Jonathon L. , Brown Hilary K. , Anderson Laura N.
Published: January 2024

Birthweight has been associated with diabetes in a reverse J-shape (highest risk at low birthweight and moderately high risk at high birthweight) and inversely associated with hypertension in adulthood with inconsistent evidence for cardiovascular disease. There is a lack of population-based studies examining the incidence of cardiometabolic outcomes in young adults born with low and high birthweights. To evaluate the association between birthweight and diabetes, hypertension, and ischemic heart disease (IHD) in young adulthood, we conducted a retrospective cohort study of 874,904 singletons born in Ontario, Canada, from 1994 to 2002, identified from population-based health administrative data. Separate Cox regression models examined birthweight in association with diabetes, hypertension, and IHD adjusting for confounders. Among adults 18–26 years, the diabetes incidence rate was 18.15 per 100,000 person-years, hypertension was 15.80 per 100,000 person-years, and IHD was 1.85 per 100,000 person-years. Adjusted hazard ratios (AHR) for the hazard of diabetes with low (<2500g) and high (>4000g), compared with normal (2500–4000g) birthweight, were 1.46 (95% CI 1.28, 1.68) and 1.09 (0.99, 1.21), respectively. AHR for hypertension with low and high birthweight were 1.34 (1.15, 1.56) and 0.86 (0.77, 0.97), respectively. AHR for IHD with low and high birthweight were 1.28 (0.80, 2.05) and 0.97 (0.71, 1.33), respectively. Overall, birthweight was associated with diabetes in young adults in a reverse J-shape and inversely with hypertension. There was insufficient evidence of an association with IHD. Further evidence is needed to understand the causal mechanisms between birthweight and cardiometabolic diseases in young adults.
Voter Approval of Bond Referendums: The Role of Bond Amount and Ballot Characteristics
Authors: Bechard Andrew , Lang Corey , Pearson-Merkowitz Shanna
Published: January 2024

Municipal and state governments are often constitutionally bound to ask voters to approve new government debt through voting on bond referendums. Generally, politicians expect voters to balk at higher-cost bonds and be more willing to approve lower-cost bonds. However, there is minimal research on how the amount of a bond affects voter support. We implement a survey experiment that presents respondents with hypothetical ballots, in which the cost of proposed bonds, the number of bonds on the ballot, and the order in which they are presented, are all randomized. Our results suggest that support is not responsive to the amount of the bond, even when the cost is well outside what is typical and within the bounds of what the government can afford. In contrast, we find other aspects of the ballot matter significantly more for bond referendum approval. The more bonds on the ballot and being placed lower on the ballot both reduce support significantly.
U.S. Animal Disease Policies and Human Health Debates
Authors: Olmstead Alan L. , Rhode Paul W.
Published: January 2024

The U.S. federal government adopted aggressive policies to control animal diseases decades before it made significant attempts to improve human health. Progressive-era reformers crafted a powerful argument that the male-dominated, rural-oriented political system valued the lives of hogs more than the well-being of babies. The invidious hog-baby comparison became a pervasive theme in debates over the Children’s Bureau, a National Department of Health, and the Sheppard-Towner Act, and it has been reproduced uncritically in recent years. This article investigates the important historical relationships between U.S. animal and human health policies. Human health champions would have been better served by embracing a One Health approach when possible, drawing more on the lessons learned in combating animal diseases.
Color liquid crystal grating based color holographic 3D display system with large viewing angle
Authors: Wang Di , Li Yi-Long , Chu Fan , Li Nan-Nan , Li Zhao-Song , Lee Sin-Doo , Nie Zhong-Quan , Liu Chao , Wang Qiong-Hua
Published: January 2024

Holographic 3D display is highly desirable for numerous applications ranging from medical treatments to military affairs. However, it is challenging to simultaneously achieve large viewing angle and high-fidelity color reconstruction due to the intractable constraints of existing technology. Here, we conceptually propose and experimentally demonstrate a simple and feasible pathway of using a well-designed color liquid crystal grating to overcome the inevitable chromatic aberration and enlarge the holographic viewing angle, thus enabling large-viewing-angle and color holographic 3D display. The use of color liquid crystal grating allows performing secondary diffraction modulation on red, green and blue reproduced images simultaneously and extending the viewing angle in the holographic 3D display system. In principle, a chromatic aberration-free hologram generation mechanism in combination with the color liquid crystal grating is proposed to pave the way for on such a superior holographic 3D display. The proposed system shows a color viewing angle of ~50.12°, which is about 7 times that of the traditional system with a single spatial light modulator. This work presents a paradigm for achieving desirable holographic 3D display, and is expected to provide a new way for the wide application of holographic display.
Driver mutation zygosity is a critical factor in predicting clonal hematopoiesis transformation risk
Authors: Kishtagari Ashwin , Khan M. A. Wasay , Li Yajing , Vlasschaert Caitlyn , Marneni Naimisha , Silver Alexander J. , von Beck Kelly , Spaulding Travis , Stockton Shannon , Snider Christina , Sochacki Andrew , Dorand Dixon , Mack Taralynn M. , Ferrell P. Brent , Xu Yaomin , Bejan Cosmin A. , Savona Michael R. , Bick Alexander G.
Published: January 2024

Clonal hematopoiesis (CH) can be caused by either single gene mutations (eg point mutations in JAK2 causing CHIP) or mosaic chromosomal alterations (e.g., loss of heterozygosity at chromosome 9p). CH is associated with a significantly increased risk of hematologic malignancies. However, the absolute rate of transformation on an annualized basis is low. Improved prognostication of transformation risk is urgently needed for routine clinical practice. We hypothesized that the co-occurrence of CHIP and mCAs at the same locus (e.g., transforming a heterozygous JAK2 CHIP mutation into a homozygous mutation through concomitant loss of heterozygosity at chromosome 9) might have important prognostic implications for malignancy transformation risk. We tested this hypothesis using our discovery cohort, the UK Biobank (n = 451,180), and subsequently validated it in the BioVU cohort (n = 91,335). We find that individuals with a concurrent somatic mutation and mCA were at significantly increased risk of hematologic malignancy (for example, In BioVU cohort incidence of hematologic malignancies is higher in individuals with co-occurring JAK2 V617F and 9p CN-LOH; HR = 54.76, 95% CI = 33.92–88.41, P < 0.001 vs. JAK2 V617F alone; HR = 44.05, 95% CI = 35.06–55.35, P < 0.001). Currently, the ‘zygosity’ of the CHIP mutation is not routinely reported in clinical assays or considered in prognosticating CHIP transformation risk. Based on these observations, we propose that clinical reports should include ‘zygosity’ status of CHIP mutations and that future prognostication systems should take mutation ‘zygosity’ into account.
Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples
Authors: Pipek Orsolya Anna , Medgyes-Horváth Anna , Stéger József , Papp Krisztián , Visontai Dávid , Koopmans Marion , Nieuwenhuijse David , Oude Munnink Bas B. ,   VEO Technical Working Group, Cochrane Guy , Rahman Nadim , Cummins Carla , Yuan David Yu , Selvakumar Sandeep , Mansurova Milena , O’Cathail Colman , Sokolov Alexey , Thorne Ross , Worp Nathalie , Amid Clara , Csabai István
Published: January 2024

Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta – Omicron BA.1 intra-host recombinants.
Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes
Authors: Fujita Ken-ichi , Ito Misa , Irie Midori , Harada Kotaro , Fujiwara Naoko , Ikeda Yuya , Yoshioka Hanae , Yamazaki Tomohiro , Kojima Masaki , Mikami Bunzo , Mayeda Akila , Masuda Seiji
Published: January 2024

mRNA export is an essential pathway for the regulation of gene expression. In humans, closely related RNA helicases, UAP56 and URH49, shape selective mRNA export pathways through the formation of distinct complexes, known as apo-TREX and apo-AREX complexes, and their subsequent remodeling into similar ATP-bound complexes. Therefore, defining the unidentified components of the apo-AREX complex and elucidating the molecular mechanisms underlying the formation of distinct apo-complexes is key to understanding their functional divergence. In this study, we identify additional apo-AREX components physically and functionally associated with URH49. Furthermore, by comparing the structures of UAP56 and URH49 and performing an integrated analysis of their chimeric mutants, we exhibit unique structural features that would contribute to the formation of their respective complexes. This study provides insights into the specific structural and functional diversification of these two helicases that diverged from the common ancestral gene Sub2.
A retrofit sensing strategy for soft fluidic robots
Authors: Zou Shibo , Picella Sergio , de Vries Jelle , Kortman Vera G. , Sakes Aimée , Overvelde Johannes T. B.
Published: January 2024

Soft robots are intrinsically capable of adapting to different environments by changing their shape in response to interaction forces. However, sensory feedback is still required for higher level decisions. Most sensing technologies integrate separate sensing elements in soft actuators, which presents a considerable challenge for both the fabrication and robustness of soft robots. Here we present a versatile sensing strategy that can be retrofitted to existing soft fluidic devices without the need for design changes. We achieve this by measuring the fluidic input that is required to activate a soft actuator during interaction with the environment, and relating this input to its deformed state. We demonstrate the versatility of our strategy by tactile sensing of the size, shape, surface roughness and stiffness of objects. We furthermore retrofit sensing to a range of existing pneumatic soft actuators and grippers. Finally, we show the robustness of our fluidic sensing strategy in closed-loop control of a soft gripper for sorting, fruit picking and ripeness detection. We conclude that as long as the interaction of the actuator with the environment results in a shape change of the interval volume, soft fluidic actuators require no embedded sensors and design modifications to implement useful sensing.
Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis
Authors: Drexhage Linnea Z. , Zhang Shengpan , Dupont Maeva , Ragaller Franziska , Sjule Ellen , Cabezas-Caballero Jose , Deimel Lachlan P. , Robertson Helen , Russell Rebecca A. , Dushek Omer , Sezgin Erdinc , Karaji Niloofar , Sattentau Quentin J.
Published: January 2024

Efferocytic clearance of apoptotic cells in general, and T cells in particular, is required for tissue and immune homeostasis. Transmembrane mucins are extended glycoproteins highly expressed in the cell glycocalyx that function as a barrier to phagocytosis. Whether and how mucins may be regulated during cell death to facilitate efferocytic corpse clearance is not well understood. Here we show that normal and transformed human T cells express a subset of mucins which are rapidly and selectively removed from the cell surface during apoptosis. This process is mediated by the ADAM10 sheddase, the activity of which is associated with XKR8-catalyzed flipping of phosphatidylserine to the outer leaflet of the plasma membrane. Mucin clearance enhances uptake of apoptotic T cells by macrophages, confirming mucins as an enzymatically-modulatable barrier to efferocytosis. Together these findings demonstrate a glycocalyx regulatory pathway with implications for therapeutic intervention in the clearance of normal and transformed apoptotic T cells.
Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data
Authors: Ehsan Nava , Kotis Bence M. , Castel Stephane E. , Song Eric J. , Mancuso Nicholas , Mohammadi Pejman
Published: January 2024

Expression Quantitative Trait Loci (eQTLs) are critical to understanding the mechanisms underlying disease-associated genomic loci. Nearly all protein-coding genes in the human genome have been associated with one or more eQTLs. Here we introduce a multi-variant generalization of allelic Fold Change (aFC), aFC-n, to enable quantification of the cis-regulatory effects in multi-eQTL genes under the assumption that all eQTLs are known and conditionally independent. Applying aFC-n to 458,465 eQTLs in the Genotype-Tissue Expression (GTEx) project data, we demonstrate significant improvements in accuracy over the original model in estimating the eQTL effect sizes and in predicting genetically regulated gene expression over the current tools. We characterize some of the empirical properties of the eQTL data and use this framework to assess the current state of eQTL data in terms of characterizing cis-regulatory landscape in individual genomes. Notably, we show that 77.4% of the genes with an allelic imbalance in a sample show 0.5 log2 fold or more of residual imbalance after accounting for the eQTL data underlining the remaining gap in characterizing regulatory landscape in individual genomes. We further contrast this gap across tissue types, and ancestry backgrounds to identify its correlates and guide future studies.
Nanoscale silicate melt textures determine volcanic ash surface chemistry
Authors: Hornby Adrian J. , Ayris Paul M. , Damby David E. , Diplas Spyridon , Eychenne Julia , Kendrick Jackie E. , Cimarelli Corrado , Kueppers Ulrich , Scheu Bettina , Utley James E. P. , Dingwell Donald B.
Published: January 2024

Explosive volcanic eruptions produce vast quantities of silicate ash, whose surfaces are subsequently altered during atmospheric transit. These altered surfaces mediate environmental interactions, including atmospheric ice nucleation, and toxic effects in biota. A lack of knowledge of the initial, pre-altered ash surface has required previous studies to assume that the ash surface composition created during magmatic fragmentation is equivalent to the bulk particle assemblage. Here we examine ash particles generated by controlled fragmentation of andesite and find that fragmentation generates ash particles with substantial differences in surface chemistry. We attribute this disparity to observations of nanoscale melt heterogeneities, in which Fe-rich nanophases in the magmatic melt deflect and blunt fractures, thereby focusing fracture propagation within aureoles of single-phase melt formed during diffusion-limited growth of crystals. In this manner, we argue that commonly observed pre-eruptive microtextures caused by disequilibrium crystallisation and/or melt unmixing can modify fracture propagation and generate primary discrepancies in ash surface chemistry, an essential consideration for understanding the cascading consequences of reactive ash surfaces in various environments.
A dicarbonate solvent electrolyte for high performance 5 V-Class Lithium-based batteries
Authors: Zhang Xiaozhe , Xu Pan , Duan Jianing , Lin Xiaodong , Sun Juanjuan , Shi Wenjie , Xu Hewei , Dou Wenjie , Zheng Qingyi , Yuan Ruming , Wang Jiande , Zhang Yan , Yu Shanshan , Chen Zehan , Zheng Mingsen , Gohy Jean-François , Dong Quanfeng , Vlad Alexandru
Published: January 2024

Rechargeable lithium batteries using 5 V positive electrode materials can deliver considerably higher energy density as compared to state-of-the-art lithium-ion batteries. However, their development remains plagued by the lack of electrolytes with concurrent anodic stability and Li metal compatibility. Here we report a new electrolyte based on dimethyl 2,5-dioxahexanedioate solvent for 5 V-class batteries. Benefiting from the particular chemical structure, weak interaction with lithium cation and resultant peculiar solvation structure, the resulting electrolyte not only enables stable, dendrite-free lithium plating-stripping, but also displays anodic stability up to 5.2 V (vs. Li/Li+), in additive or co-solvent-free formulation, and at low salt concentration of 1 M. Consequently, the Li | |LiNi0.5Mn1.5O4 cells using the 1 M LiPF6 in 2,5-dioxahexanedioate based electrolyte retain >97% of the initial capacity after 250 cycles, outperforming the conventional carbonate-based electrolyte formulations, making this, and potentially other dicarbonate solvents promising for future Lithium-based battery practical explorations.
Cyto-molecular characterization of rDNA and chromatin composition in the NOR-associated satellite in Chestnut (Castanea spp.)
Authors: Islam-Faridi Nurul , Hodnett George L. , Zhebentyayeva Tetyana , Georgi Laura L. , Sisco Paul H. , Hebard Frederick V. , Nelson C. Dana
Published: January 2024

The American chestnut (Castanea dentata, 2n = 2x = 24), once known as the “King of the Appalachian Forest”, was decimated by chestnut blight during the first half of the twentieth century by an invasive fungus (Cryphonectria parasitica). The Chinese chestnut (C. mollissima,2n = 2x = 24), in contrast to American chestnut, is resistant to this blight. Efforts are being made to transfer this resistance to American chestnut through backcross breeding and genetic engineering. Both chestnut genomes have been genetically mapped and recently sequenced to facilitate gene discovery efforts aimed at assisting molecular breeding and genetic engineering. To complement and extend this genomic work, we analyzed the distribution and organization of their ribosomal DNAs (35S and 5S rDNA), and the chromatin composition of the nucleolus organizing region (NOR)-associated satellites. Using fluorescent in situ hybridization (FISH), we have identified two 35S (one major and one minor) and one 5S rDNA sites. The major 35S rDNA sites are terminal and sub-terminal in American and Chinese chestnuts, respectively, originating at the end of the short arm of the chromosome, extending through the secondary constriction and into the satellites. An additional 5S locus was identified in certain Chinese chestnut accessions, and it was linked distally to the major 35S site. The NOR-associated satellite in Chinese chestnut was found to comprise a proximal region packed with 35S rDNA and a distinct distal heterochromatic region. In contrast, the American chestnut satellite was relatively small and devoid of the distal heterochromatic region.
Quantum discriminator for binary classification
Authors: Date Prasanna , Smith Wyatt
Published: January 2024

Quantum computers have the unique ability to operate relatively quickly in high-dimensional spaces—this is sought to give them a competitive advantage over classical computers. In this work, we propose a novel quantum machine learning model called the Quantum Discriminator, which leverages the ability of quantum computers to operate in the high-dimensional spaces. The quantum discriminator is trained using a quantum-classical hybrid algorithm in $$\mathcal {O}(N\log N)$$

O
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time, and inferencing is performed on a universal quantum computer in $$\mathcal {O}(N)$$

O
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time. The quantum discriminator takes as input the binary features extracted from a given datum along with a prediction qubit, and outputs the predicted label. We analyze its performance on the Iris and Bars and Stripes data sets, and show that it can attain 99% accuracy in simulation.
A CIC-related-epigenetic factors-based model associated with prediction, the tumor microenvironment and drug sensitivity in osteosarcoma
Authors: Yu Bin , Geng Chengkui , Wu Zhongxiong , Zhang Zhongzi , Zhang Aili , Yang Ze , Huang Jiazheng , Xiong Ying , Yang Huiqin , Chen Zhuoyuan
Published: January 2024

Osteosarcoma is generally considered a cold tumor and is characterized by epigenetic alterations. Although tumor cells are surrounded by many immune cells such as macrophages, T cells may be suppressed, be inactivated, or not be presented due to various mechanisms, which usually results in poor prognosis and insensitivity to immunotherapy. Immunotherapy is considered a promising anti-cancer therapy in osteosarcoma but requires more research, but osteosarcoma does not currently respond well to this therapy. The cancer immunity cycle (CIC) is essential for anti-tumor immunity, and is epigenetically regulated. Therefore, it is possible to modulate the immune microenvironment of osteosarcoma by targeting epigenetic factors. In this study, we explored the correlation between epigenetic modulation and CIC in osteosarcoma through bioinformatic methods. Based on the RNA data from TARGET and GSE21257 cohorts, we identified epigenetic related subtypes by NMF clustering and constructed a clinical prognostic model by the LASSO algorithm. ESTIMATE, Cibersort, and xCell algorithms were applied to analyze the tumor microenvironment. Based on eight epigenetic biomarkers (SFMBT2, SP140, CBX5, HMGN2, SMARCA4, PSIP1, ACTR6, and CHD2), two subtypes were identified, and they are mainly distinguished by immune response and cell cycle regulation. After excluding ACTR6 by LASSO regression, the prognostic model was established and it exhibited good predictive efficacy. The risk score showed a strong correlation with the tumor microenvironment, drug sensitivity and many immune checkpoints. In summary, our study sheds a new light on the CIC-related epigenetic modulation mechanism of osteosarcoma and helps search for potential drugs for osteosarcoma treatment.
Biologically informed deep learning for explainable epigenetic clocks
Authors: Prosz Aurel , Pipek Orsolya , Börcsök Judit , Palla Gergely , Szallasi Zoltan , Spisak Sandor , Csabai István
Published: January 2024

Ageing is often characterised by progressive accumulation of damage, and it is one of the most important risk factors for chronic disease development. Epigenetic mechanisms including DNA methylation could functionally contribute to organismal aging, however the key functions and biological processes may govern ageing are still not understood. Although age predictors called epigenetic clocks can accurately estimate the biological age of an individual based on cellular DNA methylation, their models have limited ability to explain the prediction algorithm behind and underlying key biological processes controlling ageing. Here we present XAI-AGE, a biologically informed, explainable deep neural network model for accurate biological age prediction across multiple tissue types. We show that XAI-AGE outperforms the first-generation age predictors and achieves similar results to deep learning-based models, while opening up the possibility to infer biologically meaningful insights of the activity of pathways and other abstract biological processes directly from the model.
Arterial and venous peripheral vascular assessment using wearable electro-resistive morphic sensors
Authors: Varaki Elham Shabani , Gargiulo Gaetano D. , Malone Matthew , Breen Paul P.
Published: January 2024

Peripheral vascular diseases (PVDs) represent a significant burden on global human health and healthcare systems. With continued growth in obesity and diabetes, it is likely that the incidence of these conditions will increase. As many PVDs remain undiagnosed, low-cost and easy to use diagnostic methods are required. This work uses newly developed wearable electro-resistive morphic sensors to assess venous and arterial competence in the lower limbs of 36 healthy subjects. Comparison of this HeMo device was made to currently available benchtop light reflection rheography and photoplethymography devices. Results indicate that HeMo can detect the physiological signals of interest for both chronic venous insufficiency and peripheral arterial disease and all subjects were interpreted as healthy by each system. However, measurement repeatability of HeMo was highlighted as an issue that requires further system development. Furthermore, as HeMo captures changes in a section of limb circumference due to changes in underlying blood movement, rather than at a single point, the recorded signal is typically damped by comparison. This factor should be considered in any future developments.
Efficacy of endophytic bacteria as promising inducers for enhancing the immune responses in tomato plants and managing Rhizoctonia root-rot disease
Authors: Abbas Mona M. , Ismael Walaa H. , Mahfouz Amira Y. , Daigham Ghadir E. , Attia Mohamed S.
Published: January 2024

Around the world, a variety of crops, including tomatoes, suffer serious economic losses due to the Rhizoctonia root-rot disease. Herein, Bacillus velezensis, Bacillus megaterium, and Herpaspirillum huttiense isolated from strawberry (Fragaria chiloensis var. ananassa) plants were pragmatic as plant growth promotors for battling the Rhizoctonia root rot disease and bringing about defense mechanisms as well as growth promotional strategies in tomato plants. These endophytic bacteria demonstrated potent antifungal activity against R. solani in vitro along in vivo. Data explained that the isolated endophytic bacteria could produce Indole acetic acid, Gibberellic acid GA, and siderophore as well as solubilize phosphate in the soil. The consortium of (Bacillus velezensis, Bacillus megaterium, and Herpaspirillum huttiense) increased the protection % against Rhizoctonia infection by (79.4%), followed by B. velezensis by (73.52%), H. huttiense by (70.5%), and B. megaterium by (67.64%), respectively. There was an increase in soluble proteins and carbohydrates in infected plants treated with a consortium of endophytic bacteria by 30.7% and 100.2% over untreated infected plants, respectively. Applying endophytic bacteria either alone or in combination lowered the level of malondialdehyde MDA and hydrogen peroxide H2O2 and improved the activities of antioxidant enzymes in both infected and uninfected plants. Also, bacterial endophytes have distinctive reactions regarding the number and concentrations of isozymes in both infected and uninfected plants. It could be recommended the commercial usage of a mixture of targeted bacterial endophyte strains as therapeutic nutrients against Rhizoctonia root-rot disease as well as plant growth inducer.