bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of a Modified Transformer Architecture Based on Relative Position Coding
Authors: Zheng Wenfeng , Gong Gu , Tian Jiawei , Lu Siyu , Wang Ruiyang , Yin Zhengtong , Li Xiaolu , Yin Lirong
Published: October 2023

Natural language processing (NLP) based on deep learning provides a positive performance for generative dialogue system, and the transformer model is a new boost in NLP after the advent of word vectors. In this paper, a Chinese generative dialogue system based on transformer is designed, which only uses a multi-layer transformer decoder to build the system and uses the design of an incomplete mask to realize one-way language generation. That is, questions can perceive context information in both directions, while reply sentences can only output one-way autoregressive. The above system improvements make the one-way generation of dialogue tasks more logical and reasonable, and the performance is better than the traditional dialogue system scheme. In consideration of the long-distance information weakness of absolute position coding, we put forward the improvement of relative position coding in theory, and verify it in subsequent experiments. In the transformer module, the calculation formula of self-attention is modified, and the relative position information is added to replace the absolute position coding of the position embedding layer. The performance of the modified model in BLEU, embedding average, grammatical and semantic coherence is ideal, to enhance long-distance attention.
Efficient and rapid control of Eurasian watermilfoil (Myriophyllum spicatum) by combining benthic mats and hand pulling
Authors: Gagné Vincent , Lavoie Claude
Published: October 2023

Eurasian watermilfoil (Myriophyllum spicatum L.) is an aquatic vascular plant that forms extensive dense beds in lakes. This invader competes with native plants, interferes with aquatic activities, and decreases riparian property values. In Canada, the use of aquatic herbicides is highly restricted. Environmental managers must therefore rely on physical methods such as hand pulling or benthic matting for control. Although these methods are not new, there has been little scientific investigation regarding their effectiveness and cost over multiple years. Benthic matting and hand pulling were used in Lac des Abénaquis (area: 1.2 km2) to control 3.6 ha of M. spicatum beds. Initiated by citizens in 2016, control procedures were scientifically studied in 2020 and 2021. Benthic fiberglass mats were deployed on dense M. spicatum patches for 10 wk. Isolated plants and patches <100 m2 were hand pulled by divers, and the harvested material surfaced via a suction hose or in hand-filled bags. By August 2021, all the M. spicatum patches had been eliminated, and only 560 widely scattered plants remained. Over the last 2 yr of control, hand pulling required 243 person-hours and removed 2,245 kg of biomass. The biomass brought to the surface was 2.4 times higher per person-hour with the suction system than with bags. The use of 1,000 m2 of benthic mats required 47 to 51 person-hours per summer season, including installation, removal, and maintenance. Intensive management (years 1 to 5) using benthic mats and hand pulling cost an estimated Can$185,000 (US$140,000) ha−1 of M. spicatum bed. Hand pulling of scattered individuals (years 6+), estimated at Can$20,000 (US$15,000) per summer, is essential to avoid reinfestation. An invasion of M. spicatum can successfully be managed in small lakes without herbicides, but control remains a costly and long-term endeavor.
Heat transfer in a quasi-one-dimensional Rayleigh–Bénard convection cell
Authors: Zhang Lu , Xia Ke-Qing
Published: October 2023

We report an experimental and numerical study on Rayleigh–Bénard convection in a slender rectangular geometry with the aspect ratio

$\varGamma$

varying from 0.05 to 0.3 and a Rayleigh number range of

$10^5\leqslant Ra\leqslant 3\times 10^9$

. The Prandtl number is fixed at

$Pr=4.38$

. It is found that the onset of convection is postponed when the convection domain approaches the quasi-one-dimensional limit. The onset Rayleigh number shows a

$Ra_c=328\varGamma ^{-4.18}$

scaling for the experiment and a

$Ra_c=810\varGamma ^{-3.95}$

scaling for the simulation, both consistent with a theoretical prediction of

$Ra_c\sim \varGamma ^{-4}$

. Moreover, the effective Nusselt–Rayleigh scaling exponent

$\beta =\partial (\log Nu)/\partial (\log Ra)$

near the onset of convection also shows a rapid increase with decreasing

$\varGamma$

. Power-law fits to the experimental and numerical data yield

$\beta =0.290\varGamma ^{-0.90}$

and

$\beta =0.564\varGamma ^{-0.92}$

, respectively. Near onset, the flow shows a stretched cell structure. In this regime, the velocity and temperature variations in a horizontal cross-section are found to be almost invariant with height in the core region of a slender domain. As the Rayleigh number increases, the system evolves from the viscous dominant regime to a plume-controlled one, a feature of which is enhancement in the heat transport efficiency. Upon further increase of

$Ra$

, the flow comes back to the classical boundary-layer-controlled regime, in which the quasi-one-dimensional geometry has no apparent effect on the global heat transfer.
Internal shear layers in librating spherical shells: the case of attractors
Authors: He Jiyang , Favier Benjamin , Rieutord Michel , Le Dizès Stéphane
Published: October 2023

Following our previous work on periodic ray paths (Heet al.,J. Fluid Mech., vol. 939, 2022, A3), we study asymptotically and numerically the structure of internal shear layers for very small Ekman numbers in a three-dimensional spherical shell and in a two-dimensional cylindrical annulus when the rays converge towards an attractor. We first show that the asymptotic solution obtained by propagating the self-similar solution generated at the critical latitude on the librating inner core describes the main features of the numerical solution. The internal shear layer structure and the scaling for its width and velocity amplitude in$E^{1/3}$and$E^{1/12}$, respectively, are recovered. The amplitude of the asymptotic solution is shown to decrease to$E^{1/6}$when it reaches the attractor, as is also observed numerically. However, some discrepancies are observed close to the particular attractors along which the phase of the wave beam remains constant. Another asymptotic solution close to those attractors is then constructed using the model of Ogilvie (J. Fluid Mech., vol. 543, 2005, pp. 19–44). The solution obtained for the velocity has an$O(E^{1/6})$amplitude, but a self-similar structure different from the critical-latitude solution. It also depends on the Ekman pumping at the contact points of the attractor with the boundaries. We demonstrate that it reproduces correctly the numerical solution. Surprisingly, the numerical solution close to an attractor with phase shift (that is, an attractor touching the axis in three or two dimensions with a symmetric forcing) is also found to be$O(E^{1/6})$, but its amplitude is much weaker. However, its asymptotic structure remains a mystery.
Fluid dynamics in intracranial aneurysms treated with flow-diverting stents: effect of multiple geometrical parameters
Authors: Chassagne Fanette , Barbour Michael C. , Levitt Michael R. , Aliseda Alberto
Published: October 2023

Characterizing the haemodynamics in intracranial aneurysms is of high interest as it impacts aneurysm growth, rupture and treatment, especially with flow-diverting stents (FDS). Flow in these geometries is known to depend on the Dean, Reynolds and Womersley numbers,$De$,$Re$,$Wo$, but is also influenced by geometrical parameters such as the sac shape or the size of the opening. Via particle image velocimetry, this parametric study aimed at evaluating the combined effects of$Re$,$De$,$Wo$and the geometry of the aneurysmal sac on the haemodynamics before and after treatment with FDS. Eight ellipsoidal idealized aneurysm models were created with two curvatures of the parent vessel, two aspect ratios of the sac and two neck sizes. Before treatment, a single counter-rotating vortex, whose strength increases with$Re$and$De$, as well as with the neck size and the aspect ratio, was observed in the sac for all but one geometry. After treatment with FDS, four different flow topologies were observed, depending on the geometry: no separation, separation for part of the cycle, two opposing vortices or a single counter-rotating vortex. A linear model with interaction revealed the predominant effect of$De$and the curvature of the parent vessel on the haemodynamics before and after treatment. This work once more demonstrated the primary role of haemodynamics in the treatment of intracranial aneurysms with FDS. Future work will consider the complexity of patient-specific geometries, and their effects on both the haemodynamics in the sac and the porosity of the FDS.
Normal families and quasiregular mappings
Authors: Fletcher Alastair N. , Nicks Daniel A.
Published: October 2023

Beardon and Minda gave a characterization of normal families of holomorphic and meromorphic functions in terms of a locally uniform Lipschitz condition. Here, we generalize this viewpoint to families of mappings in higher dimensions that are locally uniformly continuous with respect to a given modulus of continuity. Our main application is to the normality of families of quasiregular mappings through a locally uniform Hölder condition. This provides a unified framework in which to consider families of quasiregular mappings, both recovering known results of Miniowitz, Vuorinen and others and yielding new results. In particular, normal quasimeromorphic mappings, Yosida quasiregular mappings and Bloch quasiregular mappings can be viewed as classes of quasiregular mappings which arise through consideration of various metric spaces for the domain and range. We give several characterizations of these classes and obtain upper bounds on the rate of growth in each class.
The Valuation of Collateral in Bank Lending
Authors: Luck Stephan , Santos João A. C.
Published: October 2023

We study the valuation of collateral by comparing spreads on loans by the same bank, to the same borrower, at the same origination date, but backed by different types of collateral. Pledging collateral reduces borrowing costs by 23 BPS on average. The effect varies across different types of collateral, with marketable securities being most valuable, and real estate and accounts receivables and inventory being more valuable than fixed assets and a blanket lien. Further, the rate reduction from pledging collateral is sensitive to the value of the underlying collateral, and collateral tends to be more valuable for smaller and private firms and for loans with longer maturity.
Development and application of recombinase polymerase amplification assay for rapid detection of Blastocystis sp.
Authors: Mei Xuefang , Su Changwei , Zhang Shanrui , Jia Luwei , Yang Zhenke , Tian Xiaowei , Zhang Zhenchao , Wang Shuai
Published: October 2023

Blastocystis sp. is a common parasite in the intestinal tract of humans and animals. The clinical diagnosis of Blastocystis sp. mainly depends on the microscopic observation of parasite, which can lead to false-negative results. An accurate and convenient diagnostic approach for Blastocystis sp. infection is crucial for effectively preventing and controlling blastocystosis. Herein, we developed a recombinase polymerase amplification (RPA) method for detecting Blastocystis sp. The results showed that the DNA amplification by RPA established in this study could be performed within 5 min at 37°C, with maximum band intensity observed at 30 min. The minimum detection limit of RPA was 100 fg μL−1, consistent with conventional polymerase chain reaction (cPCR). Furthermore, the RPA method exhibited no cross-reactivity with 7 other non-target pathogens in the intestinal tract. Next, the newly established RPA method was used to analyse 40 fecal samples collected clinically, and the detection results were consistent with cPCR. These results corroborate that the newly developed RPA method has good sensitivity and specificity and offers the advantage of short detection times, which can be harnessed for differential diagnosis and rapid detection of Blastocystis sp.
Aquinas's science-engaged theology
Authors: Silva Ignacio , Recio Gonzalo
Published: October 2023

Science-engaged theology has emerged as a new way of conducting research within the vast field of science and religion, with the aim of, at least in one way of understanding it today, solving theological puzzles. In this article we suggest that an analysis of the diversity of approaches in which thirteenth-century philosopher and theologian Thomas Aquinas engaged theological questions with the best knowledge of the natural world available at the time allows twenty-first century science-engaged theologians to move forward the discussion about the different ways of engaging theology with the contemporary natural sciences.
SERMONS, HOMILIARIES AND PLAINSONG FOR THE NIGHT OFFICE: THE CASE OF STEPHEN THE PROTOMARTYR
Authors: Brand Benjamin
Published: October 2023

While the great majority of Franco-Roman plainsong features lyrics adapted from the Bible, a long recognised but little studied minority sets excerpts from patristic sermons and commentaries. The antiphons and responsories for the night office on the feast of St Stephen are a case study of such literary borrowing. The lyrics of these chants feature a wide range of verbal debts and reminiscences from sermons written or inspired by Augustine, the majority of which were transmitted in the seventh-century Roman homiliary and thus recited as lessons at matins. Together, the plainsong and lessons develop a distinctively Augustinian portrait of Stephen as a kind, compassionate advocate for his persecutors rather than as the hard-nosed rhetorician he is depicted to be in the Bible. They thus illuminate the working methods and theological priorities of Roman lyricists as they crafted verbal texts for sung delivery in the Divine Office.
Transmediation, Transgression and Popularization: A Study of the Cantonese Opera Film White Snake
Authors: Feng Wei
Published: October 2023

The preservation of declining xiqu heritage through remediation and transmediation has often been ineffective in attracting a wider audience. The Cantonese opera film White Snake (2021), with its unusual utilization of computer-generated technology and transgressive combination of various media, offers a fresh approach to popularizing xiqu among younger audiences. To overcome aesthetic differences between cinema and xiqu, the film transforms medium specificities and transmedial potentials of Song landscape paintings and martial-arts film, adapting them to a new scenic and choreographic setting. By altering the original play’s sensory and semiotic modalities, White Snake’s transmedia aspects blaze a new trail for popularizing xiqu heritage for a new generation.
Towards an Intermedial Theory of Medial Agency: Environing Media
Authors: Bruhn Jørgen
Published: October 2023

Based on a rough conceptual divide of (parts of) media studies, including intermedial studies, this article presents two positions based on interests in media as transmission and representation, or media as ecological frame, or media agency. Following that, the article discusses how a new concept in environmental studies, ‘environing media’ or ‘environing technologies’ – where representation and media ecological agency seem to find a fruitful meeting point – is discussed in more detail. That description and discussion are put into a debate with central ideas of intermedial studies, before the final part of the article briefly exemplifies the theoretical ideas in the case of the IPCC report’s Summary for Policymakers (2021).
Where you stand depends on where you sit: inconsistencies in Taiwan legislators' positions on importing US meat
Authors: Chen Ian Tsung-yen , Wu Kayden Yi-hsun
Published: October 2023

This study examines the political dynamics that shape legislators' policy positions on importing US meat into Taiwan during the past decade, focusing on the cases of US beef in 2012 and US pork in 2021. The trade policy surrounding this issue has become politically contentious, involving conflicting national interests and constituency preferences. Legislators face a dilemma, torn between prioritizing the interests of their constituents and aligning with their party's interests. The central argument posits that legislators affiliated with the ruling party are more inclined to advocate for or adjust their stances to support the removal of import bans on American meat, while those associated with the opposition party tend to exhibit a greater reluctance to endorse such a stance. Factors such as the legislators' constituent's interests, district vs party-list affiliations, the urban–rural divide, or education level do not consistently explain legislators' positions on the US meat trade policy. To examine these arguments, this study employs a mixed-method approach, incorporating quantitative analysis and two case studies of individual legislators. The findings of this study offer empirical support for the central proposition.
Parsi capital and imperial infrastructure: Shipping and shopping in the port of Aden, 1840-1888
Authors: Toussia Cohen Itamar
Published: October 2023

For a century following the opening of the Suez Canal, the scale and scope of global capital and information flows was predicated on a chain of imperial outposts like Aden, where ships could replenish their fuel supplies while shorefront godowns and telegraph stations gathered commodities and information to be received, processed, and relayed; by the 1950s, over 5,000 vessels called on the harbour annually, making Aden the second busiest port in the world after New York. This article explores the role of Indian-Zoroastrian (Parsi) capital in shaping the material and institutional development of the port of Aden. Parsi firms mediated between international shipping and the hostile environment of the desert colony, supplying provisions and providing brokerage and agency, or dubash services, literally meaning ‘translator’ in the vernacular. More than a particularly successful comprador community, however, Aden Parsis developed an elaborate transoceanic trade predicated on self-financed, capital-intensive infrastructure projects. Tracing the outsourcing of imperial statecraft to dubashes in Aden allows us to provincialize the making of first-wave globalization, as it was predominantly Parsi capitalists rather than European businessmen who were the driving forces of Aden’s development.
Home is Together: Sounds of Belonging in the Correspondence of Two Japanese American Families Separated by Wartime Incarceration
Authors: Barbour Alecia D.
Published: October 2023

During World War II, Japanese nationals and U.S. residents Shigezo Iwata and Masaru Ben Akahori were arrested and interned while their wives and children were incarcerated separately. Though wartime correspondence sent from Mr. Akahori to his wife and daughter and from Mrs. Iwata to her husband clearly identifies the United States as “home,” the primary emphasis on home is as a marker of familial reunification. This article posits that the memories and sounds imaginatively recollected and conveyed within the correspondence sent from Sonoko Iwata to her husband, Shigezo, and from Masaru Ben Akahori to his wife, Kiku, and their daughter, served to signify and nurture an ongoing sense of belonging to and togetherness with their respective family members with whom they hoped to once again be home, together.
Increasing the safeguarding of protected areas threatened by warfare through international environmental law
Authors: de Hemptinne Jérôme
Published: October 2023

Vulnerable ecological areas are often seriously impacted by armed conflicts. In theory, these areas could benefit from the safeguards offered by the international humanitarian law (IHL) regimes of “demilitarized zones” and “undefended localities”, but in practice, these regimes – which are designed to protect human beings from the violence of hostilities, and whose application entirely depends on the goodwill of belligerents – are rarely triggered to protect the environment as such. However, international environmental law (IEL) contains a rich and diversified normative framework which organizes the establishment and management of areas of major ecological importance. While this framework has not primarily been conceived to apply to war-related situations, it could nonetheless play a substantive role in strengthening the IHL normative regimes in two respects. Firstly, it could provide interpretative guidance for these regimes so that they can be oriented towards more “ecocentric” purposes and can be read in accordance with the most advanced IEL standards and mechanisms governing biodiversity hotspots (the “environmentalization” of IHL). Secondly, IEL norms and practices could directly apply during warfare and thus complement IHL in many respects. That said, the co-application of IEL and IHL raises difficult issues of compatibility between these regimes, requiring inter alia that the IEL framework governing protected areas be adapted to the needs and specificities of armed conflicts (the “humanitarization” of IEL).
Gesundheitspolitik
Authors: Rosenstock Rolf , Gerlinger Thomas
Published: October 2023

Gesundheitspolitische Grundfragen, übertragen auf das Gesundheitswesen
Gesundheitspolitik ist mehr als die Steuerung und Finanzierung der Krankenversorgung. Vielmehr wird sie in diesem Buch verstanden als gesellschaftliches Management von Gesundheitsrisiken vor und nach ihrem Eintritt – also in Prävention und Krankenversorgung. Dabei sollte Gesundheitspolitik das Ziel verfolgen, den Gesundheitszustand und die Versorgungsqualität für die gesamte Bevölkerung zu verbessern. Damit wird ein moderner und systematischer Zugang zu diesem Gegenstand eröffnet, der sowohl gesundheitswissenschaftliche als auch sozial- und politikwissenschaftliche Aspekte zusammenführt, und sich an den Zielen Effizienz und Chancengleichheit orientiert.
Diese aktualisierte vierte Auflage analysiert Interessen, Institutionen, Normen, Akteure und Ressourceneinsatz im Hinblick auf ihren tatsächlichen und möglichen Beitrag zu einer so verstandenen Gesundheitspolitik. Themen des Buches sind u.a.:
•   Geschichte und Typen von Gesundheitspolitik
•   Prävention und Gesundheitsförderung
•   Strukturen und Finanzierung des Krankenversicherungssystems
•   Krankenversorgung (ambulante und stationäre Versorgung sowie Arzneimittelversorgung)
•   Rehabilitation und Langzeitpflege
The Real-Time Application of an Additional HRV Reduction Algorithm to Detect Negative Psychosocial States
Authors: Rominger Christian , Schwerdtfeger Andreas R.
Published: October 2023

Abstract: Unobtrusively identifying adverse psychosocial states in everyday life would offer intriguing possibilities to trigger just-in-time adaptive interventions (JITAIs). Previously, we simulated algorithms to predict psychosocial states by means of cardiac data (so-called, additional, nonmetabolic heart rate variability reductions; AddHRVr). For the first time, this study implemented the AddHRVr algorithm in real-time mode to evaluate whether we could predict stress, perseverative cognition, or low-quality social interactions. We applied an ecological momentary assessment (EMA) in a sample of 36 participants for five consecutive days. The functioning of the AddHRVr algorithm did not translate into real-world application, and higher stress, perseverative cognition, or low-quality social interactions following the AddHRVr trigger could not be confirmed. Further data simulations were conducted to evaluate the reasons for the algorithm’s malfunctioning. We provide recommendations for future studies and call for further research and technical refinements to better align simulation approaches with real-time applications.
Response of Dissolved Trace Metals to Dust Storms, Sediment Resuspension, and Flash Floods in Oligotrophic Oceans
Authors: Benaltabet T. , Lapid G. , Torfstein A.
Published: October 2023

Trace metals (TM) delivered by atmospheric dust play a key role in oceanic biogeochemical cycles. However, the impact of short‐term environmental perturbations such as dust storms and sediment resuspension events on the oceanic water column is poorly constrained due to the low temporal sampling resolution and episodic nature of these events. The Gulf of Aqaba (GoA), Red Sea, is a highly accessible deep oligotrophic water body featuring exceptionally high atmospheric deposition fluxes that provide the main source of TMs to the GoA surface water. Here, we present a 2‐year time series of dissolved manganese, cobalt, nickel, copper, zinc, cadmium, and phosphate concentration profiles sampled in the GoA. The study focuses on daily time scale dust storms and episodes of sediment resuspension to quantify the immediate impact of these events on dissolved TM cycling. Counter‐intuitively, upper mixed layer TM inventories decrease with increasing aerosol loads, with the effects of aerosol‐induced TM scavenging and dissolution peaking 5–6 days after aerosol deposition. Dust storms promote intense TM scavenging, with TM inventories decreasing by up to 44%, but seldom lead to TM enrichment. Similarly, sediment resuspension and flash flood events triggered significant TM scavenging. These findings highlight the potential dual role of atmospheric deposition in the oceans as a long‐term source of dissolved TMs and a short‐term sink. The in situ observations presented here may be used to understand and quantify the global impact of abrupt environmental events on oceanic chemical compositions.
The Geometry, Spatial Distribution and Texture of Slate‐Hosted Calcite Veins in the Helvetic Flysch Units—Insights in Structural and Fluid Processes Within a Paleo‐Accretionary Complex
Authors: Akker Ismay Vénice , Schrank Christoph , Herwegh Marco , Berger Alfons , Jones Michael , Kewish Cameron M.
Published: October 2023

The exhumed Infrahelvetic Flysch Units in the eastern central Alps in Switzerland are a field analog to modern accretionary wedges at active plate boundaries. In these seismically active convergent settings, water‐saturated sediments undergo consolidation, and diagenetic to low‐grade metamorphic processes cause complex fluid‐rock interactions. To contribute to the understanding of structural and fluid processes and their interaction with seismic activity, we present quantitative information on the geometrical and spatial distribution of slate‐hosted calcite veins from the Infrahelvetic Flysch Units that show mutual overprinting relationships with the ductile phyllosilicate‐rich matrix. Two vein systems that form in the deeper part of the inner wedge are characterized: (a) layer‐parallel veins (meter‐scale) forming spatially repetitive vein‐arrays and (b) pervasively distributed, steep micron‐veinlets, that cross‐cut the thicker layer‐parallel veins and the ductile matrix. Synchrotron X‐ray Fluorescence Microscopy (XFM) is instrumental in detecting previously unseen densely spaced micron‐veinlets. The spatial distribution of micron‐veinlets indicates pervasive layer‐perpendicular fluid transport in response to dissolution‐precipitation creep through the wedge. Layer‐parallel veins form vein‐arrays with thicknesses on the meter‐scale suggesting that fluids are progressively localized in channels up‐scale. Both vein sets form in an alternating fashion with two different enhanced flux directions, which could be indicative for a critically stressed wedge with near‐lithostatic fluid pressures. The layer‐parallel veins and vein‐arrays could represent seismic events with low magnitude earthquakes (Mw up to 4.0) or slow‐slip events currently found at active plate boundaries, while micron‐veinlets and dissolution‐precipitation processes accommodate slow interseismic deformation.
Decadal Modulation of the Relationship Between Tropical Southern Atlantic SST and Subsequent ENSO by Pacific Decadal Oscillation
Authors: Zhang Shaoyu , Liu Yimin , Dong Buwen , Sheng Chen
Published: October 2023

This study identifies the relationship between tropical southern Atlantic (TSA) sea surface temperature anomaly (SSTA) and the El Niño‐Southern Oscillation (ENSO) and focuses on how the Pacific Decadal Oscillation (PDO) modulates this relationship. Results suggest a significant but non‐stationary interannual TSA‐ENSO relationship which undergoes a significant decadal shift. A strong TSA‐ENSO relationship is observed during the positive PDO phase, while this relationship is weak during the negative PDO phase. Two processes, involving the anomalous Pacific Walker circulation (PWC) and the intensity of air‐sea interactions over the Pacific, are proposed for this decadal shift. During the positive PDO phase, the weak and variable PWC and strong air‐sea interaction facilitate the development of SSTA in the tropical Pacific triggered by TSA SSTA, resulting in a strong TSA‐ENSO relationship and vice versa. These findings emphasize the important role of the modulation of PDO on the TSA‐ENSO relationship.
Identification and cultivation of anaerobic bacterial scavengers of dead cells
Authors: Hirakata Yuga , Mei Ran , Morinaga Kana , Katayama Taiki , Tamaki Hideyuki , Meng Xian-ying , Watari Takahiro , Yamaguchi Takashi , Hatamoto Masashi , Nobu Masaru K
Published: October 2023

The cycle of life and death and Earth’s carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
Chromatin-modifying enzymes as modulators of nuclear size during lineage differentiation
Authors: Meng Lingjun
Published: October 2023

The mechanism of nuclear size determination and alteration during normal lineage development and cancer pathologies which is not fully understood. As recently reported, chromatin modification can change nuclear morphology. Therefore, we screened a range of pharmacological chemical compounds that impact the activity of chromatin-modifying enzymes, in order to get a clue of the specific types of chromatin-modifying enzymes that remarkably effect nuclear size and shape. We found that interrupted activity of chromatin-modifying enzymes is associated with nuclear shape abnormalities. Furthermore, the activity of chromatin-modifying enzymes perturbs cell fate determination in cellular maintenance and lineage commitment. Our results indicated that chromatin-modifying enzyme regulates cell fate decision during lineage differentiation and is associate with nuclear size alteration.
Domain adapted brain network fusion captures variance related to pubertal brain development and mental health
Authors: Kraft Dominik , Alnæs Dag , Kaufmann Tobias
Published: October 2023

Puberty demarks a period of profound brain dynamics that orchestrates changes to a multitude of neuroimaging-derived phenotypes. This complexity poses a dimensionality problem when attempting to chart an individual’s brain development over time. Here, we illustrate that shifts in subject similarity of brain imaging data relate to pubertal maturation in the longitudinal ABCD study. Given that puberty depicts a critical window for emerging mental health issues, we additionally show that our model is capable of capturing variance in the adolescent brain related to psychopathology in a population-based and a clinical cohort. These results suggest that low-dimensional reference spaces based on subject similarities render useful to chart variance in brain development in youths.
A deep population reference panel of tandem repeat variation
Authors: Ziaei Jam Helyaneh , Li Yang , DeVito Ross , Mousavi Nima , Ma Nichole , Lujumba Ibra , Adam Yagoub , Maksimov Mikhail , Huang Bonnie , Dolzhenko Egor , Qiu Yunjiang , Kakembo Fredrick Elishama , Joseph Habi , Onyido Blessing , Adeyemi Jumoke , Bakhtiari Mehrdad , Park Jonghun , Javadzadeh Sara , Jjingo Daudi , Adebiyi Ezekiel , Bafna Vineet , Gymrek Melissa
Published: October 2023

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.
A non-canonical striatopallidal Go pathway that supports motor control
Authors: Labouesse Marie A. , Torres-Herraez Arturo , Chohan Muhammad O. , Villarin Joseph M. , Greenwald Julia , Sun Xiaoxiao , Zahran Mysarah , Tang Alice , Lam Sherry , Veenstra-VanderWeele Jeremy , Lacefield Clay O. , Bonaventura Jordi , Michaelides Michael , Chan C. Savio , Yizhar Ofer , Kellendonk Christoph
Published: October 2023

In the classical model of the basal ganglia, direct pathway striatal projection neurons (dSPNs) send projections to the substantia nigra (SNr) and entopeduncular nucleus to regulate motor function. Recent studies have re-established that dSPNs also possess axon collaterals within the globus pallidus (GPe) (bridging collaterals), yet the significance of these collaterals for behavior is unknown. Here we use in vivo optical and chemogenetic tools combined with deep learning approaches in mice to dissect the roles of dSPN GPe collaterals in motor function. We find that dSPNs projecting to the SNr send synchronous motor-related information to the GPe via axon collaterals. Inhibition of native activity in dSPN GPe terminals impairs motor activity and function via regulation of Npas1 neurons. We propose a model by which dSPN GPe axon collaterals (striatopallidal Go pathway) act in concert with the canonical terminals in the SNr to support motor control by inhibiting Npas1 neurons.
A reprogrammable mechanical metamaterial with origami functional-group transformation and ring reconfiguration
Authors: Hu Xinyu , Tan Ting , Wang Benlong , Yan Zhimiao
Published: October 2023

Recent advancements in reprogrammable metamaterials have enabled the development of intelligent matters with variable special properties in situ. These metamaterials employ intra-element physical reconfiguration and inter-element structural transformation. However, existing mono-characteristic homo-element mechanical metamaterials have limited reprogramming functions. Here, we introduce a reprogrammable mechanical metamaterial composed of origami elements with heterogeneous mechanical properties, which achieves various mechanical behavior patterns by functional group transformations and ring reconfigurations. Through the anisotropic assembly of two heterogeneous elements into a functional group, we enable mechanical behavior switching between positive and negative stiffness. The resulting polygonal ring exhibits rotational deformation, zero Poisson’s ratio stretching/compression deformation, and negative Poisson’s ratio auxetic deformation. Arranging these rings periodically yields homogeneous metamaterials. The reconfiguration of quadrilateral rings allows for continuous fine-tunability of the mechanical response and negative Poisson’s ratio. This mechanical metamaterial could provide a versatile material platform for reprogrammable mechanical computing, multi-purpose robots, transformable vehicles and architectures at different scales.
The liver microenvironment orchestrates FGL1-mediated immune escape and progression of metastatic colorectal cancer
Authors: Li Jia-Jun , Wang Jin-Hong , Tian Tian , Liu Jia , Zheng Yong-Qiang , Mo Hai-Yu , Sheng Hui , Chen Yan-Xing , Wu Qi-Nian , Han Yi , Liao Kun , Pan Yi-Qian , Zeng Zhao-Lei , Liu Ze-Xian , Yang Wei , Xu Rui-Hua , Ju Huai-Qiang
Published: October 2023

Colorectal cancer (CRC) patients with liver metastases usually obtain less benefit from immunotherapy, and the underlying mechanisms remain understudied. Here, we identify that fibrinogen-like protein 1 (FGL1), secreted from cancer cells and hepatocytes, facilitates the progression of CRC in an intraportal injection model by reducing the infiltration of T cells. Mechanistically, tumor-associated macrophages (TAMs) activate NF-ĸB by secreting TNFα/IL-1β in the liver microenvironment and transcriptionally upregulate OTU deubiquitinase 1 (OTUD1) expression, which enhances FGL1 stability via deubiquitination. Disrupting the TAM-OTUD1-FGL1 axis inhibits metastatic tumor progression and synergizes with immune checkpoint blockade (ICB) therapy. Clinically, high plasma FGL1 levels predict poor outcomes and reduced ICB therapy benefits. Benzethonium chloride, an FDA-approved antiseptics, curbs FGL1 secretion, thereby inhibiting liver metastatic tumor growth. Overall, this study uncovers the critical roles and posttranslational regulatory mechanism of FGL1 in promoting metastatic tumor progression, highlighting the TAM-OTUD1-FGL1 axis as a potential target for cancer immunotherapy.
Synapsin condensation controls synaptic vesicle sequestering and dynamics
Authors: Hoffmann Christian , Rentsch Jakob , Tsunoyama Taka A. , Chhabra Akshita , Aguilar Perez Gerard , Chowdhury Rajdeep , Trnka Franziska , Korobeinikov Aleksandr A. , Shaib Ali H. , Ganzella Marcelo , Giannone Gregory , Rizzoli Silvio O. , Kusumi Akihiro , Ewers Helge , Milovanovic Dragomir
Published: October 2023

Neuronal transmission relies on the regulated secretion of neurotransmitters, which are packed in synaptic vesicles (SVs). Hundreds of SVs accumulate at synaptic boutons. Despite being held together, SVs are highly mobile, so that they can be recruited to the plasma membrane for their rapid release during neuronal activity. However, how such confinement of SVs corroborates with their motility remains unclear. To bridge this gap, we employ ultrafast single-molecule tracking (SMT) in the reconstituted system of native SVs and in living neurons. SVs and synapsin 1, the most highly abundant synaptic protein, form condensates with liquid-like properties. In these condensates, synapsin 1 movement is slowed in both at short (i.e., 60-nm) and long (i.e., several hundred-nm) ranges, suggesting that the SV-synapsin 1 interaction raises the overall packing of the condensate. Furthermore, two-color SMT and super-resolution imaging in living axons demonstrate that synapsin 1 drives the accumulation of SVs in boutons. Even the short intrinsically-disordered fragment of synapsin 1 was sufficient to restore the native SV motility pattern in synapsin triple knock-out animals. Thus, synapsin 1 condensation is sufficient to guarantee reliable confinement and motility of SVs, allowing for the formation of mesoscale domains of SVs at synapses in vivo.
How myosin VI traps its off-state, is activated and dimerizes
Authors: Canon Louise , Kikuti Carlos , Planelles-Herrero Vicente J. , Lin Tianming , Mayeux Franck , Sirkia Helena , Lee Young il , Heidsieck Leila , Velikovsky Léonid , David Amandine , Liu Xiaoyan , Moussaoui Dihia , Forest Emma , Höök Peter , Petersen Karl J. , Morgan Tomos E. , Di Cicco Aurélie , Sirés-Campos Julia , Derivery Emmanuel , Lévy Daniel , Delevoye Cédric , Sweeney H. Lee , Houdusse Anne
Published: October 2023

Myosin VI (Myo6) is the only minus-end directed nanomotor on actin, allowing it to uniquely contribute to numerous cellular functions. As for other nanomotors, the proper functioning of Myo6 relies on precise spatiotemporal control of motor activity via a poorly defined off-state and interactions with partners. Our structural, functional, and cellular studies reveal key features of myosin regulation and indicate that not all partners can activate Myo6. TOM1 and Dab2 cannot bind the off-state, while GIPC1 binds Myo6, releases its auto-inhibition and triggers proximal dimerization. Myo6 partners thus differentially recruit Myo6. We solved a crystal structure of the proximal dimerization domain, and show that its disruption compromises endocytosis in HeLa cells, emphasizing the importance of Myo6 dimerization. Finally, we show that the L926Q deafness mutation disrupts Myo6 auto-inhibition and indirectly impairs proximal dimerization. Our study thus demonstrates the importance of partners in the control of Myo6 auto-inhibition, localization, and activation.
Lipocalin 2 regulates mitochondrial phospholipidome remodeling, dynamics, and function in brown adipose tissue in male mice
Authors: Su Hongming , Guo Hong , Qiu Xiaoxue , Lin Te-Yueh , Qin Chao , Celio Gail , Yong Peter , Senders Mark , Han Xianlin , Bernlohr David A. , Chen Xiaoli
Published: October 2023

Mitochondrial function is vital for energy metabolism in thermogenic adipocytes. Impaired mitochondrial bioenergetics in brown adipocytes are linked to disrupted thermogenesis and energy balance in obesity and aging. Phospholipid cardiolipin (CL) and phosphatidic acid (PA) jointly regulate mitochondrial membrane architecture and dynamics, with mitochondria-associated endoplasmic reticulum membranes (MAMs) serving as the platform for phospholipid biosynthesis and metabolism. However, little is known about the regulators of MAM phospholipid metabolism and their connection to mitochondrial function. We discover that LCN2 is a PA binding protein recruited to the MAM during inflammation and metabolic stimulation. Lcn2 deficiency disrupts mitochondrial fusion-fission balance and alters the acyl-chain composition of mitochondrial phospholipids in brown adipose tissue (BAT) of male mice. Lcn2 KO male mice exhibit an increase in the levels of CLs containing long-chain polyunsaturated fatty acids (LC-PUFA), a decrease in CLs containing monounsaturated fatty acids, resulting in mitochondrial dysfunction. This dysfunction triggers compensatory activation of peroxisomal function and the biosynthesis of LC-PUFA-containing plasmalogens in BAT. Additionally, Lcn2 deficiency alters PA production, correlating with changes in PA-regulated phospholipid-metabolizing enzymes and the mTOR signaling pathway. In conclusion, LCN2 plays a critical role in the acyl-chain remodeling of phospholipids and mitochondrial bioenergetics by regulating PA production and its function in activating signaling pathways.
UV-induced G4 DNA structures recruit ZRF1 which prevents UV-induced senescence
Authors: De Magis Alessio , Limmer Michaela , Mudiyam Venkat , Monchaud David , Juranek Stefan , Paeschke Katrin
Published: October 2023

Senescence has two roles in oncology: it is known as a potent tumor-suppressive mechanism, which also supports tissue regeneration and repair, it is also known to contribute to reduced patient resilience, which might lead to cancer recurrence and resistance after therapy. Senescence can be activated in a DNA damage-dependent and -independent manner. It is not clear which type of genomic lesions induces senescence, but it is known that UV irradiation can activate cellular senescence in photoaged skin. Proteins that support the repair of DNA damage are linked to senescence but how they contribute to senescence after UV irradiation is still unknown. Here, we unraveled a mechanism showing that upon UV irradiation multiple G-quadruplex (G4) DNA structures accumulate in cell nuclei, which leads to the recruitment of ZRF1 to these G4 sites. ZRF1 binding to G4s ensures genome stability. The absence of ZRF1 triggers an accumulation of G4 structures, improper UV lesion repair, and entry into senescence. On the molecular level loss of ZRF1 as well as high G4 levels lead to the upregulation of DDB2, a protein associated with the UV-damage repair pathway, which drives cells into senescence.
Pathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections
Authors: Toledo Alejandro Gomez , Bratanis Eleni , Velásquez Erika , Chowdhury Sounak , Olofsson Berit , Sorrentino James T. , Karlsson Christofer , Lewis Nathan E. , Esko Jeffrey D. , Collin Mattias , Shannon Oonagh , Malmström Johan
Published: October 2023

Group A streptococcus (GAS) is a major bacterial pathogen responsible for both local and systemic infections in humans. The molecular mechanisms that contribute to disease heterogeneity remain poorly understood. Here we show that the transition from a local to a systemic GAS infection is paralleled by pathogen-driven alterations in IgG homeostasis. Using animal models and a combination of sensitive proteomics and glycoproteomics readouts, we documented the progressive accumulation of IgG cleavage products in plasma, due to extensive enzymatic degradation triggered by GAS infection in vivo. The level of IgG degradation was modulated by the route of pathogen inoculation, and mechanistically linked to the combined activities of the bacterial protease IdeS and the endoglycosidase EndoS, upregulated during infection. Importantly, we show that these virulence factors can alter the structure and function of exogenous therapeutic IgG in vivo. These results shed light on the role of bacterial virulence factors in shaping GAS pathogenesis, and potentially blunting the efficacy of antimicrobial therapies.
Switchable photothermal conversion efficiency for reprogrammable actuation
Authors: He Yongcheng , Liu Haojun , Luo Jiajia , Li Nuo , Li Lihua , Xiong Puxian , Gan Jiulin , Yang Zhongmin
Published: October 2023

Reprogrammable soft matter brings flexibility to soft robots so that they can display various motions, which is flourishing in soft robotics. However, the reprogramming of photoresponsive materials used in soft robots is time-consuming using existing methods. In this study, we promote a strategy for rapid reprogramming via switchable photothermal conversion efficiency (PCE). The liquid crystalline elastomers doped with semiconductor bismuth compounds (Bi-LCE) used in this work exhibited large photothermal actuation with over 35% shrinkage in 5 s at high PCE state, which demonstrated little deformation at low PCE state. Furthermore, the material was capable of being reprogrammed up to 10 times, with only 20 min required for one PCE reversible switch. Based on this switchable PCE effect, the same Bi-LCE film displayed various shape changes through different programmable pattern. Additionally, a reprogrammable hollow tube made of PCE reprogrammable materials could tune the diameter, cross-section configuration, and surface morphology, which was crucial for microfluidics field. Reprogrammable materials provide endless possibilities for reusability and sustainability in robotics.