bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying the impact of X-band InSAR penetration bias on elevation change and mass balance estimation
Authors: Abdullahi Sahra , Burgess David , Wessel Birgit , Copland Luke , Roth Achim
Published: February 2024

Interferometric synthetic aperture radar (InSAR) data suffer from an elevation bias due to signal penetration into the firn and ice surface, rendering the height information unusable for elevation and mass-change detection. This study estimates the penetration bias in X-band InSAR data to quantify its impact on elevation and mass-change detection and to demonstrate the applicability of TanDEM-X digital elevation models (DEMs) for cryosphere research. To achieve this, a multiple linear regression model is applied to a time series of four TanDEM-X DEMs acquired between 2010 and 2018 over the Sverdrup Glacier basin (SGB), Devon Ice Cap, Canada. The resulting penetration corrected TanDEM-X DEMs agreed to within ±14 cm of spatially and temporally coincident precise in situ kinematic dGPS data (±10 cm RMSE). Additionally, multi-year estimations of mass change for the SGB derived from differencing TanDEM-X DEMs over multi-year periods between 2010 and 2018, showed good agreement with mean deviation of 338 ± 166 mm w.e. with independent measurements of mass change derived from annual in situ surface mass balance over the same time periods. The results show that the penetration bias can vary significantly, leading to random under- and overestimations in the detection of elevation and mass changes.
A virtual recruitment protocol promotes enrollment of underrepresented groups in a diabetes prevention trial
Authors: Ritchie Natalie D. , Turk Melanie T. , Holtrop Jodi Summers , Durfee Michael Josh , Dickinson L. Miriam , Kaufmann Peter G.
Published: February 2024

Strategies are needed to ensure greater participation of underrepresented groups in diabetes research. We examined the impact of a remote study protocol on enrollment in diabetes research, specifically the Pre-NDPP clinical trial. Recruitment was conducted among 2807 diverse patients in a safety-net healthcare system. Results indicated three-fold greater odds of enrolling in remote versus in-person protocols (AOR 2.90;P< 0.001 [95% CI 2.29–3.67]). Priority populations with significantly higher enrollment included Latinx and Black individuals, Spanish speakers, and individuals who had Medicaid or were uninsured. A remote study design may promote overall recruitment into clinical trials, while effectively supporting enrollment of underrepresented groups.
The Methodologically Flawed Discussion about Deep Disagreement
Authors: Melchior Guido
Published: February 2024

Questions surrounding deep disagreement have gained significant attention in recent years. One of the central debates is metaphysical, focusing on the features that make a disagreement deep. Proposals for what makes disagreements deep include theories about hinge propositions and first epistemic principles. In this paper, I criticize this metaphysical discussion by arguing that it is methodologically flawed. Deep disagreement is a technical or semi-technical term, but the metaphysical discussion mistakenly treats it as a common-sense concept to be analyzed and captured by our pre-theoretical intuitions. Since the literature on deep disagreement is subject to this fundamental confusion and deep disagreement is not a helpful umbrella term either, I propose eliminating the notion of deep disagreement from the philosophical discourse. Instead of analyzing the nature of deep disagreement, we should develop theories about different forms of disagreement, including disagreement about hinge propositions and disagreement about epistemic principles, and, in particular, a theory of rationally irresolvable disagreement.
ON SOME PECULIAR TERRACOTTA NAILS FOUND IN AMYAN (KURDISTAN REGION OF IRAQ)
Authors: Couturaud Barbara
Published: February 2024

In 2019, three fragments of terracotta nails were discovered at the site of Amyan (Kurdistan region of Iraq, Duhok Governorate), probably dated to the second half of the second millennium B.C. Typologically unprecedented, they nonetheless belong to the well-known category of nails found throughout Mesopotamia and Susiana, dating from the fourth to first millennia B.C. This article publishes the nails from Amyan and also contextualises them by comparing them to other terracotta nails found in northern Mesopotamia and dated to the second half of the second millennium B.C. By doing so, I ultimately propose an initial typology of these objects.
Self-similarity of the dipole–multipole transition in rapidly rotating dynamos
Authors: Majumder Debarshi , Sreenivasan Binod , Maurya Gaurav
Published: February 2024

The dipole–multipole transition in rapidly rotating dynamos is investigated through the analysis of forced magnetohydrodynamic waves in an unstably stratified fluid. The focus of this study is on the inertia-free limit applicable to planetary cores, where the Rossby number is small not only on the core depth but also on the length scale of columnar convection. By progressively increasing the buoyant forcing in a linear magnetoconvection model, the slow magnetic–Archimedean–Coriolis (MAC) waves are significantly attenuated so that their kinetic helicity decreases to zero; the fast MAC wave helicity, on the other hand, is practically unaffected. In turn, polarity reversals in low-inertia spherical dynamos are shown to occur when the slow MAC waves disappear under strong forcing. Two dynamically similar regimes are identified – the suppression of slow waves in a strongly forced dynamo and the excitation of slow waves in a moderately forced dynamo starting from a small seed field. While the former regime results in polarity reversals, the latter regime produces the axial dipole from a chaotic multipolar state. For either polarity transition, a local Rayleigh number based on the mean wavenumber of the energy-containing scales bears the same linear relationship with the square of the peak magnetic field measured at the transition. The self-similarity of the dipole–multipole transition can place a constraint on the Rayleigh number for polarity reversals in the Earth.
Effects of porous substrates on the structure of turbulent boundary layers
Authors: Jaiswal P. , Ganapathisubramani B.
Published: February 2024

Three different porous substrates (with different pore sizes,

$s$

, and permeabilities,

$K$

) are used to examine their effect on the structure of boundary layer flow over them. The flow is characterised with single-point hot-wire measurements as well as planar particle image velocimetry. In order to elucidate differences in shallow and deep flows past porous substrates, foams with two different thicknesses (

$h$

) are used (for all three substrates). A wide range of friction Reynolds numbers (

$2000< Re_\tau <13\,500$

) and permeability-based Reynolds numbers (

$1< Re_K< 50$

) are attained. For substrates with

$Re_K \sim 1$

, the flow behaviour remains similar to flow over impermeable smooth walls and as such Townsend's hypothesis remains valid. Very large-scale motions are observed over permeable foams even when the

$Re_K > 1$

. In contrast, a substantial reduction in velocity disturbances and associated length scales is achieved for permeable foams with intermediate values of pore density and relative foam thickness (

$h/s$

), which affects outer-layer similarity. As permeability is increased by increasing pore size, the foam becomes sparse relative to viscous scales at high Reynolds numbers. For such foams, the flow conforms to outer-layer similarity and is more akin to flow over rough surfaces. Permeability attenuates the wavelengths associated with the outer-layer peak.
The role of hyperparameters in machine learning models and how to tune them
Authors: Arnold Christian , Biedebach Luka , Küpfer Andreas , Neunhoeffer Marcel
Published: February 2024

Hyperparameters critically influence how well machine learning models perform on unseen, out-of-sample data. Systematically comparing the performance of different hyperparameter settings will often go a long way in building confidence about a model's performance. However, analyzing 64 machine learning related manuscripts published in three leading political science journals (APSR, PA, and PSRM) between 2016 and 2021, we find that only 13 publications (20.31 percent) report the hyperparameters and also how they tuned them in either the paper or the appendix. We illustrate the dangers of cursory attention to model and tuning transparency in comparing machine learning models’ capability to predict electoral violence from tweets. The tuning of hyperparameters and their documentation should become a standard component of robustness checks for machine learning models.
The Earth Is Sweet. On Cottica Ndyuka (De)compositions
Authors: da Cunha Olívia Maria Gomes
Published: February 2024

How can we remain attentive to the scale of the environmental damage caused in traditional Maroon territories by the effects of the Plantationocene and the material vestiges of colonial and racial violence left by capitalism? Dwelling on conversations held with Maroon Cottica Ndyuka women living in Moengo, a small town established on the Cottica River in Eastern Suriname to support a bauxite industrial plant in the early twentieth century, this text seeks to illuminate what Maria Puig de la Bellacasa (2021) calls “elemental affinities,” relationships in which humans and more-than-humans interact in composing body and earth through refractive and diffractive effects. The paper observes how the women mixed and modeled clay, turning it into sculpted balls known as pemba or pemba doti, frequently used as a therapeutical and spiritual substance, and as food. In so doing, the text deals with processes such as creating, composing, undoing, decomposing, and perishing once the earth—as soil—takes part in and renders possible the existence of diverse creatures. This is a contribution toward an ethnography of (de)compositions of the earth that sets out from the affinities between earth and bodies, attentive to certain metamorphic possibilities, the multiplicities of relations in which soils act.
Transcanal endoscopic carbon dioxide laser resection of early-stage (A1–B1) glomus tympanicum tumours: single-centre case series
Authors: Remacha Joan , Pujol Laura , Caballero-Borrego Miguel , Sandoval Marta , Viza Ignacio , Codina Alberto , Bernal-Sprekelsen Manuel , Larrosa Francisco
Published: February 2024

Objective

To report a single-centre experience in the endoscopic carbon dioxide laser-assisted approach to glomus tympanicum tumours.

Methods

A retrospective case review was conducted of patients diagnosed with class A1 to B1 glomus tympanicum tumours who underwent exclusive transcanal endoscopic carbon dioxide laser surgery.

Results

Seven patients fulfilled the inclusion criteria. All patients (100 per cent) were women, with a mean age of 65.4 years (standard deviation, 13.6). There were five A2 tumours, one A1 tumour and one B1 tumour. One patient presented with a delayed tympanic membrane perforation needing myringoplasty on follow up. There were no substantial post-operative complications. The mean hospitalisation time was 9.5 hours (standard deviation, 9.8). The mean follow-up period was 32.7 months (standard deviation, 13.1), with all cases having resolution of pulsatile tinnitus and no tumour recurrence.

Conclusion

The study provides further evidence on the safety and efficacy of endoscopic carbon dioxide laser surgery as a minimally invasive technique for treating early-stage glomus tympanicum tumours.
Social cognition and social motivation in schizophrenia and bipolar disorder: are impairments linked to the disorder or to being socially isolated?
Authors: Green Michael F. , Wynn Jonathan K. , Eisenberger Naomi I. , Horan William P. , Lee Junghee , McCleery Amanda , Miklowitz David J. , Reavis Eric A. , Reddy L. Felice
Published: February 2024

Background

People with schizophrenia on average are more socially isolated, lonelier, have more social cognitive impairment, and are less socially motivated than healthy individuals. People with bipolar disorder also have social isolation, though typically less than that seen in schizophrenia. We aimed to disentangle whether the social cognitive and social motivation impairments observed in schizophrenia are a specific feature of the clinical condition v. social isolation generally.

Methods

We compared four groups (clinically stable patients with schizophrenia or bipolar disorder, individuals drawn from the community with self-described social isolation, and a socially connected community control group) on loneliness, social cognition, and approach and avoidance social motivation.

Results

Individuals with schizophrenia (n = 72) showed intermediate levels of social isolation, loneliness, and social approach motivation between the isolated (n = 96) and connected control (n = 55) groups. However, they showed significant deficits in social cognition compared to both community groups. Individuals with bipolar disorder (n = 48) were intermediate between isolated and control groups for loneliness and social approach. They did not show deficits on social cognition tasks. Both clinical groups had higher social avoidance than both community groups

Conclusions

The results suggest that social cognitive deficits in schizophrenia, and high social avoidance motivation in both schizophrenia and bipolar disorder, are distinct features of the clinical conditions and not byproducts of social isolation. In contrast, differences between clinical and control groups on levels of loneliness and social approach motivation were congruent with the groups' degree of social isolation.
Confidence in research findings depends on theory
Authors: Gal David , Sternthal Brian , Calder Bobby J.
Published: February 2024

Almaatouq et al. view the purpose of research is to map variable-to-variable relationships (e.g., the effect of X on Y). They also view theory as this mapping of variable-to-variable relationships rather than an explanation of why the relationships occur. However, it is theory as explanation that allows us to reconcile disparate findings and that should guide application.
Diversity of contributions is not efficient but is essential for science
Authors: Shea Catherine T. , Woolley Anita Williams
Published: February 2024

Dominant paradigms in science foster integration of research findings, but at what cost? Forcing convergence requires centralizing decision-making authority, and risks reducing the diversity of methods and contributors, both of which are essential for the breakthrough ideas that advance science.
Integrative design for thought-experiments
Authors: Dohrn Daniel , Mezzadri Angelica
Published: February 2024

Integrative experiment design should be extended to thought-experiments. Thought-experiments are closely connected to “real” experiments. They are involved in devising the design space of theories and possible experiments. The latter may be partitioned into experiments to be really performed and mere thought-experiments. The proposed extension of integrative experiment design lends guidance to a more methodical performance of thought-experiments.
Experiment commensurability does not necessitate research consolidation
Authors: Tsvetkova Milena
Published: February 2024

Integrative experiment design promises to foster cumulative knowledge by changing how we design experiments, build theories, and conduct research. I support the push to increase commensurability across experimental research but raise several reservations regarding results-driven and large-team-based research. I argue that it is vital to preserve academic diversity and adversarial debate via independent efforts.
Riotous Lives and Subversive Literatures: New Directions in Global Histories of Resistance
Authors: Aziz Zaib un Nisa
Published: February 2024

Over the past two decades, the relatively young field of global history has generated remarkable excitement among students, scholars, and readers who want to read scholarship that crosses borders and brings many worlds to a single methodological framework. Global perspectives have been particularly fruitful for telling political histories that have defined the modern world. Today, there is increasing scholarly interest in writing global intellectual histories of decolonisation and anti-colonialism. In the pages that follow, I consider new work, situated in several disciplines, that pushes the methodological boundaries of historical inquiry into our connected pasts. These works include Daniel Elam's World Literature for the Wretched of the Earth; Madhumita Lahiri's Imperfect Solidarities; Peace on Our Terms by Mona L. Siegel; and The Fury Archives by Juno Jill Richards.
EXPERIMENTAL ECONOMICS, POVERTY, AND ECONOMIC GROWTH
Authors: Noussair Charles N.
Published: February 2024

As in other sciences, an economic experiment is an artificial situation created by a researcher for the purpose of answering one or more scientific questions. Experiments of various types are used in economics to understand the causes of poverty and how it might be alleviated. The methods can identify causal relationships between variables and thereby isolate factors that can lead to poverty as well as to document the behavioral consequences of poverty. Experiments can also be used to provide test beds for proposed policies to alleviate poverty. This essay describes a variety of ways in which experiments have been employed to understand and combat poverty. A line of laboratory experiments that considers which economic institutions are conducive to economic growth is discussed in detail. The results show that decentralized markets are conducive to allowing an economy to operate as efficiently as it can. However, in an economy with a theoretical “poverty trap,” the market works more efficiently if accompanied by a democratic voting process and freedom of communication.
FOREIGN AID AND FREEDOM
Authors: Tesón Fernando R.
Published: February 2024

This essay examines the many problems with public and private development aid and argues that global liberalization of trade and immigration would have a greater direct effect in reducing global poverty. It also examines and rejects the view that people in rich countries have a strong moral obligation to give to the global poor. Such an obligation is in tension with an ethic that prizes personal projects. A political morality of equal respect and concern is congenial not with foreign aid, but with recognizing the agency of the global poor by lifting the many obstacles they currently face to participating in the market as producers and consumers.
GROUP RIGHTS, GENDER JUSTICE, AND WOMEN’S SELF-HELP GROUPS: EXIT, VOICE, AND LOYALTY IN AN INDIGENOUS COMMUNITY IN INDIA
Authors: Kabeer Naila , Narain Nivedita , Arora Varnica , Lal Vinitika
Published: February 2024

This essay addresses tensions within political philosophy between group rights, which allow historically marginalized communities some self-governance in determining its own rules and norms, and the rights of marginalized subgroups, such as women, within these communities. Community norms frequently uphold patriarchal structures that define women as inferior to men, assign them a subordinate status within the community, and cut them off from the individual rights enjoyed by women in other sections of society. As feminists point out, the capacity for voice and exit cannot be taken for granted, for community norms may be organized in ways that deny women any voice in its decision-making forums as well as the resources they would need to survive outside the community. This essay draws on research among the Gond, an indigenous community in India, to explore this debate. Given the strength of the forces within the community militating against women’s capacity for voice or exit, the question motivating our research is: Can external organizations make a difference? We explore the impacts of two external development organizations that sought to work with women within these communities in order to answer this question.
Population size is not a reliable indicator of seed germination
Authors: Baskin Jerry M. , Baskin Carol C.
Published: February 2024

Small isolated plant populations are one of the consequences of fragmentation of natural habitats by humans. We asked what effect does the creation of smaller populations from larger ones has on the plant fitness-related trait seed germination. Using information on 119 species (142 species entries) in 50 families, we found that seeds in only 35.2% of the species entries from larger populations germinated to higher percentages than those from smaller populations. In the other entries, seeds from large and small populations germinated equally well (57.7% of total entries) or seeds from small populations germinated better (7.0% of total entries) than those from large populations. These results indicate that population size is not a reliable predictor of seed germinability. Furthermore, there was little relationship between seed germination and either seed mass, genetic diversity or degree of population isolation, or between population size and genetic diversity.
Increasing food insecurity severity is associated with lower diet quality
Authors: Kent Katherine , Schumacher Tracy , Kocar Sebastian , Seivwright Ami , Visentin Denis , Collins Clare E , Lester Libby
Published: February 2024

Objective:

Food insecurity may reduce diet quality, but the relationship between food insecurity severity and diet quality is under-researched. This study aimed to examine the relationship between diet quality and severity of household food insecurity.

Design:

A cross-sectional, online survey used the United States Department of Agriculture Household Food Security Six-item Short Form to classify respondents as food secure or marginally, moderately or severely food insecure. The Australian Recommended Food Score (ARFS; scored 0–73) determined diet quality (ARFS total and sub-scale scores). Survey-weighted linear regression (adjusted for age, sex, income, education, location and household composition) was conducted.

Setting:

Tasmania, Australia.

Participants:

Community-dwelling adults (aged 18 years and over).

Results:

The mean ARFS total for the sample (n 804, 53 % female, 29 % aged > 65 years) was 32·4 (sd = 9·8). As the severity of household food insecurity increased, ARFS total decreased. Marginally food-insecure respondents reported a mean ARFS score three points lower than food-secure adults (B = –2·7; 95 % CI (–5·11, –0·34); P = 0·03) and reduced by six points for moderately (B = –5·6; 95 % CI (–7·26, –3·90); P < 0·001) and twelve points for severely food-insecure respondents (B = –11·5; 95 % CI (–13·21, –9·78); P < 0·001). Marginally food-insecure respondents had significantly lower vegetable sub-scale scores, moderately food-insecure respondents had significantly lower sub-scale scores for all food groups except dairy and severely food-insecure respondents had significantly lower scores for all sub-scale scores.

Conclusions:

Poorer diet quality is evident in marginally, moderately and severely food-insecure adults. Interventions to reduce food insecurity and increase diet quality are required to prevent poorer nutrition-related health outcomes in food-insecure populations in Australia.
DDX3X interacts with SIRT7 to promote PD-L1 expression to facilitate PDAC progression
Authors: Zhao Tianming , Zhu Hanlong , Zou Tianhui , Zhao Si , Zhou Lin , Ni Muhan , Liu Feng , Zhu Hao , Dou Xiaotan , Di Jian , Xu Bing , Wang Lei , Zou Xiaoping
Published: February 2024

Pancreatic ductal adenocarcinoma (PDAC) is recognized as the most aggressive and fatal malignancy. A previous study reported that PDAC patients who exhibit elevated levels of DDX3X have a poor prognosis and low overall survival rate. However, the underlying molecular mechanism remains unclear. This study aimed to investigate the specific roles of DDX3X in PDAC. Multiple bioinformatics analyses were used to evaluate DDX3X expression and its potential role in PDAC. In vitro and in vivo studies were performed to assess the effects of DDX3X on PDAC cell growth. Furthermore, Western blotting, quantitative PCR, immunohistochemistry, immunofluorescence, mass spectrometry, coimmunoprecipitation and multiplexed immunohistochemical staining were conducted to identify the specific regulatory mechanism in PDAC. The results verified that DDX3X expression is notably upregulated in the tumor tissue vs. normal tissue of PDAC patients. DDX3X knockdown markedly suppressed the proliferation, invasion and migration of PDAC cells in vitro and inhibited tumor growth in vivo. Conversely, overexpression of DDX3X induced the opposite effect. Further studies supported that the DDX3X protein can associate with sirtuin 7 (SIRT7) to stimulate PDAC carcinogenesis and progression. Furthermore, SIRT7 inhibition significantly impeded DDX3X-mediated tumor growth both ex vivo and in vivo. The results also revealed that programmed death ligand 1 (PD-L1) expression is positively correlated with DDX3X expression. These results reveal significant involvement of the DDX3X-SIRT7 axis in the initiation and advancement of PDAC and offer previously undiscovered therapeutic options for PDAC management.
Targeting the prefrontal-supplementary motor network in obsessive-compulsive disorder with intensified electrical stimulation in two dosages: a randomized, controlled trial
Authors: Alizadehgoradel Jaber , Molaei Behnam , Barzegar Jalali Khandan , Pouresmali Asghar , Sharifi Kiomars , Hallajian Amir-Homayun , Nejati Vahid , Glinski Benedikt , Vicario Carmelo M. , Nitsche Michael A. , Salehinejad Mohammad Ali
Published: February 2024

Obsessive-compulsive disorder (OCD) is associated with a high disease burden, and treatment options are limited. We used intensified electrical stimulation in two dosages to target a main circuitry associated with the pathophysiology of OCD, left dorsolateral prefrontal cortex (l-DLPFC), and pre-supplementary motor area (pre-SMA) and assessed clinical outcomes, neuropsychological performance, and brain physiology. In a double-blind, randomized controlled trial, thirty-nine patients with OCD were randomly assigned to three groups of sham, 2-mA, or 1-mA transcranial direct current stimulation (tDCS) targeting the l-DLPFC (F3) and pre-SMA (FC2) with anodal and cathodal stimulation respectively. The treatment included 10 sessions of 20-minute stimulation delivered twice per day with 20-min between-session intervals. Outcome measures were reduction in OCD symptoms, anxiety, and depressive states, performance on a neuropsychological test battery (response inhibition, working memory, attention), oscillatory brain activities, and functional connectivity. All outcome measures except EEG were examined at pre-intervention, post-intervention, and 1-month follow-up times. The 2-mA protocol significantly reduced OCD symptoms, anxiety, and depression states and improved quality of life after the intervention up to 1-month follow-up compared to the sham group, while the 1-mA protocol reduced OCD symptoms only in the follow-up and depressive state immediately after and 1-month following the intervention. Both protocols partially improved response inhibition, and the 2-mA protocol reduced attention bias to OCD-related stimuli and improved reaction time in working memory performance. Both protocols increased alpha oscillatory power, and the 2-mA protocol decreased delta power as well. Both protocols increased connectivity in higher frequency bands at frontal-central areas compared to the sham. Modulation of the prefrontal-supplementary motor network with intensified tDCS ameliorates OCD clinical symptoms and results in beneficial cognitive effects. The 2-mA intensified stimulation resulted in larger symptom reduction and improved more converging outcome variables related to therapeutic efficacy. These results support applying the intensified prefrontal-SMA tDCS in larger trials.
IL-17 promotes osteoclast-induced bone loss by regulating glutamine-dependent energy metabolism
Authors: Peng Renpeng , Dong Yimin , Zheng Meng , Kang Honglei , Wang Pengju , Zhu Meipeng , Song Kehan , Wu Wei , Li Feng
Published: February 2024

Osteoclasts consume an amount of adenosine triphosphate (ATP) to perform their bone resorption function in the development of osteoporosis. However, the mechanism underlying osteoclast energy metabolism has not been fully elucidated. In addition to glucose, glutamine (Glu) is another major energy carrier to produce ATP. However, the role of Glu metabolism in osteoclasts and the related molecular mechanisms has been poorly elucidated. Here we show that Glu is required for osteoclast differentiation and function, and that Glu deprivation or pharmacological inhibition of Glu transporter ASCT2 by V9302 suppresses osteoclast differentiation and their bone resorptive function. In vivo treatment with V9302 improved OVX-induced bone loss. Mechanistically, RNA-seq combined with in vitro and in vivo experiments suggested that Glu mediates the role of IL-17 in promoting osteoclast differentiation and in regulating energy metabolism. In vivo IL-17 treatment exacerbated OVX-induced bone loss, and this effect requires the participation of Glu or its downstream metabolite α-KG. Taken together, this study revealed a previously unappreciated regulation of IL-17 on energy metabolism, and this regulation is Glu-dependent. Targeting the IL-17–Glu–energy metabolism axis may be a potential therapeutic strategy for the treatment of osteoporosis and other IL-17 related diseases.
The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome
Authors: Krischuns Tim , Arragain Benoît , Isel Catherine , Paisant Sylvain , Budt Matthias , Wolff Thorsten , Cusack Stephen , Naffakh Nadia
Published: February 2024

The current model is that the influenza virus polymerase (FluPol) binds either to host RNA polymerase II (RNAP II) or to the acidic nuclear phosphoprotein 32 (ANP32), which drives its conformation and activity towards transcription or replication of the viral genome, respectively. Here, we provide evidence that the FluPol-RNAP II binding interface, beyond its well-acknowledged function in cap-snatching during transcription initiation, has also a pivotal role in replication of the viral genome. Using a combination of cell-based and in vitro approaches, we show that the RNAP II C-terminal-domain, jointly with ANP32, enhances FluPol replication activity. We observe successive conformational changes to switch from a transcriptase to a replicase conformation in the presence of the bound RNPAII C-terminal domain and propose a model in which the host RNAP II is the anchor for transcription and replication of the viral genome. Our data open new perspectives on the spatial coupling of viral transcription and replication and the coordinated balance between these two activities.
Designing lithium halide solid electrolytes
Authors: Wang Qidi , Zhou Yunan , Wang Xuelong , Guo Hao , Gong Shuiping , Yao Zhenpeng , Wu Fangting , Wang Jianlin , Ganapathy Swapna , Bai Xuedong , Li Baohua , Zhao Chenglong , Janek Jürgen , Wagemaker Marnix
Published: February 2024

All-solid-state lithium batteries have attracted widespread attention for next-generation energy storage, potentially providing enhanced safety and cycling stability. The performance of such batteries relies on solid electrolyte materials; hence many structures/phases are being investigated with increasing compositional complexity. Among the various solid electrolytes, lithium halides show promising ionic conductivity and cathode compatibility, however, there are no effective guidelines when moving toward complex compositions that go beyond ab-initio modeling. Here, we show that ionic potential, the ratio of charge number and ion radius, can effectively capture the key interactions within halide materials, making it possible to guide the design of the representative crystal structures. This is demonstrated by the preparation of a family of complex layered halides that combine an enhanced conductivity with a favorable isometric morphology, induced by the high configurational entropy. This work provides insights into the characteristics of complex halide phases and presents a methodology for designing solid materials.
Synergistic denitrification mechanism of domesticated aerobic denitrifying bacteria in low-temperature municipal wastewater treatment
Authors: Wang Fan , Cui Qin , Liu Wenai , Jiang Weiqing , Ai Shengshu , Liu Wanqi , Bian Dejun
Published: February 2024

To address the problems of low efficacy and low microbial activity in low-temperature municipal wastewater treatment, this study utilized an air-lift micro-pressure internal circulation integrated reactor (AMICIR). Through controlling the amount of aeration and dissolved oxygen (DO) in the reactor, AMICIR creates alternating aerobic and anaerobic environments, explores the enrichment conditions of aerobic denitrifying bacteria, examines the changes in pollutant removal efficiency and the characteristics of bacterial colony structure during the process of enrichment of aerobic denitrifying bacteria in the system, and reveals the mechanism of nitrogen removal by aerobic denitrifying bacteria cooperating with anaerobic denitrifying bacteria in the low-temperature municipal wastewater treatment system. Experimental results showed average removal rates of NH4+-N, chemical oxygen demand (COD), total phosphorus (TP), and total nitrogen (TN) reaching 93.85%, 89.30%, 92.75%, and 75.4%, respectively. The microorganisms secreted large amounts of proteins and polysaccharides, forming zoogloea and anaerobic microenvironments conducive to traditional denitrification reactions. IlluminaMiSeq sequencing analysis revealed the presence of anaerobic phyla. The system was enriched with a large number of microorganisms, and aerobic denitrifying bacteria (Flavobacterium, Rhodoferax, and Pseudomonas) were successfully cultured. Flavobacterium emerged as the dominant species, with relative abundance ranging from 18.56% to 22.60%. Functional gene prediction indicated high abundance of aerobic denitrification genes, such as napA. Aerobic denitrifying bacteria were successfully enriched in the system to improve nitrogen removal from municipal wastewater at low temperatures.
Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores
Authors: Datler Julia , Hansen Jesse M. , Thader Andreas , Schlögl Alois , Bauer Lukas W. , Hodirnau Victor-Valentin , Schur Florian K. M.
Published: February 2024

Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.
Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair
Authors: Kokic Goran , Yakoub George , van den Heuvel Diana , Wondergem Annelotte P. , van der Meer Paula J. , van der Weegen Yana , Chernev Aleksandar , Fianu Isaac , Fokkens Thornton J. , Lorenz Sonja , Urlaub Henning , Cramer Patrick , Luijsterburg Martijn S.
Published: February 2024

During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by the CRL4CSA ubiquitin ligase, a process that is facilitated by ELOF1 in an unknown way. Using cryogenic electron microscopy, biochemical assays and cell biology approaches, we found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4CSA on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. In the presence of ELOF1, a transcription factor IIS (TFIIS)-like element in UVSSA gets ordered and extends through the Pol II pore, thus preventing reactivation of Pol II by TFIIS. Our results provide the structural basis for Pol II ubiquitylation and inactivation in TCR.
A general class of improved population variance estimators under non-sampling errors using calibrated weights in stratified sampling
Authors: Pandey M. K. , Singh G. N. , Zaman Tolga , Mutairi Aned Al , Mustafa Manahil SidAhmed
Published: February 2024

This paper proposes a new calibration estimator for population variance within a stratified two-phase sampling design. It takes into account random non-response and measurement errors, specifically applying this method to estimate the variance in Gas turbine exhaust pressure data. The study integrates additional information from two highly positively correlated auxiliary variables to develop a general class of estimators tailored for the stratified two-phase sampling scheme. The properties of these estimators, in terms of their biases and mean square errors, have been thoroughly examined and extensively analyzed through numerical and simulation studies. Furthermore, the calibrated weights of the strata are derived. The proposed estimators outperform the natural estimator of population variance. Finally, suitable recommendations have been made for survey statisticians intending to apply these findings to real-life problems.
Deep brain stimulation of the central thalamus restores arousal and motivation in a zolpidem-responsive patient with akinetic mutism after severe brain injury
Authors: Arnts Hisse , Tewarie Prejaas , van Erp Willemijn , Schuurman Rick , Boon Lennard I. , Pennartz Cyriel M. A. , Stam Cornelis J. , Hillebrand Arjan , van den Munckhof Pepijn
Published: February 2024

After severe brain injury, zolpidem is known to cause spectacular, often short-lived, restorations of brain functions in a small subgroup of patients. Previously, we showed that these zolpidem-induced neurological recoveries can be paralleled by significant changes in functional connectivity throughout the brain. Deep brain stimulation (DBS) is a neurosurgical intervention known to modulate functional connectivity in a wide variety of neurological disorders. In this study, we used DBS to restore arousal and motivation in a zolpidem-responsive patient with severe brain injury and a concomitant disorder of diminished motivation, more than 10 years after surviving hypoxic ischemia. We found that DBS of the central thalamus, targeted at the centromedian-parafascicular complex, immediately restored arousal and was able to transition the patient from a state of deep sleep to full wakefulness. Moreover, DBS was associated with temporary restoration of communication and ability to walk and eat in an otherwise wheelchair-bound and mute patient. With the use of magnetoencephalography (MEG), we revealed that DBS was generally associated with a marked decrease in aberrantly high levels of functional connectivity throughout the brain, mimicking the effects of zolpidem. These results imply that ‘pathological hyperconnectivity’ after severe brain injury can be associated with reduced arousal and behavioral performance and that DBS is able to modulate connectivity towards a ‘healthier baseline’ with lower synchronization, and, can restore functional brain networks long after severe brain injury. The presence of hyperconnectivity after brain injury may be a possible future marker for a patient’s responsiveness for restorative interventions, such as DBS, and suggests that lower degrees of overall brain synchronization may be conducive to cognition and behavioral responsiveness.
Minimizing artifact-induced false-alarms for seizure detection in wearable EEG devices with gradient-boosted tree classifiers
Authors: Ingolfsson Thorir Mar , Benatti Simone , Wang Xiaying , Bernini Adriano , Ducouret Pauline , Ryvlin Philippe , Beniczky Sandor , Benini Luca , Cossettini Andrea
Published: February 2024

Electroencephalography (EEG) is widely used to monitor epileptic seizures, and standard clinical practice consists of monitoring patients in dedicated epilepsy monitoring units via video surveillance and cumbersome EEG caps. Such a setting is not compatible with long-term tracking under typical living conditions, thereby motivating the development of unobtrusive wearable solutions. However, wearable EEG devices present the challenges of fewer channels, restricted computational capabilities, and lower signal-to-noise ratio. Moreover, artifacts presenting morphological similarities to seizures act as major noise sources and can be misinterpreted as seizures. This paper presents a combined seizure and artifacts detection framework targeting wearable EEG devices based on Gradient Boosted Trees. The seizure detector achieves nearly zero false alarms with average sensitivity values of $$65.27\%$$

65.27
%

for 182 seizures from the CHB-MIT dataset and $$57.26\%$$

57.26
%

for 25 seizures from the private dataset with no preliminary artifact detection or removal. The artifact detector achieves a state-of-the-art accuracy of $$93.95\%$$

93.95
%

(on the TUH-EEG Artifact Corpus dataset). Integrating artifact and seizure detection significantly reduces false alarms—up to $$96\%$$

96
%

compared to standalone seizure detection. Optimized for a Parallel Ultra-Low Power platform, these algorithms enable extended monitoring with a battery lifespan reaching 300 h. These findings highlight the benefits of integrating artifact detection in wearable epilepsy monitoring devices to limit the number of false positives.
Finger flexor rigidity in the healthy population
Authors: Grinbaum Erez , Shulman Igor , Rozen Nimrod , Rubin Guy
Published: February 2024

The involvement of the hand flexors in trigger finger is not clear. This study aimed to examine the rigidity of the flexor tendon in the first pulley territory in the hand by using ultrasound in a healthy population, as well as to create a reference scale of rigidity for the flexor tendons to compare those values in trigger fingers. We tested 35 healthy volunteers using a linear ultrasound transducer and the color Doppler method. Rigidity levels below the first pulley were examined and compared between the different fingers of the hand and the relationship between rigidity and sex and the three different age groups was evaluated. In the healthy population, the rigidity of the flexor tendons of the hand in the territory of the first pulley varied between 233.1 and 962.8 kPa, with an average of 486.42 kPa and standard deviation of 114.85. We showed that the flexors in the dominant hand were more rigid, there was a difference between the rigidity of the flexor tendons of the thumb and the other fingers of the same hand, and the ring finger of the dominant hand had stiffer flexor tendons than the fingers of the other hand in the male population. We created a value scale for the rigidity of the flexor tendons of the fingers. This base scale can be compared between different pathologies, including trigger finger. The study and all experimental protocols were approved by the local ethical committee.
A method for rapid demolition of a crossline arch bridge: a case study
Authors: Zhu Cixiang , He Xiongjun , Xiao Junyao
Published: February 2024

To reduce the adverse impact of demolition of the symmetrical rigid frame arch bridge overcrossing the highway with over-saturated traffic flow, a rapid demolition method based on the Self-Propelled Modular Transporter (SPMT) technique was developed in this study. The calculation formulae for reaction forces of the supporting brackets, as well as driving force and stability of SPMTs, were derived by analyzing the stability, synchronization, and influencing parameters of the cut bridge body—transport system. In addition, a monitoring system during the whole process was developed to ensure the demolition safety. An application of demolishing a crossline symmetrical rigid frame arch bridge in China within 5 h has been presented. The results showed that the proposed method can be successfully applied in real projects, leading to significant reduction in traffic impact, energy consumption, and environmental pollution.
Waveform-based classification of dentate spikes
Authors: Santiago Rodrigo M. M. , Lopes-dos-Santos Vítor , Aery Jones Emily A. , Huang Yadong , Dupret David , Tort Adriano B. L.
Published: February 2024

Synchronous excitatory discharges from the entorhinal cortex (EC) to the dentate gyrus (DG) generate fast and prominent patterns in the hilar local field potential (LFP), called dentate spikes (DSs). As sharp-wave ripples in CA1, DSs are more likely to occur in quiet behavioral states, when memory consolidation is thought to take place. However, their functions in mnemonic processes are yet to be elucidated. The classification of DSs into types 1 or 2 is determined by their origin in the lateral or medial EC, as revealed by current source density (CSD) analysis, which requires recordings from linear probes with multiple electrodes spanning the DG layers. To allow the investigation of the functional role of each DS type in recordings obtained from single electrodes and tetrodes, which are abundant in the field, we developed an unsupervised method using Gaussian mixture models to classify such events based on their waveforms. Our classification approach achieved high accuracies (> 80%) when validated in 8 mice with DG laminar profiles. The average CSDs, waveforms, rates, and widths of the DS types obtained through our method closely resembled those derived from the CSD-based classification. As an example of application, we used the technique to analyze single-electrode LFPs from apolipoprotein (apo) E3 and apoE4 knock-in mice. We observed that the latter group, which is a model for Alzheimer’s disease, exhibited wider DSs of both types from a young age, with a larger effect size for DS type 2, likely reflecting early pathophysiological alterations in the EC-DG network, such as hyperactivity. In addition to the applicability of the method in expanding the study of DS types, our results show that their waveforms carry information about their origins, suggesting different underlying network dynamics and roles in memory processing.