bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender Inequality and Biological Supremacy: A Sex Equality Analysis of Patrick Parkinson’s “Neutral” Proposal
Authors: Gilreath Shannon
Published: January 2023

In this essay, a response to an article by Patrick Parkinson, Shannon Gilreath disputes Parkinson’s claim that religiously motivated discrimination against transgender people should be the subject of special exceptions to prevailing antidiscrimination law, especially where the transgender person does not seek to conform to the traditional male/female gender binary. Gilreath maps the ways in which Parkinson’s proposal is an argument for biological superiority, which has been the rationalization for systematic and systemic social inferiority throughout history, including most notably in the contexts of race, gender, and sexuality oppression. In concluding that Parkinson’s proposal is little more than a restatement of the faulty differences-based approach to equality through law, Gilreath ultimately concludes that its principles are wholly inconsistent with the legitimate purposes of antidiscrimination law.
On k-folding map-germs and hidden symmetries of surfaces in the Euclidean 3-space
Authors: Peñafort Sanchis Guillermo , Tari Farid
Published: January 2023

We obtain a complete topological classification of $k$-folding map-germs on generic surfaces in $\mathbb {R}^3$, discover new robust features of surfaces and recover, in a unified way, many of the robust features that were obtained previously by considering the contact of a surface with lines, planes or spheres.
Holocene evolution of parabolic dunes, White River Badlands, South Dakota, USA, revealed by high-resolution mapping
Authors: Baldauf Paul Evans , Baker Gregory S. , Miles Maraina L. , Burkhart Patrick A. , Gontz Allen , Rinka Madelyn , Levenson Michael
Published: January 2023

The White River Badlands (WRB) of South Dakota record eolian activity spanning the late Pleistocene through the latest Holocene (21 ka to modern), reflecting the effects of the last glacial period and Holocene climate fluctuations (Holocene Thermal Maximum, Medieval Climate Anomaly, and Little Ice Age). The WRB dune fields are important paleoclimate indicators in an area of the Great Plains with few climate proxies. The goal of this study is to use 1 m/pixel-resolution digital elevation models from drone imagery to distinguish Early to Middle Holocene parabolic dunes from Late Holocene parabolic dunes. Results indicate that relative ages of dunes are distinguished by slope and roughness (terrain ruggedness index). Morphological differences are attributed to postdepositional wind erosion, soil formation, and mass wasting. Early to Middle Holocene and Late Holocene paleowind directions, 324°± 13.1° (N = 7) and 323° ± 3.0° (N = 19), respectively, are similar to the modern wind regime. Results suggest significant landscape resilience to wind erosion, which resulted in preservation of a mosaic of Early and Late Holocene parabolic dunes. Quantification of dune characteristics will help refine the chronology of eolian activity in the WRB, provide insight into drought-driven landscape evolution, and integrate WRB eolian activity in a regional paleoenvironmental context.
Longitudinal concordance of body composition and anthropometric assessment by a novel smartphone application across a 12-week self-managed weight loss intervention
Authors: Smith Marc K. , Staynor Jonathan M. D. , El-Sallam Amar , Ebert Jay R. , Ackland Tim R.
Published: January 2023

Smartphone applications (SPA) now offer the ability to provide accessible in-home monitoring of relevant individual health biomarkers. Previous cross-sectional validations of similar technologies have reported acceptable accuracy with high-grade body composition assessments; this research assessed longitudinal agreement of a novel SPA across a self-managed weight loss intervention of thirty-eight participants (twenty-one males, seventeen females). Estimations of body mass (BM), body fat percentage (BF%), fat-free mass (FFM) and waist circumference (WC) from the SPA were compared with ground truth (GT) measures from a dual-energy X-ray absorptiometry scanner and expert technician measurement. Small mean differences (MD) and standard error of estimate (SEE) were observed between method deltas (ΔBM: MD = 0·12 kg, SEE = 2·82 kg; ΔBF%: MD = 0·06 %, SEE = 1·65 %; ΔFFM: MD = 0·17 kg, SEE = 1·65 kg; ΔWC: MD = 1·16 cm, SEE = 2·52 cm). Concordance correlation coefficient (CCC) assessed longitudinal agreement between the SPA and GT methods, with moderate concordance (CCC: 0·55–0·73) observed for all measures. The novel SPA may not be interchangeable with high-accuracy medical scanning methods yet offers significant benefits in cost, accessibility and user comfort, in conjunction with the ability to monitor body shape and composition estimates over time.
Secondary sexual dimorphism in biomass production of Ilex paraguariensis progenies associated with their provenances and morphotypes
Authors: Rakocevic Miroslava , Maia Aline de Holanda Nunes , Duarte Manoela Mendes , Wendling Ivar
Published: January 2023

Secondary sexual dimorphism (SSD) in flowering plants is expressed as differences in sexual characteristics that are not directly related to gamete production, involving a wide variety of morphological and physiological traits. Yerba mate (Ilex paraguariensis) is an evergreen dioecious tree native to South America. It was hypothesized that: (1) in early years, the two yerba-mate genders would segregate with lower frequency in biomass production than during later years; (2) in the case of SSD, higher biomass production would be seen for female plants when compared to male plants at a more advanced age; (3) higher SSD would appear in morphotypes that represent leaf adaptations to full sunlight cultivation; and (4) progenies originated from provenances from higher altitudes will show greater SSD in biomass production. One experiment with 135 progenies originated from six provenances with different altitudes was established in 1997 in a monoculture (under full sunlight conditions). Biomass production (leaves and thin twigs) per plant was evaluated during four harvests (1999, 2001, 2003, and 2015). The frequency of SSD in biomass production did not change throughout the plant’s life. Males were more productive than females in 1999, 2001, and 2003, while the increased frequency of more productive female plants was observed during the most recent harvest (2015), resulting in an equal frequency of female and male progenies. Sexual segregation was observed in dully green, sassafras, and gray morphotypes that are characterized by their waxy leaf structures, an adaptation to elevated irradiance and UV. As a result of adaptative responses to stressful conditions and elevated interplant variability, the relationship between SSD and biomass production of progenies originated from the highest altitudes segregated with higher frequency when compared to the lowest altitudes.
Genomic evaluation of threshold traits in different scenarios of threshold number using parametric and non-parametric statistical methods
Authors: Ghasemi M. , Ghafouri-Kesbi F. , Zamani P.
Published: January 2023

The aim was to study the effect of the threshold number on the accuracy of genomic evaluation of the threshold traits using support vector machine (SVM), genomic best linear unbiased prediction (GBLUP) and Bayesian method B (BayesB). For this purpose, a genome consisting of three chromosomes was simulated for 1000 individuals on which 3000 bi-allelic single nucleotide polymorphism markers were evenly distributed. Genomic breeding values were predicted in different scenarios of threshold number (1–6 thresholds), QTL number (30 and 300 QTLs) and heritability level (0.1, 0.3 and 0.5). By increasing the number of thresholds from 1 to 6 thresholds, especially at higher levels of heritability, the accuracy of genomic evaluation increased; however, the increase in accuracy was not linear so that it was much more noticeable when the number of thresholds increased from 1 to 2 thresholds. In the most studied scenarios, SVM showed a very poor performance compared to other methods. BayesB ranked first regarding prediction accuracy, though in some cases the observed differences with GBLUP was not significant. While increase in heritability increased the accuracy of genomic evaluation, change in the QTL number had a slight effect on the prediction accuracy. According to the results, the SVM is not recommended for genomic evaluation of threshold traits, especially those which have only one threshold and instead, use of GBLUP and BayesB is recommended. For traits with more than one threshold, fortunately we can achieve accuracy similar to continuous traits by applying traditional genomic evaluation methods.
Recent occurrence of marine mammals and sea turtles off Angola and first report of right whales since the whaling era
Authors: Whitt Amy D. , Warde Ann M. , Blair Lenisa , Deslarzes Ken J. P. , Chaineau Claude-Henri
Published: January 2023

Marine megafauna occurrence was recorded in the deep-sea region bordering the abyssal plain ~400 km north-west of Luanda, Angola. The survey took place during an Environmental Baseline Study (EBS), prior to drilling exploration activities, with the goal of characterizing the habitat and biodiversity of the region. Offshore shipboard surveys were conducted during September 2018 in water depths ranging from 2350–3850 m. We recorded daytime sightings of marine mammals and sea turtles and at night made audio recordings using passive acoustic monitoring (PAM) methods focused on capturing the sounds of vocalizing marine mammals. A variety of species were visually detected, including the humpback whale (Megaptera novaeangliae), sperm whale (Physeter macrocephalus), common dolphin (Delphinusspp.), striped dolphin (Stenella coeruleoalba), Atlantic spotted dolphin (S. frontalis), and olive ridley turtle (Lepidochelys olivacea). Acoustic click bouts similar to those made by several odontocete species, possibly including beaked whales, were recorded within the 25–48 kHz range. The humpback whale was the most frequently sighted species, accounting for 56% of mammal sightings, indicating a potential far offshore migratory habitat in this region. Most notably, right whales (probableEubalaena australis) were visually observed. This is the first confirmed record of right whales in Angolan waters since the early 1900s. As development expands in this offshore region, these data can usefully inform future monitoring and mitigation strategies focused on minimizing impacts to wildlife.
Pythagorean-Hodograph curves-based trajectory planning for pick-and-place operation of Delta robot with prescribed pick and place heights
Authors: Su Tingting , Liang Xu , Zeng Xiang , Liu Shengda
Published: January 2023

In this paper, a Pythagorean-Hodograph (PH) curve-based pick-and-place operation trajectory planning method for Delta parallel robots is proposed, which realizes the flexible control of pick-and-place operations to meet the requirements of various practical scenarios. First, according to the geometric relationship of pick-and-place operation path, different pick-and-place operations are classified. Then trajectory planning is carried out for different situations, respectively, and in each case, the different polynomial motion laws adopted by the linear motion segment and the curved motion segment are solved. Trajectory optimization is performed with the motion period as optimization objective. The proposed method is easier to implement, and at the same time satisfies the safety, optimization, mobility, and stability of the robot; that is, the proposed method realizes obstacle avoidance, optimal time, flexible control of the robot trajectory, and stable motion. Simulations and experiments verify the effectiveness of the method proposed in this paper. The proposed method can not only realize the fast, accurate, and safe operation in intelligent manufacturing fields such as rapid classification, palletizing, grasping, warehousing, etc., but its research route can also provide a reference for trajectory planning of intelligent vehicles in logistics system.
Construction and validation of a questionnaire to study engagement in informal second language learning
Authors: Arndt Henriette L.
Published: January 2023

This article reports on the development and validation of the Informal Second Language Engagement questionnaire (ISLE) for capturing various aspects of learner engagement with informal second language practices. Whereas other questionnaires have primarily focused on learner behavior (the frequency, quantity, and diversity of informal activities in which learners engage), the ISLE additionally targets affective, cognitive, and linguistic aspects of engagement. Consequently, this questionnaire has the potential to help second language acquisition researchers better understand individual differences and variability in informal language engagement, how it changes over time, and the ways in which engagement affects language learning. The ISLE was developed and evaluated in three stages with a total of 382 German secondary school learners of English as a foreign language. The initial instrument development was informed by qualitative findings from focus group interviews. Subsequently, the questionnaire was piloted, and Exploratory Factor Analysis was applied to the data to uncover the underlying factor structures and reduce the number of items per construct. Finally, the revised instrument was evaluated further using Confirmatory Factor Analysis.
Improving measurement performance via fusion of classical and quantum accelerometers
Authors: Wang Xuezhi , Kealy Allison , Gilliam Christopher , Haine Simon , Close John , Moran Bill , Talbot Kyle , Williams Simon , Hardman Kyle , Freier Chris , Wigley Paul , White Angela , Szigeti Stuart , Legge Sam
Published: January 2023

While quantum accelerometers sense with extremely low drift and low bias, their practical sensing capabilities face at least two limitations compared with classical accelerometers: a lower sample rate due to cold atom interrogation time; and a reduced dynamic range due to signal phase wrapping. In this paper, we propose a maximum likelihood probabilistic data fusion method, under which the actual phase of the quantum accelerometer can be unwrapped by fusing it with the output of a classical accelerometer on the platform. Consequently, the recovered measurement from the quantum accelerometer is used to estimate bias and drift of the classical accelerometer which is then removed from the system output. We demonstrate the enhanced error performance achieved by the proposed fusion method using a simulated 1D accelerometer precision test scenario. We conclude with a discussion on fusion error and potential solutions.
Invasive pneumococcal surveillance to assess the potential benefits of extended spectrum conjugate vaccines (PCV15/PCV20) in older adults
Authors: Humphreys Hilary , Corcoran Mary , Mereckiene Jolita , Cunney Robert , Cotter Suzanne
Published: January 2023

The introduction of pneumococcal conjugate vaccines (PCV) into the childhood vaccination programme has reduced invasive pneumococcal disease (IPD). Although anticipated from data elsewhere, surveillance in Ireland has confirmed reductions in IPD amongst those ⩾65 years of age due to a decline of PCV serotypes in this age group. Currently, direct protection against IPD in the elderly is focused on immunisation with the 23-valent pneumococcal polysaccharide vaccine (PPV23). However, immunity may not be as effective as with PCV and, furthermore, PPV23 uptake is poor in Ireland. Hence, consideration should be given to providing a PCV to this age group.
A multilevel developmental psychopathology model of childbirth and the perinatal transition
Authors: Kaliush Parisa R. , Conradt Elisabeth , Kerig Patricia K. , Williams Paula G. , Crowell Sheila E.
Published: January 2023

Despite recent applications of a developmental psychopathology perspective to the perinatal period, these conceptualizations have largely ignored the role that childbirth plays in the perinatal transition. Thus, we present a conceptual model of childbirth as a bridge between prenatal and postnatal health. We argue that biopsychosocial factors during pregnancy influence postnatal health trajectories both directly and indirectly through childbirth experiences, and we focus our review on those indirect effects. In order to frame our model within a developmental psychopathology lens, we first describe “typical” biopsychosocial aspects of pregnancy and childbirth. Then, we explore ways in which these processes may deviate from the norm to result in adverse or traumatic childbirth experiences. We briefly describe early postnatal health trajectories that may follow from these birth experiences, including those which are adaptive despite traumatic childbirth, and we conclude with implications for research and clinical practice. We intend for our model to illuminate the importance of including childbirth in multilevel perinatal research. This advancement is critical for reducing perinatal health disparities and promoting health and well-being among birthing parents and their children.
Zurück ins Leben
Authors: Vetter Stefan
Published: January 2023

Was ist zu diesem Thema bereits bekannt?

Im ambulanten Setting wird empfohlen, Psychopharmaka in kleinen Schritten behutsam zu reduzieren. Trotzdem können massive Rebound-Effekte entstehen, die sich gegen Ende des Reduktionsprozesses nochmals massiv verschärfen können.

Wie wird eine neue Perspektive eingebracht?

In diesem Reduktionsprozess kann eine kontinuierliche Bezugspflege Sicherheit vermitteln. Dabei sollte die Pflege stets dazu ermutigen, Rebound-Effekte nicht zu bekämpfen, sondern ihnen freundschaftlich zu begegnen.

Was sind die Auswirkungen für die Praxis?

Die ambulante Pflege sollte ein Konzept dafür entwickeln, wie Rebound-Effekte identifiziert, angenommen, ausgehalten und überwunden werden können. Zudem sollte die Pflege verstärkt darüber diskutieren, wie ein Leben mit weniger Medikamenten oder auch ohne Medikamente gelingen kann.
Thermal Properties of Pressure Core Samples Recovered From Nankai Trough Wells Before and After Methane Hydrate Dissociation
Authors: Muraoka M. , Yoneda J. , Jin Y. , Hattori T. , Imai T. , Suzuki K.
Published: January 2023

The thermal properties of methane hydrate (MH)‐bearing sediments are necessary for developing gas production technologies (e.g., gas production rate prediction). The direct thermal property measurement of a general MH reservoir is difficult because it demands an advanced coring and measuring technology. Therefore, a good thermal property value estimation model for a system containing sediment grains, water, MH, and gas is necessary. In 2018, the pressure core samples were recovered from the AT‐CW1 and AT‐CW2 wells in Nankai Trough of Japan. Using a single‐sided transient plane source method, we measure herein the thermal property values of those core samples and estimate their thermal conductivity by improving existing models. The measured thermal conductivity (λ), specific heat (ρCp), and thermal diffusivity (α) of the MH‐bearing sediments before and after MH dissociation are obtained. The de Vries model agrees well with the measured thermal conductivity values before and after the MH dissociation. For the random distribution (geometric mean) model, the difference between the estimation values and the data after the MH dissociation increases as the gas saturation Sg′ increases. In the worst case, the distribution model shows an 87.6% error, while the de Vries model yields 5.2% of the same. We propose and use an estimation method of the thermal property values in an MH reservoir, which requires classical thermophysical models and well log data. The in‐situ thermal property values can be estimated when the log data are highly accurate.
The Potential Benefits of Handling Mixture Statistics via a Bi‐Gaussian EnKF: Tests With All‐Sky Satellite Infrared Radiances
Authors: Chan Man‐Yau , Chen Xingchao , Anderson Jeffrey L.
Published: January 2023

The meteorological characteristics of cloudy atmospheric columns can be very different from their clear counterparts. Thus, when a forecast ensemble is uncertain about the presence/absence of clouds at a specific atmospheric column (i.e., some members are clear while others are cloudy), that column's ensemble statistics will contain a mixture of clear and cloudy statistics. Such mixtures are inconsistent with the ensemble data assimilation algorithms currently used in numerical weather prediction. Hence, ensemble data assimilation algorithms that can handle such mixtures can potentially outperform currently used algorithms. In this study, we demonstrate the potential benefits of addressing such mixtures through a bi‐Gaussian extension of the ensemble Kalman filter (BGEnKF). The BGEnKF is compared against the commonly used ensemble Kalman filter (EnKF) using perfect model observing system simulated experiments (OSSEs) with a realistic weather model (the Weather Research and Forecast model). Synthetic all‐sky infrared radiance observations are assimilated in this study. In these OSSEs, the BGEnKF outperforms the EnKF in terms of the horizontal wind components, temperature, specific humidity, and simulated upper tropospheric water vapor channel infrared brightness temperatures. This study is one of the first to demonstrate the potential of a Gaussian mixture model EnKF with a realistic weather model. Our results thus motivate future research toward improving numerical Earth system predictions though explicitly handling mixture statistics.
Breakup of Pangea and the Cretaceous Revolution
Authors: Le Pichon Xavier , Şengör A. M. Celal , Jellinek Mark , Lenardic Adrian , İmren Caner
Published: January 2023

A 250 Ma, Pangea had just reached an equatorial position of dynamic equilibrium, after a 60° northward migration due to True Polar Wandering. It then began oscillating about itself for the next 150 Myr. The resulting extensional stresses triggered three successive phases of breakup, controlled by the mechanical resistance of a crescent of thick lithosphere, surrounding the Tethyan realm, which had adjusted the supercontinent to its hemispheric shape. The fracturing of the crescent was produced in three successive generations, each new generation corresponding to Coulomb fractures, conjugates of the preceding set. Flood basalts were associated with these deep fractures within the thick lithosphere crescent. We consider unlikely that this highly ordered pattern of fracturing was determined by the locations of the impacts of successive plumes. Between 260 and 180 Ma, thermal isolation was maximal and the asthenosphere of Pangea was about 150°C warmer than below Panthalassa. From 180 to 100 Ma, the breakup elongated Pangea by about 3,000 km in a north‐northwest–south‐southeast direction, producing gaps in the subduction girdle. Lateral mixing began, leading to a continuous rise in global sea level and progressive return to a globally homogeneous upper mantle with sea‐level at its maximum 100 Ma. This Cretaceous Revolution marked the end of the Pangea tectonics, radically different from our present plate tectonics. Neither post‐Cretaceous plate kinematic inferences, nor mantle dynamic and associated planetary cooling inferences are extendable to Pangea times.
Increasing Flood Frequencies Under Warming in the West‐Central Himalayas
Authors: Swarnkar Somil , Mujumdar Pradeep
Published: January 2023

The west‐central Himalayan River basins face significant damage caused by extreme floods annually. We selected the upper Ganga basin (UGB), the west‐central Himalayan basin, to demonstrate how maximum cumulative storm and total rainfall received during monsoon control the extreme flow variability. In addition, the downscaled CMIP6 data sets were used for projections of extremes. The results suggest that historically Alaknanda basin receives a relatively higher magnitude of monsoon and storm rainfall than the other regions in the UGB, which manifested into significant extreme flow variability at the Alaknanda outlet. The extreme flows at the UGB outlet are projected to be more frequent under warming scenarios. The nonstationary flood frequency magnitudes are higher than those obtained from the stationary frequency method, implying a need for a review of return periods used in the designs of flood control structures in the region.
Loss of muscle mass in the immediate post-operative period is associated with inadequate dietary protein and energy intake
Authors: Hardy E. J. , Deane C. S. , Lund J. N. , Phillips B. E.
Published: January 2023

Despite the implementation of ‘Enhanced Recovery After Surgery’ (ERAS) protocols, major abdominal surgery is still associated with significant and detrimental losses of muscle mass and function in the post-operative period. Although ERAS protocols advocate both early mobility and dietary intake, dietary composition in the immediate post-operative period is poorly characterised, despite muscle losses being greatest in this period. Herein, we show in 15 patients (66 ± 6 y, 12:3 M:F) who lost ~10% m. vastus lateralis muscle mass in the 5 days after open colorectal resective surgery, mean energy intake was only ~25% of the minimum ESPEN recommendation of 25 kcal/kg/d and daily dietary protein intake was only ~12% of the ESPEN recommended guidelines of 1.5 g/kg/d. Given the known importance of nutrition for muscle mass maintenance, innovative dietary interventions are needed in the immediate post-operative period, accounting for specific patient dietary preference to maximise compliance (e.g., soft-textured foods).
A non-academic perspective on the future of lithium-based batteries
Authors: Frith James T. , Lacey Matthew J. , Ulissi Ulderico
Published: January 2023

In the field of lithium-based batteries, there is often a substantial divide between academic research and industrial market needs. This is in part driven by a lack of peer-reviewed publications from industry. Here we present a non-academic view on applied research in lithium-based batteries to sharpen the focus and help bridge the gap between academic and industrial research. We focus our discussion on key metrics and challenges to be considered when developing new technologies in this industry. We also explore the need to consider various performance aspects in unison when developing a new material/technology. Moreover, we also investigate the suitability of supply chains, sustainability of materials and the impact on system-level cost as factors that need to be accounted for when working on new technologies. With these considerations in mind, we then assess the latest developments in the lithium-based battery industry, providing our views on the challenges and prospects of various technologies.
Microtubule nucleation and γTuRC centrosome localization in interphase cells require ch-TOG
Authors: Ali Aamir , Vineethakumari Chithran , Lacasa Cristina , Lüders Jens
Published: January 2023

Organization of microtubule arrays requires spatio-temporal regulation of the microtubule nucleator γ-tubulin ring complex (γTuRC) at microtubule organizing centers (MTOCs). MTOC-localized adapter proteins are thought to recruit and activate γTuRC, but the molecular underpinnings remain obscure. Here we show that at interphase centrosomes, rather than adapters, the microtubule polymerase ch-TOG (also named chTOG or CKAP5) ultimately controls γTuRC recruitment and activation. ch-TOG co-assembles with γTuRC to stimulate nucleation around centrioles. In the absence of ch-TOG, γTuRC fails to localize to these sites, but not the centriole lumen. However, whereas some ch-TOG is stably bound at subdistal appendages, it only transiently associates with PCM. ch-TOG’s dynamic behavior requires its tubulin-binding TOG domains and a C-terminal region involved in localization. In addition, ch-TOG also promotes nucleation from the Golgi. Thus, at interphase centrosomes stimulation of nucleation and γTuRC attachment are mechanistically coupled through transient recruitment of ch-TOG, and ch-TOG’s nucleation-promoting activity is not restricted to centrosomes.
TadA reprogramming to generate potent miniature base editors with high precision
Authors: Zhang Shuqian , Song Liting , Yuan Bo , Zhang Cheng , Cao Jixin , Chen Jinlong , Qiu Jiayi , Tai Yilin , Chen Jingqi , Qiu Zilong , Zhao Xing-Ming , Cheng Tian-Lin
Published: January 2023

Although miniature CRISPR-Cas12f systems were recently developed, the editing efficacy and targeting range of derived miniature cytosine and adenine base editors (miniCBEs and miniABEs) have not been comprehensively addressed. Moreover, functional miniCBEs have not yet be established. Here we generate various Cas12f-derived miniCBEs and miniABEs with improved editing activities and diversified targeting scopes. We reveal that miniCBEs generated with traditional cytidine deaminases exhibit wide editing windows and high off-targeting effects. To improve the editing signatures of classical CBEs and derived miniCBEs, we engineer TadA deaminase with mutagenesis screening to generate potent miniCBEs with high precision and minimized off-target effects. We show that newly designed miniCBEs and miniABEs are able to correct pathogenic mutations in cell lines and introduce genetic mutations efficiently via adeno-associated virus delivery in the brain in vivo. Together, this study provides alternative strategies for CBE development, expands the toolkits of miniCBEs and miniABEs and offers promising therapeutic tools for clinical applications.
Biomolecular condensates formed by designer minimalistic peptides
Authors: Baruch Leshem Avigail , Sloan-Dennison Sian , Massarano Tlalit , Ben-David Shavit , Graham Duncan , Faulds Karen , Gottlieb Hugo E. , Chill Jordan H. , Lampel Ayala
Published: January 2023

Inspired by the role of intracellular liquid-liquid phase separation (LLPS) in formation of membraneless organelles, there is great interest in developing dynamic compartments formed by LLPS of intrinsically disordered proteins (IDPs) or short peptides. However, the molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated, rendering on-demand design of synthetic condensates with tailored physico-chemical functionalities a significant challenge. To address this need, here we design a library of LLPS-promoting peptide building blocks composed of various assembly domains. We show that the LLPS propensity, dynamics, and encapsulation efficiency of compartments can be tuned by changes to the peptide composition. Specifically, with the aid of Raman and NMR spectroscopy, we show that interactions between arginine and aromatic amino acids underlie droplet formation, and that both intra- and intermolecular interactions dictate droplet dynamics. The resulting sequence-structure-function correlation could support the future development of compartments for a variety of applications.
Variable temperature thresholds of melt pond formation on Antarctic ice shelves
Authors: van Wessem J. Melchior , van den Broeke Michiel R. , Wouters Bert , Lhermitte Stef
Published: January 2023

It has been argued that the −5 °C annual mean 2 m air temperature isotherm defines a limit of ice shelf viability on the Antarctic Peninsula as melt ponding increases at higher temperatures. It is, however, presently unknown whether this threshold can also be applied to other Antarctic ice shelves. Here we use two present-day and three future high-resolution Antarctic climate simulations to predict warming thresholds for Antarctic ice shelf melt pond formation on the basis of the melt-over-accumulation ratio. The associated warming thresholds match well with observed melt pond volumes and are found to be spatially highly variable and controlled by snow accumulation. For relatively wet ice shelves, the −5 °C temperature threshold was confirmed; but cold and dry ice shelves such as Amery, Ross and Filchner-Ronne are more vulnerable than previously thought, with threshold temperatures well below −15 °C. Coupled Model Intercomparison Project Phase 6 models predict that towards the end of this century these thresholds can be reached on many ice shelves, even on cold ice shelves and under moderate warming scenarios.
Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora
Authors: Wood Daniel P. , Holmberg Jon A. , Osborne Owen G. , Helmstetter Andrew J. , Dunning Luke T. , Ellison Amy R. , Smith Rhian J. , Lighten Jackie , Papadopulos Alexander S. T.
Published: January 2023

Phenotypic plasticity in ancestral populations is hypothesized to facilitate adaptation, but evidence is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel adaptive changes has not been explored. The most general finding is that ancestral responses to a new environment are reversed following adaptation (known as reversion). We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared with zinc-sensitive plants. We show that ancestral plasticity that moves expression closer to the optimum value in the new environment influences the evolution of gene expression among genes that are likely to be involved in adaptation and increases the chance that genes are recruited repeatedly during adaptation. However, despite convergence in gene expression levels between independently adapted lineages, ancestral plasticity does not influence how similar expression values of adaptive genes become. Surprisingly, we also observed that ancestral plasticity that increases fitness often becomes genetically determined and fixed, that is, genetically assimilated. These results emphasize the important role of ancestral plasticity in parallel adaptation.
Evidence for lunar tide effects in Earth’s plasmasphere
Authors: Xiao Chao , He Fei , Shi Quanqi , Liu Wenlong , Tian Anmin , Guo Ruilong , Yue Chao , Zhou Xuzhi , Wei Yong , Rae I. Jonathan , Degeling Alexander W. , Angelopoulos Vassilis , Masongsong Emmanuel V. , Liu Ji , Zong Qiugang , Fu Suiyan , Pu Zuyin , Zhang Xiaoxin , Wang Tieyan , Wang Huizi , Zhang Zhao
Published: January 2023

Tides are universal and affect spatially distributed systems, ranging from planetary to galactic scales. In the Earth–Moon system, effects caused by lunar tides were reported in the Earth’s crust, oceans, neutral gas-dominated atmosphere (including the ionosphere) and near-ground geomagnetic field. However, whether a lunar tide effect exists in the plasma-dominated regions has not been explored yet. Here we show evidence of a lunar tide-induced signal in the plasmasphere, the inner region of the magnetosphere, which is filled with cold plasma. We obtain these results by analysing variations in the plasmasphere’s boundary location over the past four decades from multisatellite observations. The signal possesses distinct diurnal (and monthly) periodicities, which are different from the semidiurnal (and semimonthly) variations dominant in the previously observed lunar tide effects in other regions. These results demonstrate the importance of lunar tidal effects in plasma-dominated regions, influencing understanding of the coupling between the Moon, atmosphere and magnetosphere system through gravity and electromagnetic forces. Furthermore, these findings may have implications for tidal interactions in other two-body celestial systems.
In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice
Authors: Bouffi Carine , Wikenheiser-Brokamp Kathryn A. , Chaturvedi Praneet , Sundaram Nambirajan , Goddard Gillian R. , Wunderlich Mark , Brown Nicole E. , Staab Janet F. , Latanich Rachel , Zachos Nicholas C. , Holloway Emily M. , Mahe Maxime M. , Poling Holly M. , Vales Simon , Fisher Garrett W. , Spence Jason R. , Mulloy James C. , Zorn Aaron M. , Wells James M. , Helmrath Michael A.
Published: January 2023

Human intestinal organoids (HIOs) derived from pluripotent stem cells provide a valuable model for investigating human intestinal organogenesis and physiology, but they lack the immune components required to fully recapitulate the complexity of human intestinal biology and diseases. To address this issue and to begin to decipher human intestinal–immune crosstalk during development, we generated HIOs containing immune cells by transplanting HIOs under the kidney capsule of mice with a humanized immune system. We found that human immune cells temporally migrate to the mucosa and form cellular aggregates that resemble human intestinal lymphoid follicles. Moreover, after microbial exposure, epithelial microfold cells are increased in number, leading to immune cell activation determined by the secretion of IgA antibodies in the HIO lumen. This in vivo HIO system with human immune cells provides a framework for future studies on infection- or allergen-driven intestinal diseases.
Dermal macrophages set pain sensitivity by modulating the amount of tissue NGF through an SNX25–Nrf2 pathway
Authors: Tanaka Tatsuhide , Okuda Hiroaki , Isonishi Ayami , Terada Yuki , Kitabatake Masahiro , Shinjo Takeaki , Nishimura Kazuya , Takemura Shoko , Furue Hidemasa , Ito Toshihiro , Tatsumi Kouko , Wanaka Akio
Published: January 2023

Cross-talk between peripheral neurons and immune cells is important in pain sensation. We identifiedSnx25as a pain-modulating gene in a transgenic mouse line with reduced pain sensitivity. Conditional deletion ofSnx25in monocytes and macrophages, but not in peripheral sensory neurons, in mice (Snx25cKOmice) reduced pain responses in both normal and neuropathic conditions. Bone marrow transplantation usingSnx25cKOand wild-type mice indicated that macrophages modulated pain sensitivity. Expression of sorting nexin (SNX)25 in dermal macrophages enhanced expression of the neurotrophic factor NGF through the inhibition of ubiquitin-mediated degradation of Nrf2, a transcription factor that activates transcription ofNgf. As such, dermal macrophages set the threshold for pain sensitivity through the production and secretion of NGF into the dermis, and they may cooperate with dorsal root ganglion macrophages in pain perception.
Persistent mutation burden drives sustained anti-tumor immune responses
Authors: Niknafs Noushin , Balan Archana , Cherry Christopher , Hummelink Karlijn , Monkhorst Kim , Shao Xiaoshan M. , Belcaid Zineb , Marrone Kristen A. , Murray Joseph , Smith Kellie N. , Levy Benjamin , Feliciano Josephine , Hann Christine L. , Lam Vincent , Pardoll Drew M. , Karchin Rachel , Seiwert Tanguy Y. , Brahmer Julie R. , Forde Patrick M. , Velculescu Victor E. , Anagnostou Valsamo
Published: January 2023

Tumor mutation burden is an imperfect proxy of tumor foreignness and has therefore failed to consistently demonstrate clinical utility in predicting responses in the context of immunotherapy. We evaluated mutations in regions of the genome that are unlikely to undergo loss in a pan-cancer analysis across 31 tumor types (n = 9,242) and eight immunotherapy-treated cohorts of patients with non-small-cell lung cancer, melanoma, mesothelioma, and head and neck cancer (n = 524). We discovered that mutations in single-copy regions and those present in multiple copies per cell constitute a persistent tumor mutation burden (pTMB) which is linked with therapeutic response to immune checkpoint blockade. Persistent mutations were retained in the context of tumor evolution under selective pressure of immunotherapy and tumors with a high pTMB content were characterized by a more inflamed tumor microenvironment. pTMB imposes an evolutionary bottleneck that cancer cells cannot overcome and may thus drive sustained immunologic tumor control in the context of immunotherapy.
A large dataset of scientific text reuse in Open-Access publications
Authors: Gienapp Lukas , Kircheis Wolfgang , Sievers Bjarne , Stein Benno , Potthast Martin
Published: January 2023

We present the Webis-STEREO-21 dataset, a massive collection of Scientific Text Reuse in Open-access publications. It contains 91 million cases of reused text passages found in 4.2 million unique open-access publications. Cases range from overlap of as few as eight words to near-duplicate publications and include a variety of reuse types, ranging from boilerplate text to verbatim copying to quotations and paraphrases. Featuring a high coverage of scientific disciplines and varieties of reuse, as well as comprehensive metadata to contextualize each case, our dataset addresses the most salient shortcomings of previous ones on scientific writing. The Webis-STEREO-21 does not indicate if a reuse case is legitimate or not, as its focus is on the general study of text reuse in science, which is legitimate in the vast majority of cases. It allows for tackling a wide range of research questions from different scientific backgrounds, facilitating both qualitative and quantitative analysis of the phenomenon as well as a first-time grounding on the base rate of text reuse in scientific publications.
Metabolic profiles and fingerprints for the investigation of the influence of nitisinone on the metabolism of the yeast Saccharomyces cerevisiae
Authors: Barchanska Hanna , Płonka Joanna , Nowak Paulina , Kostina-Bednarz Marianna
Published: January 2023

Nitisinone (2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione, NTBC) is considered a potentially effective drug for the treatment of various metabolic diseases associated with disorders of l-tyrosine metabolism however, side-effects impede its widespread use. This work aimed to broaden the knowledge of the influence of NTBC and its metabolites 2-amino-4-(trifluoromethyl)benzoic acid (ATFA), 2-nitro-4-(trifluoromethyl)benzoic acid (NTFA), and cyclohexane-1,3-dione (CHD) on the catabolism of l-tyrosine and other endogenous compounds in Saccharomyces cerevisiae. Based on a targeted analysis performed by LC–ESI–MS/MS, based on multiple reaction monitoring, it was found that the dissipation kinetics of the parent compound and its metabolites are compatible with a first-order reaction mechanism. Moreover, it has been proven that formed NTBC metabolites, such as CHD, cause a decrease in l-tyrosine, l-tryptophan, and l-phenylalanine concentrations by about 34%, 59% and 51%, respectively, compared to the untreated model organism. The overall changes in the metabolism of yeast exposed to NTBC or its derivatives were evaluated by non-targeted analysis via LC–ESI–MS/MS in the ion trap scanning mode. Based on principal components analysis, a statistically significant similarity between metabolic responses of yeast treated with ATFA or NTFA was observed. These findings facilitate further studies investigating the influence of NTBC on the human body and the mechanism of its action.
Early evolution of enamel matrix proteins is reflected by pleiotropy of physiological functions
Authors: Spoutil Frantisek , Aranaz-Novaliches Goretti , Prochazkova Michaela , Wald Tomas , Novosadova Vendula , Kasparek Petr , Osicka Radim , Reseland Janne E. , Lyngstadaas Staale P. , Tiainen Hanna , Bousova Kristyna , Vondrasek Jiri , Sedlacek Radislav , Prochazka Jan
Published: January 2023

Highly specialized enamel matrix proteins (EMPs) are predominantly expressed in odontogenic tissues and diverged from common ancestral gene. They are crucial for the maturation of enamel and its extreme complexity in multiple independent lineages. However, divergence of EMPs occured already before the true enamel evolved and their conservancy in toothless species suggests that non-canonical functions are still under natural selection. To elucidate this hypothesis, we carried out an unbiased, comprehensive phenotyping and employed data from the International Mouse Phenotyping Consortium to show functional pleiotropy of amelogenin, ameloblastin, amelotin, and enamelin, genes, i.e. in sensory function, skeletal morphology, cardiovascular function, metabolism, immune system screen, behavior, reproduction, and respiratory function. Mice in all KO mutant lines, i.e. amelogenin KO, ameloblastin KO, amelotin KO, and enamelin KO, as well as mice from the lineage with monomeric form of ameloblastin were affected in multiple physiological systems. Evolutionary conserved motifs and functional pleiotropy support the hypothesis of role of EMPs as general physiological regulators. These findings illustrate how their non-canonical function can still effect the fitness of modern species by an example of influence of amelogenin and ameloblastin on the bone physiology.
Genetic determinants and absence of breast cancer in Xavante Indians in Sangradouro Reserve, Brazil
Authors: Zhou Yan , Russo Jose , Rueff José , Pires Marcelo A. M. , de Castro Guilherme Bezerra
Published: January 2023

Genetic compositions of distinct human populations are different. How genomic variants influence many common and rare genetic diseases is always of great medical and anthropological interest, and understanding of genetic architectures of population groups in relation to diseases can advance our knowledge of medicine. Here, we have studied the genomic architecture of a group of Xavante Indians, an indigenous population in Brazil, and compared them with normal populations from the 1000 Genomes Projects. Principal component analysis (PCA) indicates that the Xavante Indians are genetically distinctive when compared to other ethnic groups. No incidence of breast cancer cases has ever been reported in the population, and polygenic risk analysis indicates extremely low breast cancer risk in this population when compared with germline TCGA (The Cancer Genome Atlas) breast cancer normal control samples. Low germinal mutation burden among this population is also observed. Our findings will help to deepen the understanding of breast cancer and might also provide new approaches to study the disease.
In situ diffraction monitoring of nanocrystals structure evolving during catalytic reaction at their surface
Authors: Zieliński Maciej , Kaszkur Zbigniew , Juszczyk Wojciech , Sobczak Janusz
Published: January 2023

With decreasing size of crystals the number of their surface atoms becomes comparable to the number of bulk atoms and their powder diffraction pattern becomes sensitive to a changing surface structure. On the example of nanocrystalline gold supported on also nanocrystalline $${\text{CeO}}_2$$

CeO
2

we show evolution of (a) the background pattern due to chemisorption phenomena, (b) peak positions due to adsorption on nonstoichiometric $${\text{CeO}}_{2-x}$$

CeO

2
-
x

particles, (c) Au peaks intensity. The results of the measurements, complemented with mass spectrometry gas analysis, point to (1) a multiply twinned structure of gold, (2) high mobility of Au atoms enabling transport phenomena of Au atoms to the surface of ceria while varying the amount of Au in the crystalline form, and (3) reversible $${\text{CeO}}_2$$

CeO
2

peaks position shifts on exposure to He–X–He where X is O2, H2, CO or CO oxidation reaction mixture, suggesting solely internal alternations of the $${\text{CeO}}_2$$

CeO
2

crystal structure. We found no evidence of ceria lattice oxygen being consumed/supplied at any stage of the process. The work shows possibility of structurally interpreting different contributions to the multi-phase powder diffraction pattern during a complex physico-chemical process, including effects of physi-, chemisorption and surface evolution. It shows a way to structurally interpret heterogeneous catalytic reactions even if no bulk phase transition is involved.