bluuebunny/crossref_metadata_2025 huggingface dataset:
Using spatial aggregation of soil multifunctionality maps to support uncertainty‐aware planning decisions
Authors: Courteille Léa , Lagacherie Philippe , Boukhelifa Nadia , Lutton Evelyne , Tardieu Léa
Published: July 2024

To ensure soil preservation, it is essential to incorporate the soil's ability to provide ecosystem services into the spatial planning process. For well‐informed planning decisions, stakeholders need spatially explicit information on the state of the soils and the functions they fulfil, with sufficient spatial resolution and quantified uncertainty. It has been shown that Digital Soil Mapping (DSM) products can provide such information. However, in some cases, fine spatial resolution coupled with high levels of uncertainty may lead stakeholders to overlook the inherent uncertainties in the information. Spatial aggregation of DSM products opens up a promising avenue for obtaining maps that are more tailored to the users' scales of decision making while facilitating uncertainty communication. In this perspective, we propose a new spatial aggregation approach relying on spatially constrained agglomerative clustering (AC). The spatial aggregation approach is applied to a 25‐m‐resolution soil potential multifunctionality index (SPMI) map developed for the coastal plain of the Occitanie Region. This DSM product was increasingly aggregated to obtain SPMI maps of different resolutions displaying two distinct areal metrics: proportions of area above a given threshold of SPMI, and mean SPMI. Each map was evaluated through a set of indicators selected for their potential impact on user decision making: mean spatial resolution, overall predicted uncertainty, quantity of information and mean within‐unit variability. The maps were compared with respect to these indicators to other maps obtained with alternative aggregation methods employed in DSM literature (maps aggregated according to some administrative units and QuadMaps). We show that all the tested aggregation methods produced a substantial decrease of the map uncertainty with moderate loss of spatial resolution. However, only AC preserved the fine spatial pattern of the initial DSM product while enabling fine tuning of the uncertainty displayed to end‐users. We show that AC can simplify the identification of extensive regions characterized by low uncertainty without losing information regarding soil multifunctionality, thereby facilitating and enhancing the efficiency of planning decisions.
Soil N2O emissions during dry fallow periods
Authors: Cardinael Rémi , Barton Louise , Corbeels Marc , Six Johan , Rowlings David , Shumba Armwell , Chikowo Regis , Farrell Mark
Published: July 2024

Shang et al. (2024) recently suggested to include nitrous oxide (N2O) emissions during the fallow period to better estimate N2O emission factors (EFs). We however highlighted several pitfalls of the proposed adjusted EFs for croplands in the specific case of dry subhumid, semiarid, and arid regions with dry fallow periods, these regions covering about 47% of the Earth's terrestrial area.
Präparierte Emotionen: Formen der Trauer im Umgang mit der Stellerschen Seekuh
Authors: Bund Romana
Published: July 2024

Wie werden Emotionen im Kontext des Artenverlusts eingesetzt? In welchem Ausmaß sind sie steuerbar und für welche Zwecke werden sie genutzt? Anhand des Beispiels der Stellerschen Seekuh fragt der Artikel nach Formen der Trauer im Umgang mit der Auslöschung und den Überresten des marinen Säugetiers. Die Stellersche Seekuh wurde Mitte des 18. Jahrhunderts an den Rändern frühmoderner Seewege im Nordpazifik entdeckt und zu Nahrungszwecken ausgerottet. Das Tier ist Teil einer speziesübergreifenden Ausrottungsgeschichte und zeigt die Verbindung der Vernichtung nicht‐menschlicher Lebewesen und indigener Gemeinschaften auf. Mithilfe der Seekuh wird untersucht, wessen Auslöschung überhaupt Trauer erfährt und wie diese mithilfe der in naturhistorischen Museen zusammengesetzten Knochengerüste her‐ und dargestellt wird. Fragen nach der Verbindung von Emotion und imperialen Machtstrukturen spielen dabei ebenso eine Rolle, wie die von Sammlungsinstitutionen genutzten Erzählungen letzter Individuen, tragischer Abgesänge und die Kommodifizierung der Überreste des Tieres. Abschließend wird Trauer als Möglichkeit berücksichtigt, über Artengrenzen hinweg zu verbinden.
Single‐cell transcriptome sequencing reveals SPP1‐CD44‐mediated macrophage–tumor cell interactions drive chemoresistance in TNBC
Authors: Liu Fuzhong , Zhang Junfeng , Gu Xiaowei , Guo Qiuyang , Guo Wenjia
Published: July 2024

Triple‐negative breast cancer (TNBC) is often considered one of the most aggressive subtypes of breast cancer, characterized by a high recurrence rate and low overall survival (OS). It is notorious for posing challenges related to drug resistance. While there has been progress in TNBC research, the mechanisms underlying chemotherapy resistance in TNBC remain largely elusive. We collect single‐cell RNA sequencing (scRNA‐seq) data from five TNBC patients susceptible to chemotherapy and five resistant cases. Comprehensive analyses involving copy number variation (CNV), pseudotime trajectory, cell–cell interactions, pseudospace analysis, as well as transcription factor and functional enrichment are conducted specifically on macrophages and malignant cells. Furthermore, we performed validation experiments on clinical samples using multiplex immunofluorescence. We identified a subset of SPP1+ macrophages that secrete SPP1 signals interacting with CD44 on malignant cell surfaces, potentially activating the PDE3B pathway within malignant cells via the integrin pathway, leading to chemotherapy resistance. The abnormally enhanced SPP1 signal between macrophages and malignant cells may serve as a factor promoting chemotherapy resistance in TNBC patients. Therefore, SPP1+ macrophages could potentially serve as a therapeutic target to reduce chemotherapy resistance.
Unveiling the limits of precision in iterative MINFLUX
Authors: Smith Carlas , Kalisvaart Dylan , Prakash Kirti
Published: July 2024

In single‐molecule microscopy, a big question is how precisely we can estimate the location of a single molecule. Our research shows that by using iterative localisation microscopy and factoring in the prior information, we can boost precision and reduce the number of photons needed. Leveraging the Van Trees inequality aids in determining the optimal precision achievable. Our approach holds promise for wider application in discerning the optimal precision across diverse imaging scenarios, encompassing various illumination strategies, point spread functions and overarching control methodologies.
Analyzing the accuracy of a cross‐mounting technique utilizing digitized interocclusal records
Authors: Kan Elena , Luu Dianne , Kim Soo‐Woo , Liu Richard , Lee Jason D. , Lee Sang J.
Published: July 2024

Purpose

To compare the accuracy of a partially digital cross‐mounting workflow of direct scans of interocclusal records to a conventional workflow by analyzing the deviations of sequentially cross‐mounted casts.

Materials and methods

A set of reference casts, comprising maxillary and mandibular full‐arch prepared casts and interim prostheses, was articulated, mounted, and scanned to generate four reference casts for cross‐mounting. In the conventional approach, 15 sets of these four casts were printed. Polyvinylsiloxane (PVS) records were made using the reference casts and utilized for sequential cross‐mounting. In the partially digital group, the same PVS interocclusal records were scanned and used for digital cross‐mounting via design software. The mean deviations of both groups from the reference cast were analyzed using a 3D inspection software program. Statistical tests, including paired t‐test and analysis of variance (ANOVA), were conducted to compare the average discrepancies between the two groups and to evaluate discrepancies in the anterior and posterior regions (α = 0.05).

Results

The range of discrepancies was similar in both the conventional and partially digital groups. The final set of related casts had a mean deviation of 201.58 ± 136.98 mm in the conventional workflow and 248.69 ± 164.71 mm in the partially digital workflow. No statistically significant difference was found between conventional and partially digital groups (p = 0.091). Error propagation was examined by comparing discrepancies at each step within the cross‐mounting process. In the conventional group, no significant difference was found (p = 0.148), but a significant difference was found among groups in the partially digital group at each step of sequential mounting (p < 0.001). A significant difference was observed between anterior and posterior deviations in the partially digital group (p < 0.001), but not in the conventional group (p = 0.143).

Conclusions

The study reveals that there is no statistically significant difference between conventional and partially digital cross‐mounting workflows. However, within the partially digital group, a significant difference in deviation emerges across cross‐mounting steps, with increased deviation in the anterior region.
Intraoral scanner‐based virtual facebow transferring: A chairside dental technique
Authors: Yang Shengtao , Wu Lei , Alabkaa Baraa , Lepidi Luca , Yue Li , Li Junying
Published: July 2024

Accurately mounting dental casts on an articulator is an essential step in prosthetic treatments. In digital dentistry, virtual articulator mounting procedures rely on virtual facebow records. However, virtual facebow records usually require devices like face scanners or jaw motion tracking systems that are not commonly available in most dental practices. The present technique report describes a straightforward intraoral scanner‐based virtual facebow transfer approach. In this technique, a reference facebow joint support was first scanned and aligned with a virtual articulator. Then, a patient's facebow joint support and bite fork assembly were scanned chairside with an intraoral scanner and aligned with the virtual articulator by matching common features with the reference facebow joint support. After aligning the patient's intraoral scans with the patient's bite fork scan that was already superimposed on the virtual articulator, a virtual mounting process was achieved. Once the corresponding reference facebow joint supports have been generated, this technique can be easily implemented with most facebow systems and be seamlessly integrated into daily clinical practice as only an intraoral scanner and a conventional facebow were required.
Screening rates for hepatitis B and C among low‐income US veterans: Data from the National Veteran Homeless and Other Poverty Experiences Study
Authors: Beydoun Hind A. , Tsai Jack
Published: July 2024

Screening for viral hepatitis is considered a high‐priority area in the Veterans Health Administration (VHA). Yet, few studies have examined viral hepatitis screening test use among low‐income veterans who are considered high‐risk with limited healthcare access. Using cross‐sectional data from 933 participants in the 2021–2022 National Veteran Homeless and Other Poverty Experiences (NV‐HOPE) study, we examined rates and correlates of lifetime screening for hepatitis B (HBV) and hepatitis C (HCV) infections. Multivariable logistic regression models evaluated characteristics associated with HBV/HCV screening. Nearly 16% and 21% reported lifetime HBV and HCV screening, respectively. These rates are considerably lower than HBV (47.3%) and HCV (92.9%) screening rates documented among contemporaneous veterans in VHA electronic health records. In the NV‐HOPE data, veterans 50–79 years were more likely than those ≥80 years of age to ever‐screen for HBV/HCV. Whereas, household income was inversely related to lifetime screening behaviours, veterans reporting ‘other’ employment types (vs. full‐time/part‐time employment) were more likely to ever‐screen for HBV/HCV. Ever‐screening for HBV was more likely among veterans reporting non‐Hispanic ‘other’ (vs. non‐Hispanic ‘white’) race, housing instability, Medicaid insurance, as well as drug use and cognitive disorder histories. Living with ≥5 members (vs. alone), histories of alcohol use, cancer, and liver disorders were also correlated with ever‐screening for HCV. HIV/AIDS history correlated with ever‐screening for HBV/HCV. In conclusion, fewer than one‐third of low‐income US veterans ever‐screened for HBV/HCV, with lower screening rates among those less likely to be exposed to viral hepatitis, thereby informing interventions aimed at promoting available screening, treatment and vaccinations for HBV/HCV.
Homogeneous selection and stochasticity overrule heterogeneous selection across biotic taxa and ecosystems
Authors: Soininen Janne , Graco‐Roza Caio
Published: July 2024

Deterministic factors including homogeneous and heterogeneous selection and stochastic factors jointly shape ecological communities. However, a quantitative synthesis of the factors underlying the balance among different assembly processes is lacking. Here, we synthesized data from 149 datasets covering major biotic groups and ecosystem types globally. We used a null model approach based on Raup–Crick dissimilarities and Bayesian meta‐regression to analyze the data. We found that communities were more under homogeneous selection than heterogeneous selection across biotic taxa and ecosystems. Environment selected species homogeneously more often at small scales while heterogeneously more often at large scales. Stochasticity also showed scale‐dependence as stochastic community assembly increased with study scale. Homogeneous and heterogeneous selection were strongest at high latitudes while stochastic factors were strongest in tropics. Marine systems had the highest degree of homogeneous selection and the lowest stochasticity. We provide the first analysis of community assembly across taxa and ecosystems which should be important for a better understanding of how communities respond to environmental change.
The double mediating effect of stress regulation and life satisfaction on music use as a coping mechanism and happiness in Chinese older adults during the COVID‐19 pandemic
Authors: Wang Jie , Suh Kyung Hyun
Published: July 2024

Background

This study investigated the relationship between music use as a coping mechanism and subjective happiness among Chinese older adults (COAs) during Coronavirus disease 2019 (COVID‐19); it also focused on the mediating effect of stress regulation by music and life satisfaction in this relationship.

Methods

Participants were 329 male and female Chinese adults aged 60 years or older. Data were collected using the Sojump application for an online survey. The double mediating effect was analyzed using PROCESS Macro 3.5 Model 6.

Results

The results revealed that music use as a coping mechanism and stress regulation by music were not significantly correlated with subjective happiness of COAs, whereas these were positively correlated with their life satisfaction. Additionally, life satisfaction of COAs was positively correlated with subjective happiness. Stress regulation by music and life satisfaction completely mediated the relationship between music use as a coping mechanism and subjective happiness of COAs during COVID‐19. In the double mediation model, music use as a coping mechanism positively influenced stress regulation by music (β = 0.704), stress regulation by music positively influenced life satisfaction (β = 0.162), and life satisfaction positively influenced subjective happiness (β = 0.498).

Conclusion

Therefore, music can promote happiness in COAs in stressful situations through stress regulation and life satisfaction.
KPP fronts in shear flows with cutoff reaction rates
Authors: Needham D. J. , Tzella A.
Published: July 2024

We consider the effect of a shear flow which has, without loss of generality, a zero mean flow rate, on a Kolmogorov–Petrovskii–Piscounov (KPP)‐type model in the presence of a discontinuous cutoff at concentration . In the long‐time limit, a permanent‐form traveling wave solution is established which, for fixed , is unique. Its structure and speed of propagation depends on (the strength of the flow relative to the propagation speed in the absence of advection) and (the square of the front thickness relative to the channel width). We use matched asymptotic expansions to approximate the propagation speed in the three natural cases , , and , with particular associated orderings on , while remains fixed. In all the cases that we consider, the shear flow enhances the speed of propagation in a manner that is similar to the case without cutoff (). We illustrate the theory by evaluating expressions (either directly or through numerical integration) for the particular cases of the plane Couette and Poiseuille flows.
Telehealth in geriatric dentistry: A comparative analysis of concordance between virtual and in‐person examinations for hospitalized older patients
Authors: Kallás Monira Samaan , Guardieiro Bruno , Henrique Expedita Angela , Silva Deise Garrido , Takashi Danilo Aoike , Marchini Leonardo
Published: July 2024

Aims

This study aims to assess the concordance between in‐person clinical and virtual oral examinations among hospitalized older adults.

Methods

A single examiner performed an in‐person clinical examination, recorded systemic health history and oral health indices, clinically documented the Bedside Oral Exam (BOE), and captured photographs for subsequent analysis during a virtual examination. Following a 90‐day washout period, a virtual examination was repeated by the same examiner and by a second examiner. Descriptive analysis and a Kappa test were used to compare proportions and evaluate the agreement between results.

Results

Intra‐examiners presented high percentage of agreement in all domains of BOE (80%–86%), with an exception for gingiva (78%). Kappa's intra‐examiners presented moderate scores in saliva, mucous membrane, gingiva and teeth/dentures domains and a strong score in the tongue domain (0.839). Inter examiners presented moderate agreement in lips and gingiva, saliva, mucous membrane, and teeth/dentures domains. Inter examiners Kappa scores were weak for lips (0.395) and gingiva (0.498) domains; moderate for saliva (0.703), mucous membrane (0.769) and teeth/dentures (0.714) domains and strong for the tongue domain (0.872).

Conclusion

In this study, a moderate level of agreement was observed between clinical and virtual oral examinations among older hospitalized patients. These findings are encouraging and warrant further investigation about how teledentistry can be used to enhance oral health access to this vulnerable population.
On the scalarity of nu‐V constructions in Taiwan Mandarin
Authors: Chen Yi‐Hsun , Chou C.‐T. Tim , Shen Po Ju
Published: July 2024

This paper investigates three puzzles concerning scalar nu‐V constructions in Taiwan Mandarin: (a) a scalar nu‐V construction is incompatible with state/achievement verbs, irrespective of the presence of a quantity phrase; (b) when combined with activity verbs, the inclusion of a quantity phrase appears obligatory for scalar nu‐V constructions in an out‐of‐the‐blue context; (c) under appropriate contextual support, bare nouns and demonstrative phrases can replace the typically obligatory quantity phrases to form a grammatical scalar nu‐V construction with an activity verb. We argue that the solutions to these puzzles lie in three core meaning components of scalar nu‐V constructions: (a) scalar presupposition; (b) association with focus; (c) volitional requirement. Specifically, we propose that (a) scalar nu is a scalar verbal modifier that forms a verbal compound with its following verb; (b) scalar nu introduces a scalar presupposition (based on the scalar associate) and the volitional requirement in scalar nu‐V constructions. If our analysis is correct, it suggests that the scalarity of a construction may come from a verbal modifier (e.g., scalar nu) in the formation of a compound verb, thereby enhancing our understanding of the compositionality of compound verbs in natural language.
Reconstructing geographies of margins: Unbounded spaces in an immobile world
Authors: Aparna Kolar
Published: July 2024

In this paper I call for unbounding Paasi's ontological position, while urging for a research agenda that shifts from Deconstructing Regional Identity to Reconstructing geographies of margins. Reconstructing geographies of margins is an agenda for building situated knowledges from experiences of movement historically produced as ‘out of place’ and ‘out of time’ to undo fixity in spatio‐temporal categories of the state but also of social‐scientific analysis. I argue that thinking and sensing from the plural epistemological and ontological positions emerging from such movement (out of one's place and time assigned by oppressive structures of domination) is essential to emancipate the categories of the migrant/refugee/other from scientific and historical ways of knowing that produced it in the first place. This agenda cannot be fixed but must be continuously aimed, as an ongoing perpetual process of unbounding research agendas of mobility, borders and migration from settling into rigid onto‐epistemic positions.
Learning English vowels: The effects of different phonetic training modes on Arabic learners' production and perception
Authors: Alshangiti Wafaa , Evans Bronwen G.
Published: July 2024

This study investigated the effect of different types of phonetic training on potential changes in the production and perception of English vowels by Arabic learners of English. Forty-six Arabic learners of English were randomly assigned to one of three high variability vowel training programs: Perception training (High Variability Phonetic Training), Production training, and a Hybrid Training program (production and perception training). Pre- and post-tests (vowel identification, category discrimination, speech recognition in noise, and vowel production) showed that all training types led to improvements in perception and production. There was some evidence that improvements were linked to training type: learners in the Perception Training condition improved in vowel identification but not vowel production, while those in the Production Training condition showed only small improvements in performance on perceptual tasks, but greater improvement in production. However, the effects of training modality were complicated by proficiency, with high proficiency learners benefitting more from different types of training regardless of training mode than lower proficiency learners.
Monoallelic de novo
AJAP1
loss-of-function variants disrupt trans-synaptic control of neurotransmitter release
Authors: Früh Simon , Boudkkazi Sami , Koppensteiner Peter , Sereikaite Vita , Chen Li-Yuan , Fernandez-Fernandez Diego , Rem Pascal D. , Ulrich Daniel , Schwenk Jochen , Chen Ziyang , Le Monnier Elodie , Fritzius Thorsten , Innocenti Sabrina M. , Besseyrias Valérie , Trovò Luca , Stawarski Michal , Argilli Emanuela , Sherr Elliott H. , van Bon Bregje , Kamsteeg Erik-Jan , Iascone Maria , Pilotta Alba , Cutrì Maria R. , Azamian Mahshid S. , Hernández-García Andrés , Lalani Seema R. , Rosenfeld Jill A. , Zhao Xiaonan , Vogel Tiphanie P. , Ona Herda , Scott Daryl A. , Scheiffele Peter , Strømgaard Kristian , Tafti Mehdi , Gassmann Martin , Fakler Bernd , Shigemoto Ryuichi , Bettler Bernhard
Published: July 2024

Adherens junction–associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic
AJAP1
variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in
Ajap1
−/−
and
Ajap1
W183C/+
mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function
AJAP1
variants.
Biochemical and biophysical drivers of the hydrogen isotopic composition of carbohydrates and acetogenic lipids
Authors: Lehmann Marco M. , Schuler Philipp , Werner Roland A. , Saurer Matthias , Wiesenberg Guido L. B. , Cormier Marc-André
Published: July 2024

The hydrogen isotopic composition (δ
2
H) of plant compounds is increasingly used as a hydroclimatic proxy; however, the interpretation of δ
2
H values is hampered by potential coeffecting biochemical and biophysical processes. Here, we studied δ
2
H values of water and carbohydrates in leaves and roots, and of leaf
n
-alkanes, in two distinct tobacco (
Nicotiana sylvestris
) experiments. Large differences in plant performance and biochemistry resulted from (a) soil fertilization with varying nitrogen (N) species ratios and (b) knockout-induced starch deficiency. We observed a strong
2
H-enrichment in sugars and starch with a decreasing performance induced by increasing NO
3
−
/NH
4
+
ratios and starch deficiency, as well as from leaves to roots. However, δ
2
H values of cellulose and
n
-alkanes were less affected. We show that relative concentrations of sugars and starch, interlinked with leaf gas exchange, shape δ
2
H values of carbohydrates. We thus provide insights into drivers of hydrogen isotopic composition of plant compounds and into the mechanistic modeling of plant cellulose δ
2
H values.
Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation
Authors: Zhao Zhaozhao , Chen Yu , Zou Xudong , Lin Limin , Zhou Xiaolan , Cheng Xiaomeng , Yang Guangrui , Xu Qiushi , Gong Lihai , Li Lei , Ni Ting
Published: July 2024

Abnormal transcription initiation from alternative first exon has been reported to promote tumorigenesis. However, the prevalence and impact of gene expression regulation mediated by alternative tandem transcription initiation were mostly unknown in cancer. Here, we developed a robust computational method to analyze alternative tandem transcription start site (TSS) usage from standard RNA sequencing data. Applying this method to pan-cancer RNA sequencing datasets, we observed widespread dysregulation of tandem TSS usage in tumors, many of which were independent of changes in overall expression level or alternative first exon usage. We showed that the dynamics of tandem TSS usage was associated with epigenomic modulation. We found that significant 5′ untranslated region shortening of gene
TIMM13
contributed to increased protein production, and up-regulation of
TIMM13
by CRISPR-mediated transcriptional activation promoted proliferation and migration of lung cancer cells. Our findings suggest that dysregulated tandem TSS usage represents an addtional layer of cancer-associated transcriptome alterations.
Nanoradian-scale precision in light rotation measurement via indefinite quantum dynamics
Authors: Xia Binke , Huang Jingzheng , Li Hongjing , Luo Zhongyuan , Zeng Guihua
Published: July 2024

The manipulation and metrology of light beams are pivotal for optical science and applications. In particular, achieving ultrahigh precision in the measurement of light beam rotations has been a long-standing challenge. Instead of using quantum probes like entangled photons, we address this challenge by incorporating a quantum strategy called “indefinite time direction” into the parameterizing process of quantum parameter estimation. Leveraging this quantum property of the parameterizing dynamics allows us to maximize the utilization of orbital angular momentum resources for measuring ultrasmall angular rotations of beam profile. Notably, a nanoradian-scale precision of light rotation measurement is lastly achieved in the experiment, which is the highest precision by far to our best knowledge. Furthermore, this scheme holds promise in various optical applications due to the diverse range of manipulable resources offered by photons.
Defect dipole stretching enables ultrahigh electrostrain
Authors: Tian Shuo , Wang Binquan , Li Bin , Guo Yiping , Zhang Shujun , Dai Yejing
Published: July 2024

Piezoelectric actuators have been extensively utilized as micro-displacement devices because of their advantages of large output displacement, high sensitivity, and immunity to electromagnetic interference. Here, we propose a straightforward approach to design <110>-oriented defect dipoles by introducing A-site vacancies and oxygen vacancies in (K
0.48
Na
0.52
)
0.99
NbO
2.995
ceramics. As a result, we achieve ultrahigh electrostrains of 0.7% at 20 kV cm
−1
(with an effective piezoelectric strain coefficient
d
33
*
= 3500 pm V
−1
), outperforming the performance of existing piezoelectric ceramics at the same driving field. The exceptional electrostrain is primarily attributed to the large stretching of defect dipoles when subjected to an applied electric field, a phenomenon that has been experimentally confirmed. Moreover, the strong interaction between these defect dipoles and <110> spontaneous polarizations plays a critical role in minimizing hysteresis and ensuring excellent fatigue resistance. Our findings present a practical and effective strategy for developing high-performance piezoelectric materials tailored for advanced actuator applications.
Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort
Authors: Camarena Marta E. , Theunissen Patrick , Ruiz Marta , Ruiz-Orera Jorge , Calvo-Serra Beatriz , Castelo Robert , Castro Carla , Sarobe Pablo , Fortes Puri , Perera-Bel Júlia , Albà M. Mar
Published: July 2024

The expression of tumor-specific antigens during cancer progression can trigger an immune response against the tumor. Here, we investigate if microproteins encoded by noncanonical open reading frames (ncORFs) are a relevant source of tumor-specific antigens. We analyze RNA sequencing data from 117 hepatocellular carcinoma (HCC) tumors and matched healthy tissue together with ribosome profiling and immunopeptidomics data. Combining human leukocyte antigen–epitope binding predictions and experimental validation experiments, we conclude that around 40% of the tumor-specific antigens in HCC are likely to be derived from ncORFs, including two peptides that can trigger an immune response in humanized mice. We identify a subset of 33 tumor-specific long noncoding RNAs expressing novel cancer antigens shared by more than 10% of the HCC samples analyzed, which, when combined, cover a large proportion of the patients. The results of the study open avenues for extending the range of anticancer vaccines.
An open-label, randomized controlled trial to assess a ketogenic diet in critically ill patients with sepsis
Authors: Rahmel Tim , Effinger David , Bracht Thilo , Griep Leonore , Koos Björn , Sitek Barbara , Hübner Max , Hirschberger Simon , Basten Jale , Timmesfeld Nina , Adamzik Michael , Kreth Simone
Published: July 2024

Patients with sepsis experience metabolic and immunologic dysfunction that may be amplified by standard carbohydrate-based nutrition. A ketogenic diet (KD) may offer an immunologically advantageous alternative, although clinical evidence is limited. We conducted a single-center, open-label, randomized controlled trial to assess whether a KD could induce stable ketosis in critically ill patients with sepsis. Secondary outcomes included assessment of feasibility and safety of KD, as well as explorative analysis of clinical and immunological characteristics. Forty critically ill adults were randomized to either a ketogenic or standard high-carbohydrate diet. Stable ketosis was achieved in all KD patients, with significant increases in β-hydroxybutyrate levels compared with controls [mean difference 1.4 milimoles per liter; 95% confidence interval (CI): 1.0 to 1.8;
P
< 0.001). No major adverse events or harmful metabolic side effects (acidosis, dysglycemia, or dyslipidemia) were observed. After day 4, none of the patients in the KD group required insulin treatment, whereas in the control group, insulin dependency ranged between 35% and 60% (
P
= 0.009). There were no differences in 30-day survival, but ventilation-free [incidence rate ratio (IRR) 1.7; 95% CI: 1.5 to 2.1;
P
< 0.001], vasopressor-free (IRR 1.7; 95% CI: 1.5 to 2.0;
P
< 0.001), dialysis-free (IRR 1.5; 95% CI: 1.3 to 1.8;
P
< 0.001), and intensive care unit–free days (IRR 1.7; 95% CI: 1.4 to 2.1;
P
< 0.001) were higher in the ketogenic group. Next-generation sequencing of CD4
+
/CD8
+
T cells and protein analyses showed reduced immune dysregulation, with decreased gene expression of T-cell activation and signaling markers and lower pro-inflammatory cytokine secretion. This trial demonstrated the safe induction of a stable ketogenic state in sepsis, warranting larger trials to investigate potential benefits in sepsis-related organ dysfunction.
Continental-scale drainage reorganization during Mesoproterozoic orogenesis: Evidence from the Belt Basin of western North America
Authors: Hirtz Jaime A.M. , Constenius Kurt N. , Horton Brian K. , Valencia Victor A. , Pratt Brian R.
Published: July 2024

The Mesoproterozoic Belt Basin of the northwestern United States and southwestern Canada contains a 5–20-km-thick metasedimentary succession deposited during an important transition in the Precambrian development of North America. Key unresolved issues for the Belt Basin include the chronology of deposition, sources of siliciclastic sediment, and regional paleogeography during Laurentian orogenesis. To address these topics, we acquired detrital zircon U-Pb geochronologic data for eastern exposures of the Belt-Purcell Supergroup in the Lewis thrust salient along the USA-Canada border. To define an integrated chronostratigraphic and provenance framework for the Belt Basin, we calculated maximum depositional ages and qualitatively and quantitatively compared our geochronologic data set to a compilation of Laurentian igneous and metamorphic zircon U-Pb ages using multidimensional scaling and an inverse Monte Carlo model. The results suggest a stratigraphic age range of ca. 1495–1380 Ma, constituting a depositional duration of ~115 m.y. with an average sediment accumulation rate of ~40 m/m.y. for the studied locality (extrapolated to ~155 m/m.y. for the basin depocenter). Variations in sediment provenance are expressed by three distinct intervals within the Belt-Purcell Supergroup. The lower Belt Supergroup succession (Waterton to lower Helena Formations; ca. 1495–1440 Ma) is dominated by Paleoproterozoic and Archean grains derived from the northeastern Canadian Shield. The middle Belt Supergroup succession (upper Helena to Sheppard Formations; ca. 1440–1420 Ma) displays mixed early Mesoproterozoic, late Paleoproterozoic, and Archean zircon age groups. The upper Belt Supergroup succession (Gateway to Roosville Formations; ca. 1420–1380 Ma) contains almost entirely late Paleoproterozoic zircons sourced from the south (Yavapai-Mazatzal and Mojave crustal provinces). We interpret sediment provenance to reflect a continental-scale, fluvial drainage reorganization during middle Belt Supergroup deposition that can be linked to the recently recognized Picuris orogeny.
Supplemental Material: Updating the Upper Cretaceous (Campanian) Two Medicine Formation of Montana (USA): Lithostratigraphic revisions, new CA-ID-TIMS U-Pb ages, and a calibrated framework for dinosaur occurrences
Authors: Rogers Raymond R. , et al.
Published: July 2024

Table S1: U-Pb isotopic data for zircon analyses from Campanian bentonites of the Two Medicine Formation, Montana, USA. Table S2: GPS coordinates for measured columns in Two Medicine Formation.
Spatiotemporal patterns of low and highly pathogenic avian influenza virus prevalence in murres in Canada from 2007 to 2022—a case study for wildlife viral monitoring
Authors: McLaughlin Angela , Giacinti Jolene , Rahman Ishraq , Wight Jordan , Hargan Kathryn , Lang Andrew S. , Mallory Mark L. , Robertson Gregory J. , Elliot Kyle , Ojkic Davor , Lair Stéphane , Jones Megan , Berhane Yohannes , Gilchrist Grant , Wilson Laurie , Wilhelm Sabina I. , Brown Michael G.C. , Provencher Jennifer F.
Published: July 2024

Migratory seabirds move across ocean basins and are one of the primary reservoirs of low pathogenic avian influenza virus (LPAIV). This includes the millions of thick-billed murres ( Uria lomvia) and common murres ( Uria aalge) that are distributed across northern hemisphere oceans. In response to increasingly frequent detections of highly pathogenic avian influenza virus (HPAIV) in Europe in 2020–2021, avian influenza virus (AIV) monitoring in wildlife has increased. We compiled data from murres tested for AIV in Canada between 2007 and 2022 to quantify spatiotemporal variation in the prevalence of LPAIV and HPAIV in these birds. No HPAIV was detected in murres prior to 2022, but HPAIV was present in 46% of both live/harvested and found dead murres in the northwestern Atlantic in 2022 with prevalence peaking at 63% among live birds in the summer. In the eastern Canadian Arctic, HPAIV prevalence in 2022 was <1% while LPAIV prevalence was 21%, which was significantly higher than previous sampling years. Power analyses suggest approximately 100 samples from breeding murres should be collected annually per colony or region to detect moderate changes in HPAIV prevalence. These analyses inform robust monitoring of viruses in wildlife, with implications for conservation, harvest management, and public health.
Viral Genome Delivery Across Bacterial Cell Surfaces
Authors: Iglesias Stephano M. , Li Fenglin , Briani Federica , Cingolani Gino
Published: July 2024

In 1952, Hershey and Chase used bacteriophage T2 genome delivery inside Escherichia coli to demonstrate that DNA, not protein, is the genetic material. Over 70 years later, our understanding of bacteriophage structure has grown dramatically, mainly thanks to the cryogenic electron microscopy revolution. In stark contrast, phage genome delivery in prokaryotes remains poorly understood, mainly due to the inherent challenge of studying such a transient and complex process. Here, we review the current literature on viral genome delivery across bacterial cell surfaces. We focus on icosahedral bacterial viruses that we arbitrarily sort into three groups based on the presence and size of a tail apparatus. We inventory the building blocks implicated in genome delivery and critically analyze putative mechanisms of genome ejection. Bacteriophage genome delivery into bacteria is a topic of growing interest, given the renaissance of phage therapy in Western medicine as a therapeutic alternative to face the antibiotic resistance crisis.
Efficacy of Risankizumab in Patients with Suboptimal Response or Failure to Ustekinumab: A Multicenter Retrospective Study in Spain
Authors: Magdaleno-Tapial Jorge , Ortiz-Salvador José María , Sánchez-Carazo José Luis , Hernández-Bel Pablo , Pérez-Ferriols Amparo , Santos-Alarcón Sergio , Sahuquillo-Torralba Antonio , Pujol-Marco Conrad , Rivera-Díaz Raquel , Belinchón-Romero Isabel , Ruiz-Geneao Diana , Romero-Maté Alberto , Ruiz-Villaverde Ricardo , Ferrán-Farrés Marta , Gallardo-Hernández Fernando , Almenara-Blasco Manuel , Alonso-Suárez Jorge , González-Cantero Álvaro , Martínez-Lorenzo Elena , Fernández-Armenteros José Manuel , de Alcázar-Viladomiu Elena , García-Latasa Javier , Rocamora-Durant Vicenç , Ara-Martín Mariano , Mateu-Puchades Almudena , Llamas-Velasco Mar , Vilarrasa-Rull Eva , Velasco-Pastor Manel , de la Cueva-Dobao Pablo , Carrascosa-Carrillo José Manuel , Martorell-Calatayud Antonio
Published: July 2024

Background. Current psoriasis treatment goals emphasize achieving complete or near‐complete skin clearance while preserving the quality of life, necessitating treatment modification for a suboptimal or inadequate response. Despite risankizumab’s demonstrated efficacy, evidence remains limited for patients switching from ustekinumab, particularly those with suboptimal or inadequate response. Objective. This study assesses risankizumab’s real‐world effectiveness in patients with suboptimal response (PASI 2‐3), inadequate response (PASI 3–5), or failure (PASI >5) to ustekinumab, based on a multicenter retrospective cohort in Spain. Method. A multicenter retrospective study across 24 Spanish hospitals included 102 patients previously treated with ustekinumab and switched to risankizumab. Results. Out of 102 patients, 78 experienced ustekinumab treatment failure (PASI >5), while 24 had an inadequate response (PASI 3–5), including 6 with a suboptimal response (PASI 2‐3). Remarkably, after one year of treatment with risankizumab, all patients demonstrated improvement, achieving near‐complete or complete skin clearance (PASI 0‐1). Conclusion. Risankizumab displayed effectiveness in patients with suboptimal/inadequate response or treatment failure to ustekinumab, aligning with the current treatment goals of complete or near‐complete skin clearance. These real‐world results corroborate clinical trial data, emphasizing risankizumab’s potential as a powerful therapeutic alternative for this patient population. Further prospective studies are essential to validate these findings.
Association of Helicobacter pylori Infection with Depression and Anxiety: A Systematic Review and Meta‐Analysis
Authors: Li Lu , Ren Yadi , Wang Zeyu , Niu Yanqing , Zhao Ying , Aihaiti Xiaherezhati , Ji Yinglan , Li Man
Published: July 2024

Introduction. The association between Helicobacter pylori (H. pylori) infection and depression and anxiety has been reported in the literature. The aim of this meta‐analysis is to investigate the association of H. pylori infection with depression and anxiety. Methods. A systematic search was conducted in PubMed, Web of Science, Embase, and Chinese databases for observational studies that reported the incidence or prevalence of depression and anxiety in patients with H. pylori infection. We conducted meta‐analysis with a random‐effects model. Results. A total of twelve studies were included in this meta‐analysis. Significant and positive association was found for H. pylori infection with anxiety (OR 2.49, 95% CI 1.83–3.39), but not depression (OR 1.40, 95% CI 0.75–2.58). Subgroup analysis from study design noted a significant positive association between H. pylori infection and anxiety (case‐control and cross‐sectional study, OR 2.36, 95% CI 1.65–3.38; cohort study, RR 1.72, 95% CI 1.28–2.32). The similar trend among studies used the Self‐Rating Anxiety Scale (OR 2.43, 95% CI 1.78–3.32) and other questionnaires (OR 2.41, 95% CI 1.50–3.87) have been observed. However, subgroup analysis of the association between H. pylori infection and depression yields different results. Subgroup analysis from cohort studies noted a significant association between H. pylori infection and depression (RR 1.99, 95% CI 1.33–2.99), but not case‐control and cross‐sectional studies (OR 1.20, 95% CI 0.59–2.46). A significant positive association has been observed among studies used the Self‐Rating Depression Scale (OR 2.03, 95% CI 1.11–3.70), as opposed to studies using other questionnaires (OR 1.03, 95% CI 0.31–3.44). Conclusion. This meta‐analysis provide the support that a significant positive association between H. pylori infection and anxiety disorders. However, the association between H. pylori infection and depression appears to be insignificant.
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: July 2024

Demographic variables stratified by low and high hypoxia scores, showing no significant differences to be controlled for in the Cox proportional hazards model described in Figure 1D.
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: July 2024

Kruskal-Walis test results comparing the deconvolved immune cell compositions between hypoxic and normoxic tumors.
Figure 5 from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: July 2024

Oxygen-responsive gene expression of Cutibacterium within model tumors. A, Volcano plot of metatranscriptomic analysis of transcripts from Cutibacterium found in low or high hypoxia score CT26 tumors grown in either immune-deficient or immune-competent host animals (1,295 total transcripts identified). B, Bar plot showing the total number of significantly enriched genes in the hypoxic and normoxic conditions enriched in each enzyme class as notated in (A). C, Table of the 34 annotated transcripts that showed significant concordant changes to hypoxia score in both datasets (48 total, 39 pos, and 9 neg).