bluuebunny/crossref_metadata_2025 huggingface dataset:
Complex dynamic systems theory: A webinar with Diane Larsen-Freeman
Authors: Larsen-Freeman Diane
Published: October 2022

The following is an edited transcript of a webinar that took place on 11 June 2022 between Diane Larsen-Freeman and seven colleagues (in alphabetical order: Anne Burns, Hossein Farhady, Mathias Schulze, Scott Thornbury, Benjamin White, Henry Widdowson, and Yasin Yazdi-Amirkhiz), who generously took the time to formulate and submit questions in advance of the webinar and to participate in the event. The focus of the webinar was on Complex Dynamic Systems Theory (CDST). Coincidentally, the webinar took place on the 25th anniversary of Larsen-Freeman's first publication on the same theme (Larsen-Freeman, 1997).
Utterance-Initial Prosodic Differences Between Statements and Questions in Infant-Directed Speech
Authors: GEFFEN Susan , BURKINSHAW Kelly , ATHANASOPOULOU Angeliki , CURTIN Suzanne
Published: October 2022

Cross-linguistically, statements and questions broadly differ in syntactic organization. To learn the syntactic properties of each sentence type, learners might first rely on non-syntactic information. This paper analyzed prosodic differences between infant-directedwh-questions and statements to determine what kinds of cues might be available. We predicted there would be a significant difference depending on the first words that appear inwh-questions (e.g., two closed-class words; meaning words from a category that rarely changes) compared to the variety of first words found in statements. We measured F0, duration, and intensity of the first two words in statements andwh-questions in naturalistic speech from 13 mother-child dyads in the Brent corpus of the CHILDES database. Results found larger differences between sentence-types when the second word was an open-class not a closed-class word, suggesting a relationship between prosodic and syntactic information in an utterance-initial position that infants may use to make sentence-type distinctions.
Opportunistic Bargaining: Negotiating Distribution in China
Authors: Han Rongbin , Du Juan , Shao Li
Published: October 2022

Using a detailed case study of house eviction in peri-urban China as well as original data from an online survey experiment, this article explores the opportunistic bargaining phenomenon in China in which citizens leverage the policy priorities of authorities with tactics that are not approved by the state to bargain for goals beyond those promised by the state. We find that opportunistic bargaining is widely accepted by Chinese citizens and that such an inclination is encouraged by successful precedents and clear signals of an opening through which to leverage government policy priorities; however, it is dampened by unclear signals and failed precedents. We also find that opportunistic bargainers tend to hold more negative perceptions of the current regime and are less likely to abide by state rules or social norms. The characteristics of opportunistic bargaining appear to be the opposite of the dominant “rightful resistance” framework.
Incidence and predictors of Escherichia coli producing extended-spectrum beta-lactamase (ESBL-Ec) in Queensland, Australia from 2010 to 2019: a population-based spatial analysis
Authors: Ling Weiping , Cadavid-Restrepo Angela , Furuya-Kanamori Luis , Harris Patrick N. A. , Paterson David L.
Published: October 2022

The dissemination of Escherichia coli producing extended-spectrum beta-lactamase (ESBL-Ec) is evident in the community. A population-based spatial analysis is necessary to investigate community risk factors for ESBL-Ec occurrence. The study population was defined as individuals with ESBL-Ec isolated in Queensland, Australia, from 2010 to 2019. Choropleth maps, global Moran's index and Getis-Ord Gi* were used to describe ESBL-Ec distribution and identify hot spots. Multivariable Poisson regression models with or without spatially structured random effects were performed. A total of 12 786 individuals with ESBL-Ec isolate were identified. The crude incidence rate increased annually from 9.1 per 100 000 residents in 2010 to 49.8 per 100 000 residents in 2019. The geographical distribution of ESBL-Ec changed from random to clustered after 2014, suggesting presence of community-specific factors that can enhance occurrence. Hot spots were more frequently identified in Outback and Far North Queensland, future public health measures to reduce transmission should prioritise these communities. Communities with higher socioeconomic status (RR = 0.66, 95% CI 0.55–0.79, per 100 units increase) and higher proportion of residents employed in the agricultural industry (RR = 0.79, 95% CI 0.67–0.95, per 10% increase) had lower ESBL-Ec incidence. Risk factors for occurrence appear differential between remote and city settings and this should be further investigated.
Imperial wet nurses in the reign of Mughal Emperor Akbar
Authors: Shivram Balkrishan
Published: October 2022

Mughal chronicles frequently refer to royal Mughal infants being entrusted to wet nurses for breastfeeding and nurturing. The women chosen for this purpose were invariably the wives of important Mughal officials. It was believed that the quality of milk the baby received determined its future disposition. Therefore, these nurses needed to possess desirable psychological qualities and moral temperaments. They were accorded a high status and usually established a lasting relationship with their charges. As a result, the children of the emperor developed a close association with their wet nurses and their families who, in turn, became the staunchest supporters of their wards. The success, influence, and prestige of these families depended on the political fortune of the royal child they had cared for. If the prince became an emperor, they gained immense power and prestige both in life and death. They were honoured with elaborate funerals and buried in imperial tombs. This article argues that the rationale behind the use of wet nurses by Mughal royalty during Emperor Akbar's reign was not simply a medical or physiological one, it was equally a political instrument for forging ties between prominent families and royalty.
‘Good for you!’ Processing social emotions in L2 discourse comprehension: an ERP study
Authors: González-García Aldariz Andrea , Rodríguez-Gómez Pablo , Romero-Rivas Carlos , Rodríguez-Cuadrado Sara , Foucart Alice , Moreno Eva M.
Published: October 2022

Social factors impact sentence comprehension in a first language (L1), suggesting that semantic processing cannot be dissociated from social and moral emotions in relation to pro/antisocial individuals. Given that integrating multiple types of information and processing emotion-laden pragmatic information is costlier in a second language (L2), we investigated whether social factors would affect discourse comprehension similarly in L2. Processing the outcomes of scenarios involving pro/antisocial protagonists provoked similar neural patterns in L2 as in L1 (Rodríguez-Gómez, Martín-Loeches, Colmenares, Romero Ferreiro & Moreno, 2020), suggesting that L2 users simultaneously integrate semantic and discourse-pragmatic information during sentence comprehension.
Valued Outcomes in the Cancer Experience (VOICE)™: Development and validation of a multidimensional measure of perceived control
Authors: Zaleta Alexandra K. , Fortune Erica E. , Miller Melissa F. , Yuen Eva Y.N. , McManus Shauna , Hurley Karen , Golant Mitch , Goldberger Sara , Shockney Lillie D. , Buzaglo Joanne S.
Published: October 2022

Objective

Enhancing cancer patients’ sense of control can positively impact psychological well-being. We developed and assessed the psychometric properties of Valued Outcomes in the Cancer Experience (VOICE)TM, a measure of patients’ perceived control over key personal priorities within their cancer experience.

Methods

VOICE construction and testing were completed in three phases with separate participant samples: (1) item generation and initial item pool testing (N = 459), (2) scale refinement (N = 623), and (3) confirmatory validation (N = 515).

Results

A 21-item measure was developed that captures cancer patients’ sense of control in seven key domains: (1) Purpose and Meaning, (2) Functional Capacity, (3) Longevity, (4) Quality Care, (5) Illness Knowledge, (6) Social Support, and (7) Financial Capability. VOICE demonstrated adequate internal consistency (full-scale α = 0.93; factor α = 0.67–0.89) and adequate to strong convergent and discriminatory validity.

Significance of results

VOICE measures cancer patients’ perceived control across a diverse range of personal priorities, creating a platform for elevating patient perspectives and identifying pathways to enhance patient well-being. VOICE is positioned to guide understanding of the patient experience and aid the development and evaluation of supportive care interventions to enhance well-being.
Arabic version of the Palliative Care Self-Efficacy Scale: Translation, adaptation, and validation
Authors: Wazqar Dhuha Youssef
Published: October 2022

Objectives

A lack of confidence among oncology nurses might be problematic when providing palliative care. No valid and reliable tool is currently available in Saudi Arabia to assess oncology nurses’ confidence in providing palliative care. This study aims to explain the process of translation, adaptation, and validation of the Palliative Care Self-Efficacy Scale (PCSS) to support its use in the Saudi context.

Methods

This was a methodological study of translation, cultural adaptation, and content validation of PCSS. The process of translation and adaptation was conducted according to the World Health Organization guidelines, including forward and backward translations, an expert panel review, and pretesting and cognitive interviewing, resulting in a final version. Two independent bilingual oncology nurses familiar with palliative care terminology translated the PCSS from English to Modern Standard Arabic. Next, the concise PCSS translation developed from the 2 translations was back-translated to English by 2 English-speaking translators and then compared to the original PCSS. The Arabic version PCSS was evaluated by Saudi professionals (N = 5) in oncology and palliative care nursing using a Likert scale for essentiality, relevance, clarity, and appropriateness. The content validity was examined using the calculation of the content validity ratio, item-level content validity index (I-CVI), and modified kappa statistics. The thinking aloud method was also used to interview Saudi oncology nurses (N = 8) who had palliative care experience.

Results

The relevance, clarity, and appropriateness of the first Arabic version PCSS were validated. It had a level of content validity index of 1.00 for all items after improvements were made based on the recommendations of experts and oncology nurses.

Significance of results

The PCSS demonstrated face and content validity in the assessment of oncology nurses’ confidence in providing palliative care. The PCSS is suitable for use in palliative cancer care units in Saudi Arabia to identify the educational needs of nurses to promote their confidence and improve the quality of care. Additional reliable and valid language versions of the PCSS allow for international and national comparisons, which may be useful for oncology nursing administrators or managers who are accountable for the quality of palliative care during the strategic health-care planning process in cancer services.
The Calcium Isotope (δ44/40Ca) Record Through Environmental Changes: Insights From the Late Triassic
Authors: Kovács Zsófia , Demangel Isaline , Baldermann Andre , Hippler Dorothee , Schmitt Anne‐Désirée , Gangloff Sophie , Krystyn Leopold , Richoz Sylvain
Published: October 2022

Calcium isotopes (δ44/40Ca) are particularly useful in palaeo‐environmental studies due to the key role of carbonate minerals in continental weathering and their formation in seawater. The calcium isotope ratio can provide hints on past changes in the calcium fluxes, environmental shifts, ecological factors and alternatively diagenesis of carbonate rocks. The investigation of the Late Triassic calcium isotope record offers a great opportunity to evaluate such factors in a time interval that witnessed important environmental and ecological turnovers, such as the first appearance of calcareous nannoplankton, ocean acidification and periods of elevated extinction rates. In this study, we present a δ44/40Ca data set from the upper Norian (Upper Triassic) through the lower Hettangian (Lower Jurassic) interval. The isotope records reveal two globally significant signals: a ∼ 0.20‰ decrease through the early Rhaetian (Upper Triassic) and a small, negative (∼0.14‰) excursion corresponding to the emplacement of the Central Atlantic Magmatic Province, at the end of the Triassic. The possible explanations for these signals are changes in the isotopic ratio of the continental calcium influx to the ocean due to the high chemical weathering rate of carbonates and possibly ocean acidification, respectively. The considerable (∼0.15–0.30‰) offset in δ44/40Ca between study areas is likely the combined result of local differences in lithology and early marine diagenesis. The major evolutionary step represented by the first occurrence of calcareous nannoplankton did not have at this time a determining role on the calcium isotopic signature of the marine carbonates.
Simultaneous Determination of I/Ca and Other Elemental Ratios in Foraminifera: Comparing Results From Acidic and Basic Solutions
Authors: Zhou Xiaoli , Hess Anya V. , Bu Kaixuan , Sagawa Takuya , Rosenthal Yair
Published: October 2022

The iodine to calcium ratio in carbonate (I/Ca) has been widely used to indicate ocean oxygenation level in the past. Given the volatility of iodine, I/Ca has been measured in alkaline solutions in previous studies. However, this limits the application of I/Ca with other element/Ca (El/Ca) proxies at the same time and in the same foraminifera because other El/Ca data are preferably analyzed in acidic solutions. This study assesses the reliability of I/Ca measurements in acidic solutions measured with other El/Ca as well as the effects of different sample pre‐treatments on measured foraminiferal I/Ca. Our results show that when samples are measured within hours of prepaparation, the pH of the final solution has an insignificant effect on I/Ca measurements of a carbonate reference material JCp‐1 and a multi‐element standard solution, consistent with the slow kinetics of iodine volatilization. We find, however, that low pH possibly reduces the measured I/Ca in foraminiferal tests in some samples. Our experiments also suggest a resolvable effect of reductive cleaning, yielding lower foraminiferal I/Ca compared to without reductive cleaning. The HNO3 concentration used to dissolve foraminiferal shells has a negligible effect. Despite the different solution pHs and cleaning and dissolving methods, our core top planktic I/Ca data are able to differentiate well‐oxygenated from oxygen‐depleted waters in the upper ocean, and after correcting for cleaning effect, our data are generally consistent with the published studies that analyzed I/Ca without reductive cleaning and in basic solutions. This study shows that measurements of I/Ca within hours of sample dissolutions yield reliable planktic I/Ca data, while also allowing the acquisition of other El/Ca values for paleoceanographic studies.
The Ocean's Biological Pump: In Situ Oxygen Measurements in the Subtropical Oceans
Authors: Emerson Steven , Yang Bo
Published: October 2022

The magnitude and distribution of the ocean's biological pump (the downward flux of organic carbon (OC) from the ocean surface) influences the pCO2 of the atmosphere and the O2 content of the deep sea, but has not been well quantified. We determine this flux in the ocean's five subtropical gyres using upper‐ocean oxygen mass balance and measurements of T, S, and pO2 by autonomous profiling floats. Our results suggest that the biological OC pump is not globally uniform among the subtropical gyres: values in the North Pacific and Atlantic indicate distinct autotrophy (1–2 mol C m−2 yr−1) while near zero values in the S. Indian Ocean suggest the possibility of net heterotrophy. There is a correlation between the surface water iron/nitrate ratio and the magnitude of the biological pump suggesting an important role for nitrogen fixation in controlling the global distribution.
Small Magnitude Events Highlight the Correlation Between Hydraulic Fracturing Injection Parameters, Geological Factors, and Earthquake Occurrence
Authors: Kemna Kilian B. , Roth Marco P. , Wache Ricarda M. , Harrington Rebecca M. , Liu Yajing
Published: October 2022

Hydraulic fracturing (HF) operations are widely associated with induced seismicity in the Western Canadian Sedimentary Basin. This study correlates injection parameters of 12,903 HF stages in the Kiskatinaw area in northeast British Columbia with an enhanced catalog containing 40,046 earthquakes using a supervised machine learning approach. It identifies relevant combinations of geological and operational parameters related to individual HF stages in efforts to decipher fault activation mechanisms. Our results suggest that stages targeting specific geological units (here, the Lower Montney formation) are more likely to induce an earthquake. Additional parameters positively correlated with earthquake likelihood include target formation thickness, injection volume, and completion date. Furthermore, the COVID‐19 lockdown may have reduced the potential cumulative effect of HF operations. Our results demonstrate the value of machine learning approaches for implementation as guidance tools that help facilitate safe development of unconventional energy technologies.
Development of Lattice‐Preferred Orientations of MgO Periclase From Strain Rate Controlled Shear Deformation Experiments Under Pressure up to 120 GPa
Authors: Park Yohan , Azuma Shintaro , Okazaki Keishi , Uesugi Kentaro , Yasutake Masahiro , Nishihara Yu , Nomura Ryuichi
Published: October 2022

The seismic anisotropy observed in Earth's lowermost mantle (D″ layer) is thought to originate from the lattice‐preferred orientation (LPO) of mantle materials induced by plastic deformation. Ferropericlase is the second most abundant mineral in the lower mantle, and its LPO induced by deformation may significantly contribute to the seismic anisotropy in the D″ layer. The slip system(s) of ferropericlase controlling the LPO in the D″ layer is still controversial, owing to technical difficulties in conducting high‐pressure deformation experiments. We conducted shear deformation experiments on MgO under pressures of up to 120 GPa and reported the LPO after the deformation experiments. Our results indicate that {100}<011> is the dominant slip system in the D″ layer. The LPO developed during shear deformation would result in shear wave splitting with VSH > VSV, consistent with seismic observations in the regions expected to accommodate large shear strain by subducted slabs in the D″ layer.
The Topographic Signature of Mantle Pressure Build‐Up Beneath Subducting Plates: Insights From Spherical Subduction Models
Authors: Holt Adam F.
Published: October 2022

Subduction zones are associated with spatially heterogeneous pressure fields that, depending on location, push/pull on Earth's surface producing dynamic topography (DT). Despite this, subduction zones, and associated pressure fields, are typically over‐simplified within global mantle flow models. Here, I use subduction models within a global domain to probe mantle pressure build‐up beneath subducting plates (SPs) and the resulting DT. Positive pressure develops beneath the SP in most subduction models. This produces positive DT (≤450 m) and tilts the SP upwards toward the trench (≤0.25 m/km). As SP size increases, the pressure magnitude increases producing greater topography/tilting. At a global scale, I find potential evidence for the modeled tilting in published residual topography. I argue that the rigorous incorporation of subduction zones into mantle flow models, and hence the inclusion of this signal, is needed to continue to bring future DT predictions and observational estimates into closer alignment.
The Helicity Sign of Flux Transfer Event Flux Ropes and Its Relationship to the Guide Field and Hall Physics in Magnetic Reconnection at the Magnetopause
Authors: Dahani S. , Kieokaew R. , Génot V. , Lavraud B. , Chen Y. , Michotte de Welle B. , Aunai N. , Tóth G. , Cassak P. A. , Fargette N. , Fear R. C. , Marchaudon A. , Gershman D. , Giles B. , Torbert R. , Burch J.
Published: October 2022

Flux Transfer Events (FTEs) are transient magnetic flux ropes typically found at the Earth's magnetopause on the dayside. While it is known that FTEs are generated by magnetic reconnection, it remains unclear how the details of magnetic reconnection controls their properties. A recent study showed that the helicity sign of FTEs positively correlates with the east‐west (By) component of the Interplanetary Magnetic Field (IMF). With data from the Cluster and Magnetospheric Multiscale missions, we performed a statistical study of 166 quasi force‐free FTEs. We focus on their helicity sign and possible association with upstream solar wind conditions and local magnetic reconnection properties. Using both in situ data and magnetic shear modeling, we find that FTEs whose helicity sign corresponds to the IMF By are associated with moderate magnetic shears while those that do not correspond to the IMF By are associated with higher magnetic shears. While uncertainty in IMF propagation to the magnetopause may lead to randomness in the determination of the flux rope core field and helicity, we rather propose that for small IMF By, which corresponds to high shear and low guide field, the Hall pattern of magnetic reconnection determines the FTE core field and helicity sign. In that context we explain how the temporal sequence of multiple X‐line formation and the reconnection rate are important in determining the flux rope helicity sign. This work highlights a fundamental connection between kinetic processes at work in magnetic reconnection and the macroscale structure of FTEs.
Record Arctic Cyclone of January 2022: Characteristics, Impacts, and Predictability
Authors: Blanchard‐Wrigglesworth Edward , Webster Melinda , Boisvert Linette , Parker Chelsea , Horvat Christopher
Published: October 2022

Arctic cyclones are a fundamental component of Arctic climate, influencing atmospheric heat and moisture transport into the region and surface energy, moisture, and momentum fluxes. Arctic cyclones can also drive changes in sea ice and energize ocean waves. Here we investigate a record low sea level pressure (SLP) Arctic cyclone which formed in East Greenland and tracked NE over the Barents and Kara seas between 21 and 27 January 2022. At its peak intensity on 24 January, the cyclone reached an estimated depth of 932.2 mb at 79.5°N 20°E. North of 70°N, this is the lowest SLP in the ERA‐5 reanalysis over 1979 to present. The cyclone resulted in a record (over the period 1979–2022) weekly loss of regional sea ice area and surface wind speeds, and generated ocean waves exceeding 8 m that impinged on sea ice in the Barents sea, observed via satellite altimetry as large waves‐in‐sea ice up to 2 m in amplitude more than 100 km into the ice pack. Surface heat fluxes were strongly impacted by the cyclone, with record atmosphere‐to‐surface turbulent fluxes. However, the direct atmospheric thermodynamic impact on sea ice loss was modest, and the record sea ice changes were likely mainly driven by dynamical and/or ocean processes. While the storm was well predicted up to 8 days in advance, subsequent changes in sea ice cover were not, likely due to biases in the forecasts' sea ice initial conditions and missing physics in the forecast model such as wave‐sea ice interaction.
Challenges and strategies in high-accuracy manufacturing of the world’s largest SiC aspheric mirror
Authors: Zhang Xuejun , Hu Haixiang , Wang Xiaokun , Luo Xiao , Zhang Ge , Zhao Wenxing , Wang Xiaoyi , Liu Zhenyu , Xiong Ling , Qi Erhui , Cui Congcong , Wang Yanchao , Li Yingjie , Wang Xu , Li Longxiang , Bai Yang , Cheng Qiang , Zhang Zhiyu , Li Ruigang , Tang Wa , Zeng Xuefeng , Deng Weijie , Zhang Feng
Published: October 2022

In the process of manufacturing the world’s largest silicon carbide (SiC) aspheric mirror, the primary difficulties are mirror blank preparation, asphere fabrication, and testing, as well as cladding and coating. Specifically, the challenges include the homogeneity of the complicated structure casting, accuracy and efficiency of the fabrication process, print-through effect, fidelity and precision of test procedure, stress and denseness of cladding process, the dynamic range of interferometric measurement, and air turbulence error due to the long optical path. To break through such a barrier of difficulties, we proposed the water-soluble room temperature vanishing mold and gel casting technology, homogeneous microstructure reaction-formed joint technology, nano-accuracy efficient compound fabrication, gravity unloading technology, high-denseness low-defect physical vapor deposition (PVD) Si-cladding technology, test data fusion method, and time-domain averaging method, etc. Based on the proposed technologies and methods, we have accomplished the world’s largest SiC aspheric mirror with a size of ⌀4.03 m. The impressive performance of the SiC aspheric mirror is validated by the characteristics of the fabricated SiC aspheric mirror. The aerial density of the SiC blank is less than 120 kg/m2, surface shape test accuracy is better than 6 nm RMS, thickness inhomogeneity of the cladding layer is less than 5%, and the final surface figure error and roughness are 15.2 nm RMS and 0.8 nm RMS, respectively.
Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population
Authors: Berding Kirsten , Bastiaanssen Thomaz F. S. , Moloney Gerard M. , Boscaini Serena , Strain Conall R. , Anesi Andrea , Long-Smith Caitriona , Mattivi Fulvio , Stanton Catherine , Clarke Gerard , Dinan Timothy G. , Cryan John F.
Published: October 2022

The impact of diet on the microbiota composition and the role of diet in supporting optimal mental health have received much attention in the last decade. However, whether whole dietary approaches can exert psychobiotic effects is largely understudied. Thus, we investigated the influence of a psychobiotic diet (high in prebiotic and fermented foods) on the microbial profile and function as well as on mental health outcomes in a healthy human population. Forty-five adults were randomized into either a psychobiotic (n = 24) or control (n = 21) diet for 4 weeks. Fecal microbiota composition and function was characterized using shotgun sequencing. Stress, overall health and diet were assessed using validated questionnaires. Metabolic profiling of plasma, urine and fecal samples was performed. Intervention with a psychobiotic diet resulted in reductions of perceived stress (32% in diet vs. 17% in control group), but not between groups. Similarly, biological marker of stress were not affected. Additionally, higher adherence to the diet resulted in stronger decreases in perceived stress. While the dietary intervention elicited only subtle changes in microbial composition and function, significant changes in the level of 40 specific fecal lipids and urinary tryptophan metabolites were observed. Lastly, microbial volatility was linked to greater changes in perceived stress scores in those on the psychobiotic diet. These results highlight that dietary approaches can be used to reduce perceived stress in a human cohort. Using microbiota-targeted diets to positively modulate gut-brain communication holds possibilities for the reduction of stress and stress-associated disorders, but additional research is warranted to investigate underlying mechanisms, including the role of the microbiota.
Visualization of BOK pores independent of BAX and BAK reveals a similar mechanism with differing regulation
Authors: Shalaby Raed , Diwan Arzoo , Flores-Romero Hector , Hertlein Vanessa , Garcia-Saez Ana J.
Published: October 2022

BOK is a poorly understood member of the BCL-2 family of proteins that has been proposed to function as a pro-apoptotic, BAX-like effector. However, the molecular mechanism and structural properties of BOK pores remain enigmatic. Here, we show that the thermal stability and pore activity of BOK depends on the presence of its C-terminus as well as on the mitochondrial lipid cardiolipin. We directly visualized BOK pores in liposomes by electron microscopy, which appeared similar to those induced by BAX, in line with comparable oligomerization properties quantified by single molecule imaging. In addition, super-resolution STED imaging revealed that BOK organized into dots and ring-shaped assemblies in apoptotic mitochondria, also reminiscent of those found for BAX and BAK. Yet, unlike BAX and BAK, the apoptotic activity of BOK was limited by partial mitochondrial localization and was independent of and unaffected by other BCL-2 proteins. These results suggest that, while BOK activity is kept in check by subcellular localization instead of interaction with BCL-2 family members, the resulting pores are structurally similar to those of BAX and BAK.
Structural basis of actin filament assembly and aging
Authors: Oosterheert Wout , Klink Björn U. , Belyy Alexander , Pospich Sabrina , Raunser Stefan
Published: October 2022

The dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and is coupled to changes in the F-actin nucleotide state1–3. It remains unclear how F-actin hydrolyses ATP and subsequently undergoes subtle conformational rearrangements that ultimately lead to filament depolymerization by actin-binding proteins. Here we present cryo-electron microscopy structures of F-actin in all nucleotide states, polymerized in the presence of Mg2+ or Ca2+ at approximately 2.2 Å resolution. The structures show that actin polymerization induces the relocation of water molecules in the nucleotide-binding pocket, activating one of them for the nucleophilic attack of ATP. Unexpectedly, the back door for the subsequent release of inorganic phosphate (Pi) is closed in all structures, indicating that Pi release occurs transiently. The small changes in the nucleotide-binding pocket after ATP hydrolysis and Pi release are sensed by a key amino acid, amplified and transmitted to the filament periphery. Furthermore, differences in the positions of water molecules in the nucleotide-binding pocket explain why Ca2+-actin shows slower polymerization rates than Mg2+-actin. Our work elucidates the solvent-driven rearrangements that govern actin filament assembly and aging and lays the foundation for the rational design of drugs and small molecules for imaging and therapeutic applications.
Phenotypic plasticity and genetic control in colorectal cancer evolution
Authors: Househam Jacob , Heide Timon , Cresswell George D. , Spiteri Inmaculada , Kimberley Chris , Zapata Luis , Lynn Claire , James Chela , Mossner Maximilian , Fernandez-Mateos Javier , Vinceti Alessandro , Baker Ann-Marie , Gabbutt Calum , Berner Alison , Schmidt Melissa , Chen Bingjie , Lakatos Eszter , Gunasri Vinaya , Nichol Daniel , Costa Helena , Mitchinson Miriam , Ramazzotti Daniele , Werner Benjamin , Iorio Francesco , Jansen Marnix , Caravagna Giulio , Barnes Chris P. , Shibata Darryl , Bridgewater John , Rodriguez-Justo Manuel , Magnani Luca , Sottoriva Andrea , Graham Trevor A.
Published: October 2022

Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather ‘plastic’. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.
Functional antibodies exhibit light chain coherence
Authors: Jaffe David B. , Shahi Payam , Adams Bruce A. , Chrisman Ashley M. , Finnegan Peter M. , Raman Nandhini , Royall Ariel E. , Tsai FuNien , Vollbrecht Thomas , Reyes Daniel S. , Hepler N. Lance , McDonnell Wyatt J.
Published: October 2022

The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1–CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2–22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
Clonal expansion and epigenetic inheritance of long-lasting NK cell memory
Authors: Rückert Timo , Lareau Caleb A. , Mashreghi Mir-Farzin , Ludwig Leif S. , Romagnani Chiara
Published: October 2022

Clonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV+ individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification.
Detectability and parameter estimation of stellar origin black hole binaries with next generation gravitational wave detectors
Authors: Pieroni Mauro , Ricciardone Angelo , Barausse Enrico
Published: October 2022

We consider stellar-origin black hole binaries, which are among the main astrophysical sources for next generation gravitational wave (GW) detectors such as the Einstein Telescope (ET) and Cosmic Explorer (CE). Using population models calibrated with the most recent LIGO/Virgo results from O3b run, we show that ET and CE will be capable of detecting tens of thousands of such sources (and virtually all of those present in our past light cone up to $$z\lesssim 0.7$$

z
≲
0.7

for ET and $$z\lesssim 1$$

z
≲
1

for CE) with a signal-to-noise ratio up to several hundreds, irrespective of the detector design. When it comes to parameter estimation, we use a Fisher-matrix analysis to assess the impact of the design on the estimation of the intrinsic and extrinsic parameters. We find that the CE detector, consisting of two distinct $$L-$$

L
-

shape interferometers, has better sky localization performance compared to ET in its triangular configuration. We also find that the network is typically capable of measuring the chirp mass, symmetric mass ratio and spins of the binary at order of $$10^{-5}$$

10

-
5

, $$10^{-4}$$

10

-
4

and $$10^{-4}$$

10

-
4

fractional error respectively. While the fractional errors for the extrinsic parameters are of order $$10^{-2}$$

10

-
2

for the sky localization, luminosity distance and inclination.
Prevalence of LA-MRSA in pigsties: analysis of factors influencing the (De)colonization process
Authors: Kobusch Iris , Schröter Iris , Linnemann Sabrina , Schollenbruch Hannah , Hofmann Franka , Boelhauve Marc
Published: October 2022

Professional pig husbandry is often associated with a more or less high load of LA-MRSA. Possible risk factors for LA-MRSA colonization in pig herds have already been identified in studies suggesting that housing conditions may affect LA-MRSA prevalence. In Europe, pigs are kept under variety of conditions. The aim of this study is to identify husbandry and housing condition factors that affect colonization with LA-MRSA. 78 pig farms were selected and assigned to three categories according to housing conditions: conventional, alternative and organic. Animal and surface samples were taken and examined for the presence of LA-MRSA at beginning and end of one fattening period per farm. Altogether, a significant (p < 0.05) decrease in colonization with LA-MRSA from beginning to end of the fattening periods in pigs and surfaces can be observed. Alternative farms showed a higher dynamic in the colonization. In organic farms, almost no colonization was found. Influencing housing condition factors that determine LA-MRSA status at the end of the fattening period are the number of pigs in the building, LA-MRSA status at the beginning of fattening period, material of the floor (straw bedding), strictness of black–white separation and antibiotic treatment during the fattening period. For pig farming in general, knowledge and measures to reduce the colonization with LA-MRSA would be important.
Real world data on the prognostic significance of monocytopenia in myelodysplastic syndrome
Authors: Diamantopoulos Panagiotis T. , Charakopoulos Emmanouil , Symeonidis Argiris , Kotsianidis Ioannis , Viniou Nora-Athina , Pappa Vassiliki , Pontikoglou Charalampos , Tsokanas Dimitrios , Drakos Georgios , Kourakli Alexandra , Solomou Elena , Hatzimichael Eleftheria , Pouli Anastasia , Kotsopoulou Maria , Asmanis Evangelos , Dimou Maria , Panayiotidis Panayiotis , Papageorgiou Sotirios , Vassilopoulos Georgios , Anagnostopoulos Achilles , Vassilakopoulos Theodoros , Papadaki Helen , Galanopoulos Athanasios
Published: October 2022

Monocytopenia is a common finding in patients with myelodysplastic syndrome (MDS), but although monocytes may exhibit prognostic significance in MDS due to their role in innate immunity, they have not been incorporated in any prognostic scoring system for MDS. In this study, we analyzed national registry data from 1719 adults with MDS. Monocytopenia was present in 29.5% of the patients and was correlated with the presence of excess blasts and higher revised international prognostic scoring system categories. Univariate analysis showed that monocytopenia was prognostic of a lower overall survival [(OS), 32.0 versus 65.0 months, p < 0.001], while it retained its prognostic significance in a multivariate model comprising anemia, neutropenia and thrombocytopenia [hazard ratio (HR) for OS, 1.320, p < 0.001]. Moreover, it was prognostic of a lower leukemia free survival (LFS) both in univariate analysis and in a multivariate model comprising cytopenias, bone marrow blasts, and cytogenetic risk (HR for LFS 1.27, p = 0.031). The findings regarding OS and LFR were exclusive or more pronounced in lower risk patients, respectively. Moreover, monocytopenia could divide the low and intermediate risk groups of IPSS-R in prognostically distinct subgroups. Our results redefine the prognostic role of monocytes in MDS and set the basis for further studies to validate our results and expand our knowledge on the prognostic significance of monocytopenia in MDS.
Ferritin thresholds for cardiac and liver hemosiderosis in β-thalassemia patients: a diagnostic accuracy study
Authors: Darvishi-Khezri Hadi , Aliasgharian Aily , Naderisorki Mohammad , Kosaryan Mehrnoush , Ghazaiean Mobin , Fallah Hanie , Zahedi Mohammad , Karami Hossein
Published: October 2022

Ferritin is frequently used to screen some dire consequences of iron overload in β-thalassemia patients. The study aimed to define the best cutoff point of ferritin to screen for cardiac and liver hemosiderosis in these cases. This was a registry-based study on β-thalassemia patients living throughout Mazandaran province, Iran (n = 1959). In this diagnostic research, the index test was ferritin levels measured by a chemiluminescent immunoassay. As a reference test, T2*-weighted magnetic resonance imaging (T2*-weighted MRI) was applied to determine cardiac and liver hemosiderosis. A cutoff point of 2027 ng/mL for ferritin showed a sensitivity of 50%, specificity 77.4%, PPV 42.1%, and NPV 82.5% for cardiac hemosiderosis (area under curve [AUC] 0.66, 95% CI 0.60–0.71, adjusted odds ratio [OR] 2.05, 95% CI 1.05–4.01). At an optimum cutoff point of 1090 ng/mL, sensitivity 66.7%, specificity 68%, PPV 82.9%, and NPV 46.8% for liver hemosiderosis were estimated (AUC 0.68, 95% CI 0.63–0.73, adjusted OR 3.93, 95% CI 2.02–7.64. The likelihood of cardiac hemosiderosis serum ferritin levels below 2027 ng/mL is 17.5%. Moreover, 82.9% of β-thalassemia patients with serum ferritin levels above 1090 ng/mL may suffer from liver hemosiderosis, regardless of the grades.
A quantum graph approach to metamaterial design
Authors: Lawrie Tristan , Tanner Gregor , Chronopoulos Dimitrios
Published: October 2022

Since the turn of the century, metamaterials have gained a large amount of attention due to their potential for possessing highly nontrivial and exotic properties—such as cloaking or perfect lensing. There has been a great push to create reliable mathematical models that accurately describe the required material composition. Here, we consider a quantum graph approach to metamaterial design. An infinite square periodic quantum graph, constructed from vertices and edges, acts as a paradigm for a 2D metamaterial. Wave transport occurs along the edges with vertices acting as scatterers modelling sub-wavelength resonant elements. These resonant elements are constructed with the help of finite quantum graphs attached to each vertex of the lattice with customisable properties controlled by a unitary scattering matrix. The metamaterial properties are understood and engineered by manipulating the band diagram of the periodic structure. The engineered properties are then demonstrated in terms of the reflection and transmission behaviour of Gaussian beam solutions at an interface between two different metamaterials. We extend this treatment to N layered metamaterials using the Transfer Matrix Method. We demonstrate both positive and negative refraction and beam steering. Our proposed quantum graph modelling technique is very flexible and can be easily adjusted making it an ideal design tool for creating metamaterials with exotic band diagram properties or testing promising multi-layer set ups and wave steering effects.
The combination of ulinastatin and somatostatin reduces complication rates in acute pancreatitis: a systematic review and meta-analysis of randomized controlled trials
Authors: Horváth István László , Bunduc Stefania , Fehérvári Péter , Váncsa Szilárd , Nagy Rita , Garmaa Gantsetseg , Kleiner Dénes , Hegyi Péter , Erőss Bálint , Csupor Dezső
Published: October 2022

Currently, there is no specific pharmaceutical agent for treating acute pancreatitis (AP). Somatostatin and its analogues have been used to prevent the autolysis of the pancreas in AP, however, their effectiveness has not been confirmed. This investigation aimed to examine the efficacy of ulinastatin, a protease inhibitor, combined with somatostatin analogues in the treatment of AP. We conducted a systematic database search in 4 databases to identify randomized controlled trials in which the efficacy of ulinastatin in combination with somatostatin analogue was compared to somatostatin analogue alone in patients with AP. Since the patient populations of analysed papers were slightly different, we used random effect models to pool odds ratios (OR) and mean differences (MD) and the corresponding 95% confidence intervals (CI). A total of 9 articles comprising 1037 patients were included in the meta-analysis. The combination therapy significantly reduced the complication rates for acute respiratory distress syndrome, acute kidney injury, and multiple organ dysfunction. Symptoms were relieved threefold with the combination therapy compared to somatostatin alone, and combination therapy significantly shortened the length of hospital stay. The decrease in mortality was not statistically significant.﻿
Foundation plant species provide resilience and microclimatic heterogeneity in drylands
Authors: Lortie C. J. , Filazzola Alessandro , Westphal Mike , Butterfield H. Scott
Published: October 2022

Climate change profoundly influences plants and animals in all ecosystems including drylands such as semi-arid and arid scrublands and grasslands. At the peak of an extended megadrought in the Southwestern USA, the microclimatic refuges provided by foundation plant species and through associated vegetation were examined. Shrubs and open interstitial spaces without a canopy but with annual plants were instrumented in 2016 and the wet season of 2017 in the central drylands of California. In both years and all seasons tested, vegetation significantly mediated fine-scale near-surface air temperature and relative soil moisture content—defined here as microclimate. The foundation species with other vegetation provided the most significant thermal refuge potential capacity for other plants and animals, but there was variation by growing season. Soil moisture content was frequently increased by the direct canopy effects of shrubs. This evidence suggests that the climate many plants and animals experience, even during an extended megadrought, is mediated by the local plants in highly impacted drylands with anthropogenic disturbance and significant water-induced challenges. Foundation species such as shrubs in drylands function as a potent starting point in examining the ecological relevance of climate at scales germane to many species locally. An ecological framework for climate resilience using shrubs will improve conservation and restoration planning in drylands.