bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic control of the operculum and capsule morphology of Eucalyptus globulus
Authors: Hernández Mariano A , Butler Jakob B , Ammitzboll Hans , Weller James L , Vaillancourt René E , Potts Brad M
Published: June 2022

Background and aims

The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures.

Methods

Samples of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers.

Key results

A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed.

Conclusions

Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
Prior knowledge facilitates low homologous protein secondary structure prediction with DSM distillation
Authors: Wang Qin , Wei Jun , Zhou Yuzhe , Lin Mingzhi , Ren Ruobing , Wang Sheng , Cui Shuguang , Li Zhen
Published: June 2022

Motivation

Protein secondary structure prediction (PSSP) is one of the fundamental and challenging problems in the field of computational biology. Accurate PSSP relies on sufficient homologous protein sequences to build the multiple sequence alignment (MSA). Unfortunately, many proteins lack homologous sequences, which results in the low quality of MSA and poor performance. In this article, we propose the novel dynamic scoring matrix (DSM)-Distil to tackle this issue, which takes advantage of the pretrained BERT and exploits the knowledge distillation on the newly designed DSM features. Specifically, we propose the DSM to replace the widely used profile and PSSM (position-specific scoring matrix) features. DSM could automatically dig for the suitable feature for each residue, based on the original profile. Namely, DSM-Distil not only could adapt to the low homologous proteins but also is compatible with high homologous ones. Thanks to the dynamic property, DSM could adapt to the input data much better and achieve higher performance. Moreover, to compensate for low-quality MSA, we propose to generate the pseudo-DSM from a pretrained BERT model and aggregate it with the original DSM by adaptive residue-wise fusion, which helps to build richer and more complete input features. In addition, we propose to supervise the learning of low-quality DSM features using high-quality ones. To achieve this, a novel teacher–student model is designed to distill the knowledge from proteins with high homologous sequences to that of low ones. Combining all the proposed methods, our model achieves the new state-of-the-art performance for low homologous proteins.

Results

Compared with the previous state-of-the-art method ‘Bagging’, DSM-Distil achieves an improvement about 5% and 7.3% improvement for proteins with MSA count ≤30 and extremely low homologous cases, respectively. We also compare DSM-Distil with Alphafold2 which is a state-of-the-art framework for protein structure prediction. DSM-Distil outperforms Alphafold2 by 4.1% on extremely low-quality MSA on 8-state secondary structure prediction. Moreover, we release a large-scale up-to-date test dataset BC40 for low-quality MSA structure prediction evaluation.

Availability and implementation

BC40 dataset: https://drive.google.com/drive/folders/15vwRoOjAkhhwfjDk6-YoKGf4JzZXIMC. HardCase dataset: https://drive.google.com/drive/folders/1BvduOr2b7cObUHy6GuEWk-aUkKJgzTUv. Code: https://github.com/qinwang-ai/DSM-Distil.
Effective drug–target interaction prediction with mutual interaction neural network
Authors: Li Fei , Zhang Ziqiao , Guan Jihong , Zhou Shuigeng
Published: June 2022

Motivation

Accurately predicting drug–target interaction (DTI) is a crucial step to drug discovery. Recently, deep learning techniques have been widely used for DTI prediction and achieved significant performance improvement. One challenge in building deep learning models for DTI prediction is how to appropriately represent drugs and targets. Target distance map and molecular graph are low dimensional and informative representations, which however have not been jointly used in DTI prediction. Another challenge is how to effectively model the mutual impact between drugs and targets. Though attention mechanism has been used to capture the one-way impact of targets on drugs or vice versa, the mutual impact between drugs and targets has not yet been explored, which is very important in predicting their interactions.

Results

Therefore, in this article we propose MINN-DTI, a new model for DTI prediction. MINN-DTI combines an interacting-transformer module (called Interformer) with an improved Communicative Message Passing Neural Network (CMPNN) (called Inter-CMPNN) to better capture the two-way impact between drugs and targets, which are represented by molecular graph and distance map, respectively. The proposed method obtains better performance than the state-of-the-art methods on three benchmark datasets: DUD-E, human and BindingDB. MINN-DTI also provides good interpretability by assigning larger weights to the amino acids and atoms that contribute more to the interactions between drugs and targets.

Availability and implementation

The data and code of this study are available at https://github.com/admislf/MINN-DTI.
Subsampling sparse graphons under minimal assumptions
Authors: Lunde Robert , Sarkar Purnamrita
Published: June 2022

We study the properties of two subsampling procedures for networks, vertex subsampling and $p$-subsampling, under the sparse graphon model. The consistency of network subsampling is demonstrated under the minimal assumptions of weak convergence of the corresponding network statistics and an expected subsample size growing to infinity more slowly than the number of vertices in the network. Furthermore, under appropriate sparsity conditions, we derive limiting distributions for the nonzero eigenvalues of an adjacency matrix under the sparse graphon model. Our weak convergence result implies the consistency of our subsampling procedures for eigenvalues under appropriate conditions.
Sensory experience modulates the reorganization of auditory regions for executive processing
Authors: Manini Barbara , Vinogradova Valeria , Woll Bencie , Cameron Donnie , Eimer Martin , Cardin Velia
Published: June 2022

Crossmodal plasticity refers to the reorganization of sensory cortices in the absence of their typical main sensory input. Understanding this phenomenon provides insights into brain function and its potential for change and enhancement. Using functional MRI, we investigated how early deafness influences crossmodal plasticity and the organization of executive functions in the adult human brain. Deaf (n = 25; age: mean = 41.68, range = 19–66, SD = 14.38; 16 female, 9 male) and hearing (n = 20; age: mean = 37.50, range = 18–66, SD = 16.85; 15 female, 5 male) participants performed four visual tasks tapping into different components of executive processing: task switching, working memory, planning and inhibition. Our results show that deaf individuals specifically recruit ‘auditory’ regions during task switching. Neural activity in superior temporal regions, most significantly in the right hemisphere, are good predictors of behavioural performance during task switching in the group of deaf individuals, highlighting the functional relevance of the observed cortical reorganization. Our results show executive processing in typically sensory regions, suggesting that the development and ultimate role of brain regions are influenced by perceptual environmental experience.
Identification of a novel fatty acid binding protein-5-CB2 receptor-dependent mechanism regulating anxiety behaviors in the prefrontal cortex
Authors: Uzuneser Taygun C , Szkudlarek Hanna J , Jones Matthew J , Nashed Mina G , Clement Timothy , Wang Hehe , Ojima Iwao , Rushlow Walter J , Laviolette Steven R
Published: June 2022

The endocannabinoid (eCB) system represents a promising neurobiological target for novel anxiolytic pharmacotherapies. Previous clinical and preclinical evidence has revealed that genetic and/or pharmacological manipulations altering eCB signaling modulate fear and anxiety behaviors. Water-insoluble eCB lipid anandamide requires chaperone proteins for its intracellular transport to degradation, a process that requires fatty acid-binding proteins (FABPs). Here, we investigated the effects of a novel FABP-5 inhibitor, SBFI-103, on fear and anxiety-related behaviors using rats. Acute intra-prelimbic cortex administration of SBFI-103 induced a dose-dependent anxiolytic response and reduced contextual fear expression. Surprisingly, both effects were reversed when a cannabinoid-2 receptor (CB2R) antagonist, AM630, was co-infused with SBFI-103. Co-infusion of the cannabinoid-1 receptor antagonist Rimonabant with SBFI-103 reversed the contextual fear response yet showed no reversal effect on anxiety. Furthermore, in vivo neuronal recordings revealed that intra-prelimbic region SBFI-103 infusion altered the activity of putative pyramidal neurons in the basolateral amygdala and ventral hippocampus, as well as oscillatory patterns within these regions in a CB2R-dependent fashion. Our findings identify a promising role for FABP5 inhibition as a potential target for anxiolytic pharmacotherapy. Furthermore, we identify a novel, CB2R-dependent FABP-5 signaling pathway in the PFC capable of strongly modulating anxiety-related behaviors and anxiety-related neuronal transmission patterns.
Effectiveness of Paxlovid in Reducing Severe Coronavirus Disease 2019 and Mortality in High-Risk Patients
Authors: Najjar-Debbiny Ronza , Gronich Naomi , Weber Gabriel , Khoury Johad , Amar Maisam , Stein Nili , Goldstein Lee Hilary , Saliba Walid
Published: June 2022

Background

Paxlovid was granted an Emergency Use Authorization for the treatment of mild to moderate coronavirus disease 2019 (COVID-19), based on the interim analysis of the Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients (EPIC-HR) trial. Paxlovid effectiveness needs to be assessed in a noncontrolled setting. In this study we used population-based real-world data to evaluate the effectiveness of Paxlovid.

Methods

The database of the largest healthcare provider in Israel was used to identify all adults aged 18 years or older with first-ever positive test for severe acute respiratory syndrome coronavirus 2 between January and February 2022, who were at high risk for severe COVID-19 and had no contraindications for Paxlovid use. Patients were included irrespective of their COVID-19 vaccination status. Cox hazard regression was used to estimate the 28-day hazard ratio (HR) for severe COVID-19 or mortality with Paxlovid examined as time-dependent variable.

Results

Overall, 180 351 eligible patients were included; of these, only 4737 (2.6%) were treated with Paxlovid, and 135 482 (75.1%) had adequate COVID-19 vaccination status. Both Paxlovid and adequate COVID-19 vaccination status were associated with significant decrease in the rate of severe COVID-19 or mortality with adjusted HRs of 0.54 (95% confidence interval [CI], .39–.75) and 0.20 (95% CI, .17–.22), respectively. Paxlovid appears to be more effective in older patients, immunosuppressed patients, and patients with underlying neurological or cardiovascular disease (interaction P < .05 for all). No significant interaction was detected between Paxlovid treatment and COVID-19 vaccination status.

Conclusions

This study suggests that in the era of Omicron and in real-life settings, Paxlovid is highly effective in reducing the risk of severe COVID-19 or mortality.
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature
Authors: Feng Baiyang , Gao Jing
Published: June 2022

Anthrax is a zoonotic infectious disease caused by Bacillus anthracis (anthrax bacterium) that affects not only domestic and wild animals worldwide but also human health. As the study develops in-depth, a large quantity of related biomedical publications emerge. Acquiring knowledge from the literature is essential for gaining insight into anthrax etiology, diagnosis, treatment and research. In this study, we used a set of text mining tools to identify nearly 14 000 entities of 29 categories, such as genes, diseases, chemicals, species, vaccines and proteins, from nearly 8000 anthrax biomedical literature and extracted 281 categories of association relationships among the entities. We curated Anthrax-related Entities Dictionary and Anthrax Ontology. We formed Anthrax Knowledge Graph (AnthraxKG) containing more than 6000 nodes, 6000 edges and 32 000 properties. An interactive visualized Anthrax Knowledge Portal(AnthraxKP) was also developed based on AnthraxKG by using Web technology. AnthraxKP in this study provides rich and authentic relevant knowledge in many forms, which can help researchers carry out research more efficiently.

Database URL: AnthraxKP is permitted users to query and download data at http://139.224.212.120:18095/.
Impact of within-visit systolic blood pressure change patterns on blood pressure classification: the Cardiovascular Risk in Young Finns Study
Authors: Meng Yaxing , Magnussen Costan G , Wu Feitong , Juonala Markus , Buscot Marie-Jeanne , Pahkala Katja , Hutri-Kähönen Nina , Kähönen Mika , Laitinen Tomi , Viikari Jorma S A , Raitakari Olli T , Sharman James E
Published: June 2022

Aims

Most international guidelines recommend that repeat blood pressure (BP) readings are required for BP classification. Two international guidelines diverge from this by recommending that no further BP measurements are required if the first clinic BP is below a hypertension threshold. The extent to which within-visit BP variability patterns change over time, and whether this could impact BP classification is unknown. We sought to examine this.

Methods and results

Data were from the Cardiovascular Risk in Young Finns Study, a prospective cohort study. Up to 2799 participants were followed from childhood (9–15 years) to adulthood (18–49 years) over up to six visits. Patterns of within-visit systolic BP (SBP) variability were defined as no-change, decrease, increase between consecutive readings (with 5 mmHg change thresholds). Classification of SBP (normal, high-normal, hypertension) using the first reading was compared with repeat readings. On average, SBP decreased with subsequent measures, but with major individual variability (no-change: 56.9–62.7%; decrease: 24.1–31.6%; increase: 11.5–16.8%). Patterns of SBP variability were broadly similar from childhood to adulthood, with the highest prevalence of an increase among participants categorized with normal SBP (12.6–20.3%). The highest prevalence of SBP reclassification occurred among participants with hypertension (28.9–45.3% reclassified as normal or high-normal). The prevalence of reclassification increased with the magnitude of change between readings.

Conclusion

There is a major individual variation of within-visit SBP change in childhood and adulthood and can influence BP classification. This highlights the importance of consistency among guidelines recommending that repeat BP measurements are needed for BP classification.
Seismicity in a weak crust: the transtensional tectonics of the Brawley Seismic Zone section of the Pacific–North America Plate Boundary in Southern California, USA
Authors: Hauksson Egill , Stock Joann M , Husker Allen L
Published: June 2022

The Brawley Seismic Zone (BSZ) is a ∼58-km-long section of the Pacific–North America Plate boundary that connects the southernmost San Andreas Fault (SAF) and the Imperial Fault in southern California. We analyse the BSZ as two segments: a north segment, dominated by SAF tectonics, and a south segment that accommodates a higher level of seismicity. The south segment includes a ∼6 km wide right lateral step-over that includes the Salton Sea geothermal field (SSGF) and Holocene subaerial lava domes at the south end of the Salton Sea, called Salton Buttes. In general, the 40 yr (1981–2021) of BSZ seismicity is characterized by transitory sequences that often are accommodated simultaneously or in quick succession on intricate ladder-like faults. These sequences rarely reactivate faults associated with previous seismicity alignments but rather activate adjacent faults, sometimes located within less than 1 km. They can include several events of similar size as the mainshock, followed by bursts of aftershocks sometimes located away from the mainshock rupture. The seismicity rate and the spatial geometrical complexity varies between the BSZ-north and BSZ-south segments. The 24-km-long BSZ-north accommodates a ∼12-km-long linear trend of seismicity that extends from the SAF terminus into the Salton Sea, where moderate-sized northeast striking sequences form the rungs in a ladder-structure in a weak crust. The seismicity in this area is most likely influenced by the stress state of the SAF. In contrast, the 34 km long BSZ-south segment, which also has a weak crust, has accommodated larger sequences that illuminate irregular ladder-type faulting, with aftershocks defining linear distributions striking either north or northeast. The focal mechanisms exhibit a mostly strike-slip style of faulting with minor dip-slip faulting in the south Salton Sea area as well as the Mesquite basin to the south. The state of stress, as determined from focal mechanisms, consists of almost horizontal σ1, and σ3 with vertical σ2. The activation angle between the trend of σ1 and the preferred nodal plane of the largest nearby event decreases systematically from north to south along the long-axis of the BSZ. In the step-over zone, the Holocene volcanism and the frequent seismicity sequences suggest crustal extension as well as associated reduced crustal strength as compared to other parts of the BSZ. The presence of weak, thin, hot crust and distributed ladder-like or conjugate predominantly strike-slip faulting suggests that the whole BSZ acts as a several kilometre wide fault zone where no prominent principal slip surfaces are required to accommodate moderate-sized (M6+) earthquakes.
Modelling autosomal dominant optic atrophy associated with OPA1 variants in iPSC-derived retinal ganglion cells
Authors: Sladen Paul E , Jovanovic Katarina , Guarascio Rosellina , Ottaviani Daniele , Salsbury Grace , Novoselova Tatiana , Chapple J Paul , Yu-Wai-Man Patrick , Cheetham Michael E
Published: June 2022

Autosomal dominant optic atrophy (DOA) is the most common inherited optic neuropathy, characterized by the preferential loss of retinal ganglion cells (RGCs), resulting in optic nerve degeneration and progressive bilateral central vision loss. More than 60% of genetically confirmed patients with DOA carry variants in the nuclear OPA1 gene, which encodes for a ubiquitously expressed, mitochondrial GTPase protein. OPA1 has diverse functions within the mitochondrial network, facilitating inner membrane fusion and cristae modelling, regulating mitochondrial DNA maintenance and coordinating mitochondrial bioenergetics. There are currently no licensed disease-modifying therapies for DOA and the disease mechanisms driving RGC degeneration are poorly understood. Here, we describe the generation of isogenic, heterozygous OPA1 null induced pluripotent stem cell (iPSC) (OPA1+/−) through clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing of a control cell line, in conjunction with the generation of DOA patient-derived iPSC carrying OPA1 variants, namely, the c.2708_2711delTTAG variant (DOA iPSC), and previously reported missense variant iPSC line (c.1334G>A, DOA plus [DOA]+ iPSC) and CRISPR/Cas9 corrected controls. A two-dimensional (2D) differentiation protocol was used to study the effect of OPA1 variants on iPSC-RGC differentiation and mitochondrial function. OPA1+/−, DOA and DOA+ iPSC showed no differentiation deficit compared to control iPSC lines, exhibiting comparable expression of all relevant markers at each stage of differentiation. OPA1+/− and OPA1 variant iPSC-RGCs exhibited impaired mitochondrial homeostasis, with reduced bioenergetic output and compromised mitochondrial DNA maintenance. These data highlight mitochondrial deficits associated with OPA1 dysfunction in human iPSC-RGCs, and establish a platform to study disease mechanisms that contribute to RGC loss in DOA, as well as potential therapeutic interventions.
The Water to Land Transition Submerged: Multifunctional Design of Pectoral Fins for Use in Swimming and in Association with Underwater Substrate
Authors: Hale Melina E , Galdston Seth , Arnold Benjamin W , Song Chris
Published: June 2022

Fins of fishes provide many examples of structures that are beautifully designed to power and control movement in water; however, some species also use their fins for substrate-associated behaviors where interactions with solid surfaces are key. Here, we examine how the pectoral fins of ray-finned fish with these multifunctional behavioral demands, in water and on solid surfaces, are structured and function. We subdivide fins used in swimming and substrate contact into two general morphological categories, regionalized vs. generalized fins. Regionalized fins have ventral rays that are free from connecting membrane or in which that membrane is reduced. Dorsally they maintain a more typical membranous fin. While all pectoral fins vary somewhat in their morphology from leading to trailing edge, generalized fins do not have the substantial membrane loss between rays that is seen in regionalized fins and the distal edge anatomy changes gradually along its margin. We add a new case study in regionalized fins with the dwarf hawkfish (Cirrhitichthys falco). Hawkfishes are most often found perching and moving on structures in their environments. During perching, the free ventral rays are in contact with the substrate and splayed. We found that unlike other fish with regionalized pectoral fins, hawkfish maintain use of the dorsal membranous region of its pectoral fin for rhythmic swimming. We found that typically hawkfish bend their ventral free rays under, toward the medial hemitrichs or hold them straight during substrate-associated postures. This appears also to be the case for the ventral free rays of other species with regionalized fins. Generalized fin use for substrate contact was reviewed in round gobies (Neogobius melanostomus). In addition, although their lobe fins are not representative of ray-finned fish anatomy, we explored fin contact on submerged substrates in the Senegal bichir (Polypterus senegalus), which has a generalized distal fin (no free fin rays or distinct membrane regions). Both groups use their pectoral fins for swimming. During substrate-based postures, unlike hawkfish, their distal rays generally bend outward toward the lateral hemitrichs and a large swath of the fin membrane can contact the surface. The alternative demands on multifunctional fins suggest specialization of the mechanosensory system. We review mechanosensation related to fin movement and surface contact. These alternative regionalized and generalized strategies for serving aquatic and substrate-based functions underwater provide opportunities to further investigate specializations, including sensory structures and systems, that accompany the evolution of substrate-based behaviors in vertebrates.
Spatio-temporal variability in drifting Fish Aggregating Device (dFAD) beaching events in the Seychelles Archipelago
Authors: MacMillan Isla , Attrill Martin J , Imzilen Taha , Lett Christophe , Walmsley Simon , Chu Clarus , Kaplan David M
Published: June 2022

Purse-seine fisheries use drifting Fish Aggregating Devices (dFADs), human-made floating objects, to facilitate the capture of tropical tunas. Currently, the majority of dFADs are constructed primarily of highly durable non-biodegradable materials and there is no legal obligation to recover dFADs after deployment, leading to beaching events and potentially negative environmental impacts. We assessed beachings as a function of intra- and inter-annual trends, water depth, distance from land, seasonality, and benthic habitat within the local context of the Seychelles Archipelago using trajectories of dFADs deployed by French purse seiners over 2008–2020. Overall, 3842 beaching events associated with 2371 distinct dFAD tracking buoys were identified. Beachings occurred most frequently during the winter monsoon (December–March). Due to the shallow Mahé Plateau, beachings occurred in both nearshore (≤ 5 km from land) and offshore (> 5 km) regions, predominantly in estimated depths less than 60 m. Despite representing < 20% of overall mapped habitat, the benthic habitat “Coral/Algae” had the highest beaching rate (35.3% of beachings), and therefore, beachings pose a significant concern for conservation. Our results provide a detailed view of the spatio-temporal pattern of beachings in the Seychelles, supporting the development of mitigation and prevention methods to reduce marine debris and perturbations to the marine environment.
The role of immune cells in the liver tumor microenvironment: an involvement of gut microbiota-derived factors
Authors: Kamiya Tomonori , Ohtani Naoko
Published: June 2022

Abstract

More than 500 species of microbiota reside in the human intestine and coexist with humans, their host. Gut microbial metabolites and components are absorbed from the intestine and influence cells in the liver, including hepatocytes and stromal cells, such as liver sinusoidal endothelial cells, hepatic stellate cells, Kupffer cells, natural killer (NK) cells, NK T cells and other immune cells. This gut-originated axis to the liver is called the “gut–liver axis”, which underscores the importance of the link between the gut and the liver. In this review, we discuss the gut microbial components and metabolites that affect cells in the liver, particularly in association with immune cells, and the related responses. We also highlight the mechanisms underlying gut microbiota-mediated liver carcinogenesis and discuss cancer prevention, including the recently clarified modulation of immune checkpoint inhibitor efficacy by the gut microbiota.
The Human Neck is Part of the Musculoskeletal Core: Cervical Muscles Help Stabilize the Pelvis During Running and Jumping
Authors: Boynton Alicia M , Carrier David R
Published: June 2022

Synopsis

During locomotion, cervical muscles must be active to stabilize the head as the body accelerates and decelerates. We hypothesized that cervical muscles are also part of the linked chain of axial muscles that provide core stabilization against torques applied to the hip joint by the extrinsic muscles of the legs. To test whether specific cervical muscles play a role in postural stabilization of the head and/or core stabilization of the pelvic girdle, we used surface electromyography to measure changes in muscle activity in response to force manipulations during constant speed running and maximum effort counter-movement jumps. We found that doubling the mass of the head during both running and maximum effort jumping had little or no effect on (1) acceleration of the body and (2) cervical muscle activity. Application of horizontal forward and rearward directed forces at the pelvis during running tripled mean fore and aft accelerations, thereby increasing both the pitching moments on the head and flexion and extension torques applied to the hip. These manipulations primarily resulted in increases in cervical muscle activity that is appropriate for core stabilization of the pelvis. Additionally, when subjects jumped maximally with an applied downward directed force that reduced acceleration and therefore need for cervical muscles to stabilize the head, cervical muscle activity did not decrease. These results suggest that during locomotion, rather than acting to stabilize the head against the effects of inertia, the superficial muscles of the neck monitored in this study help to stabilize the pelvis against torques imposed by the extrinsic muscles of the legs at the hip joint. We suggest that a division of labor may exist between deep cervical muscles that presumably provide postural stabilization of the head versus superficial cervical muscles that provide core stabilization against torques applied to the pelvic and pectoral girdles by the extrinsic appendicular muscles.
Political Agency, Victimhood, and Gender in Contexts of Armed Conflict: Moving beyond Dichotomies
Authors: Kreft Anne-Kathrin , Schulz Philipp
Published: June 2022

In this article, we nuance the relationships between political agency, victimhood, and gender during armed conflicts. Dominant narratives often spotlight individuals as either passive victims or active agents. These representations are especially pronounced for sexual violence against women in conflict, where gendered conceptions of victimhood and agency remain particularly salient. Recent scholarship challenges this dichotomized way of thinking, showing how victimhood and agency sit alongside each other. We extend this growing body of scholarship by proposing a relational conception of agency that helps us better understand exactly how victimhood and agency intersect and can even be co-constitutive. Specifically, we propose that conceptualizing agency as relational—to others, to contextual structures, to own vulnerabilities and prior victimization—is particularly well suited to overcome inadequate dichotomizations, and to illuminate the spectrum of political agency, ranging from formalized politicized spaces to more mundane forms of agency within the quotidian. Drawing on qualitative fieldwork in Colombia and Uganda, we empirically tease out these complex intersections in a context of (gendered) vulnerability.
Cancer-associated mutations in SF3B1 disrupt the interaction between SF3B1 and DDX42
Authors: Zhao Bo , Li Zhuang , Qian Rui , Liu Gang , Fan Mingyue , Liang Zehua , Hu Xin , Wan Youzhong
Published: June 2022

While cancer-associated SF3B1 mutations causes alternative RNA splicing, the molecular mechanism underlying the alternative RNA splicing is not fully elucidated. Here, we analysed the proteins that interacted with the wild-type and K700E-mutated SF3B1 and found that the interactions of two RNA helicases, DDX42 and DDX46, with the mutated SF3B1 were reduced. Overexpression of DDX42 restored the decreased interaction between DDX42 and the K700E-mutated SF3B1, and suppressed some alternative RNA splicing associated with the SF3B1 mutation. Mutation that decreased the ATP hydrolysis activities of DDX42 abolished the suppressive effects of DDX42 on the alternative RNA splicing, suggesting that the ATP hydrolysis activity of DDX42 is involved in the mechanism of the altered RNA splicing associated with the SF3B1 mutation. Our study demonstrates an important function of the interaction between DDX42 and SF3B1 on regulating RNA splicing and revealed a potential role of DDX42 in the altered RNA splicing associated with the SF3B1 mutation.
The extinction law in the inner 3 × 3 deg2 of the Milky Way and the red clump absolute magnitude in the inner bar-bulge
Authors: Sanders Jason L , Smith Leigh , González-Fernández Carlos , Lucas Philip , Minniti Dante
Published: June 2022

The extinction law from 0.9 to 8 microns in the inner $3\times 3\deg ^2$ of the Milky Way is measured using data from VISTA Variables in the Via Lactea, GLIMPSE, and WISE. Absolute extinction ratios are found by requiring that the observed red clump density peaks at the GRAVITY collaboration distance to the Galactic centre. When combined with selective extinction ratios measured from the bulge giant colour–colour diagrams, we find an extinction law of $A_Z:A_Y:A_J:A_H:A_{K_s}:A_{W1}:A_{[3.6]}:A_{[4.5]}:A_{W2}:A_{[5.8]}:A_{[8.0]} =7.19(0.30):5.11(0.20):3.23(0.11):1.77(0.04):1:0.54(0.02):0.46(0.03):0.34(0.03):0.32(0.03):0.24(0.04):0.28(0.03)$ valid for low extinctions where non-linearities are unimportant. These results imply an extinction law from the Rayleigh Jeans colour excess method of $A_{K_s}=0.677(H-[4.5]-0.188)$. We find little evidence for significant selective extinction ratio variation over the inspected region (around $5\, \mathrm{per\, cent}$). Assuming the absolute extinction ratios do not vary across the inspected region gives an independent measurement of the absolute Ks magnitude of the red clump at the Galactic Centre of $(-1.61\pm 0.07)\, \mathrm{mag}$. This is very similar to the value measured for solar neighbourhood red clump stars giving confidence in the use of red clump stars as standard candles across the Galaxy. As part of our analysis, we inspect the completeness of PSF photometry from the VVV survey using artificial star tests, finding $90\, \mathrm{per\, cent}$ completeness at $K_s\approx 16 \, (17)$ in high (low) density regions and good agreement with the number counts with respect to the GALACTICNUCLEUS and DECAPS catalogues over small regions of the survey.
Twenty-year monitoring of the surface magnetic fields of chemically peculiar stars
Authors: Giarrusso M , Cecconi M , Cosentino R , Munari M , Ghedina A , Ambrosino F , Boschin W , Leone F
Published: June 2022

Magnetic chemically peculiar stars of the main sequence can present rotational periods as long as many decades. Here we report the results of an observational campaign started in 2001 aimed at establishing these very long periods from the variability of the integrated magnetic field modulus, the so-called surface magnetic field Bs, as measured from the Zeeman splitting of the Fe ii 6149.258 Å spectral line. 36 stars have been monitored with various high-resolution spectrographs at different telescopes, totalling 412 newly collected spectra. To improve the phase coverage, we have also exploited all public archives containing high-resolution spectra, many not yet published. On the basis of these new Bs variability curves, we (1) confirm or revisit the periods of 24 stars, (2) extend the lower limits to the periods of HD 55719 (P > 38 yr), HD 165474 (P > 27 yr), and HD 177765 (P > 37 yr), (3) establish for the first time the periods of HD 29578 (P = 10.95 yr), HD 47103 (P = 17.683 d), HD 150562 (P = 5.7 yr), and HD 216018 (P = 34.044 d), and (4) set lower limits to the periods of HD 75445 (P »14 yr), HD 110066 (P » 29 yr), HD 116114 (P > 48 yr), and HD 137949 (P > 27 yr). As to γ Equ, whose period must exceed 90 yr, we point out a clear decrease in the field modulus, the maximum of which coincides within the uncertainties with the minimum of the variation in the integrated longitudinal field.
Swift heavy ions irradiation of water ice at different temperatures: hydrogen peroxide and ozone synthesis and sputtering yield
Authors: Mejía C , de Barros A L F , Rothard H , Boduch P , da Silveira E F
Published: June 2022

Water ices at 15 and 144 K were bombarded by swift heavy ions, 45.8 MeV 58Ni11 + and 606 MeV 64Zn26 +, to measure the induced chemical and physical effects. The column densities of water and the synthesized species, hydrogen peroxide (H2O2) and ozone (O3), were monitored via infrared spectroscopy. The formation and destruction cross-sections of precursor and products were determined and compared with literature. The H2O2 formation and destruction cross-sections  reveal a linear dependence with electronic stopping power, σ ∝ Se. The sputtering yield (Y0) shows a power law with electronic energy lost, $Y_0\propto S_\mathrm{e}^2$, and an exponential increase with the sample temperature. The findings indicate that the radiolysis rate of water ice is higher at low temperatures while the desorption yield increases at higher temperatures. A large amount of water ice is located in the grain mantles of the circumstellar envelopes and the interstellar medium regions, which are exposed to galactic cosmic rays (GCRs). The synthesis of H2O2 and O3 molecules as a function of absorbed doses of GCR irradiation and their irradiation time is analysed in detail. Besides, the extrapolation of the sputtering yield rates, as a function of time and temperature, for astrophysical conditions can contribute to a better understanding of non-thermal sputtering of water ices.
The DESI N-body Simulation Project – II. Suppressing sample variance with fast simulations
Authors: Ding Zhejie , Chuang Chia-Hsun , Yu Yu , Garrison Lehman H , Bayer Adrian E , Feng Yu , Modi Chirag , Eisenstein Daniel J , White Martin , Variu Andrei , Zhao Cheng , Zhang Hanyu , Meneses Rizo Jennifer , Brooks David , Dawson Kyle , Doel Peter , Gaztanaga Enrique , Kehoe Robert , Krolewski Alex , Landriau Martin , Palanque-Delabrouille Nathalie , Poppett Claire
Published: June 2022

Dark Energy Spectroscopic Instrument (DESI) will construct a large and precise three-dimensional map of our Universe. The survey effective volume reaches $\sim 20\, h^{-3}\, \mathrm{Gpc}^{3}$. It is a great challenge to prepare high-resolution simulations with a much larger volume for validating the DESI analysis pipelines. AbacusSummit is a suite of high-resolution dark-matter-only simulations designed for this purpose, with $200\, h^{-3}\, \mathrm{Gpc}^{3}$ (10 times DESI volume) for the base cosmology. However, further efforts need to be done to provide a more precise analysis of the data and to cover also other cosmologies. Recently, the CARPool method was proposed to use paired accurate and approximate simulations to achieve high statistical precision with a limited number of high-resolution simulations. Relying on this technique, we propose to use fast quasi-N-body solvers combined with accurate simulations to produce accurate summary statistics. This enables us to obtain 100 times smaller variance than the expected DESI statistical variance at the scales we are interested in, e.g. $k \lt 0.3\, h\, \mathrm{Mpc}^{-1}$ for the halo power spectrum. In addition, it can significantly suppress the sample variance of the halo bispectrum. We further generalize the method for other cosmologies with only one realization in AbacusSummit suite to extend the effective volume ∼20 times. In summary, our proposed strategy of combining high-fidelity simulations with fast approximate gravity solvers and a series of variance suppression techniques sets the path for a robust cosmological analysis of galaxy survey data.
Multi-wavelength studies of the X-ray binary MAXI J1727 − 203: constraining system parameters
Authors: Wang Sili , Kawai Nobuyuki , Shidatsu Megumi , Murata Katsuhiro , Hosokawa Ryohei , Hanayama Hidekazu , Horiuchi Takashi , Morihana Kumiko
Published: June 2022

We report on the evolution of X-ray spectral and timing properties of the X-ray binary MAXI J1727 − 203 based on NICER/XTI and MAXI/GSC observations. Over the course of the outburst, a transition from the intermediate state to the high/soft state, and then back to the low/hard state was observed. During the high/soft state, the innermost radius estimated from the multi-colour disc model remained constant at $\sim 145.0\ (\frac{D}{10\ \mathrm{kpc}}) \ {(\frac{\cos i}{\cos 0^{\circ }})}^{-1/2}$ km, where D is the source distance and i is the inclination. Assuming that the binary system contain a Schwarzschild black hole and has an inclination angle of 0°–84°, and considering the typical Eddington ratio at the transition back to the low/hard state, the black hole mass was estimated to be M ≥ 11.5 M⊙ for a distance of D ≥ 5.9 kpc. We also attempted to constrain the black hole mass and distance with a different method by combining the results from optical and near-infrared photometric observations. We modelled the near-infrared to X-ray spectral energy distributions obtained in the outburst period with an irradiated disk model, and estimated the lower limit of the black hole mass for a given distance, assuming both accretion disk and companion star fill their Roche lobe. The lower limit was, however, found to be much higher than the constraint obtained from the X-ray data. We discuss several possible causes of this inconsistency. It is difficult to fully resolve the conflict by a single cause and hence a combination of causes is required.
Functional Diversity and Evolution of Bitter Taste Receptors in Egg-Laying Mammals
Authors: Itoigawa Akihiro , Hayakawa Takashi , Zhou Yang , Manning Adrian D. , Zhang Guojie , Grutzner Frank , Imai Hiroo
Published: June 2022

Egg-laying mammals (monotremes) are a sister clade of therians (placental mammals and marsupials) and a key clade to understand mammalian evolution. They are classified into platypus and echidna, which exhibit distinct ecological features such as habitats and diet. Chemosensory genes, which encode sensory receptors for taste and smell, are believed to adapt to the individual habitats and diet of each mammal. In this study, we focused on the molecular evolution of bitter taste receptors (TAS2Rs) in monotremes. The sense of bitter taste is important to detect potentially harmful substances. We comprehensively surveyed agonists of all TAS2Rs in platypus (Ornithorhynchus anatinus) and short-beaked echidna (Tachyglossus aculeatus) and compared their functions with orthologous TAS2Rs of marsupial and placental mammals (i.e., therians). As results, the agonist screening revealed that the deorphanized monotreme receptors were functionally diversified. Platypus TAS2Rs had broader receptive ranges of agonists than those of echidna TAS2Rs. While platypus consumes a variety of aquatic invertebrates, echidna mainly consumes subterranean social insects (ants and termites) as well as other invertebrates. This result indicates that receptive ranges of TAS2Rs could be associated with feeding habits in monotremes. Furthermore, some orthologous receptors in monotremes and therians responded to β-glucosides, which are feeding deterrents in plants and insects. These results suggest that the ability to detect β-glucosides and other substances might be shared and ancestral among mammals.
On the rate of phytoplankton respiration in the light
Authors: Bender Michael L , Zhu Xin-Guang , Falkowski Paul , Ma Fangfang , Griffin Kevin
Published: June 2022

The rate of algal and cyanobacterial respiration in the light is an important ecophysiological term that remains to be completely characterized and quantified. To address this issue, we exploited process-specific decarboxylation rates from flux balance analysis and isotopically nonstationary metabolic flux analysis. Our study, based on published data, suggested that decarboxylation is about 22% of net CO2 assimilation when the tricarboxylic acid cycle is completely open (characterized by the commitment of alpha ketoglutarate to amino acid synthesis and very low rates of succinate formation). This estimate was supported by calculating the decarboxylation rates required to synthesize the major components of biomass (proteins, lipids, and carbohydrates) at their typical abundance. Of the 22 CO2 molecules produced by decarboxylation (normalized to net assimilation = 100), approximately 13 were from pyruvate and 3 were from isocitrate. The remaining six units of decarboxylation were in the amino acid synthesis pathways outside the tricarboxylic acid cycle. A small additional flux came from photorespiration, decarboxylations of six phosphogluconate in the oxidative pentose phosphate pathway, and decarboxylations in the syntheses of lower-abundance compounds, including pigments and ribonucleic acids. This general approach accounted for the high decarboxylation rates in algae and cyanobacteria compared to terrestrial plants. It prompts a simple speculation for the origin of the Kok effect and helps constrain the photoautotrophic respiration rate, in the light, in the euphotic zone of the ocean and lakes.
Human IgE monoclonal antibody recognition of mite allergen Der p 2 defines structural basis of an epitope for IgE cross-linking and anaphylaxis in vivo
Authors: Khatri Kriti , Richardson Crystal M , Glesner Jill , Kapingidza Anyway Brenda , Mueller Geoffrey A , Zhang Jian , Dolamore Cole , Vailes Lisa D , Wünschmann Sabina , Peebles R Stokes , Chapman Martin D , Smith Scott A , Chruszcz Maksymilian , Pomés Anna
Published: June 2022

Immunoglobulin E (IgE) antibody is a critical effector molecule for adaptive allergen-induced immune responses, which affect up to 40% of the population worldwide. Allergens are usually innocuous molecules but induce IgE antibody production in allergic subjects. Allergen cross-linking of IgE bound to its high affinity receptor (FcεRI) on mast cells and basophils triggers release of histamine and other mediators that cause allergic symptoms. Little is known about the direct allergen–IgE antibody interaction due to the polyclonal nature of serum IgE and the low frequency of IgE-producing B cells in blood. Here, we report the X-ray crystal structure of a house dust mite allergen, Der p 2, in complex with Fab of a human IgE monoclonal antibody (mAb) isolated by hybridoma technology using human B cells from an allergic subject. This IgE mAb, 2F10, has the correct pairing of heavy and light chains as it occurs in vivo. Key amino acids forming the IgE epitope on Der p 2 were identified. Mutation of these residues ablated their functional ability to cross-link IgE in a mouse model of passive systemic anaphylaxis. These analyses revealed an important conformational epitope associated with the IgE antibody repertoire to a major mite allergen.
Chordomas: From Stem to Stern
Authors: Freiburg Luke , Demos Terrence C.
Published: June 2022

Although rare, chordomas can affect the entire axial skeleton, and they are the most common primary malignant bone tumor in both the sacrum and the spine. This article details tumor origin, epidemiology, pathology, and imaging features, in an effort to improve the ability of the radiologist to diagnose, provide a differential diagnosis, and further understand treatment of patients with chordomas.