bluuebunny/crossref_metadata_2025 huggingface dataset:
A Case Study of Cumulus Convection Over Land in Cloud‐Resolving Simulations With a Coupled Ray Tracer
Authors: Veerman M. A. , van Stratum B. J. H. , van Heerwaarden C. C.
Published: December 2022

We present simulations of cumulus convection over land with shortwave radiation computed by a Monte Carlo ray tracer coupled to the flow solver. Ray tracing delivers very realistic in‐cloud heating rates and global horizontal irradiance fields. The necessary performance of the ray tracer has been enabled by the raw power of graphics processing unit computing and from techniques for accelerating data lookup and ray tracer convergence. We used a case study over a grassland in the Netherlands to compare simulations with a coupled ray tracer to those with a conventional two‐stream solver, and to test ray tracer convergence. We demonstrate that the simulated cloud evolution is insensitive to the convergence of the ray tracing across a wide range of samples per pixel per spectral quadrature point. Furthermore, simulations with a coupled ray tracer produce surface irradiance patterns that resemble observations and that strongly feed back to the evolution of clouds via locally enhanced surface heat fluxes.
High and Dry: Billion‐Year Trends in the Aridity of River‐Forming Climates on Mars
Authors: Kite Edwin S. , Noblet Axel
Published: December 2022

Mars' wet‐to‐dry transition is a major environmental catastrophe, yet the spatial pattern, tempo, and cause of drying are poorly constrained. We built a globally distributed database of constraints on Mars late‐stage paleolake size relative to catchment area (aridity index (AI)), and found evidence for climate zonation as Mars was drying out. Aridity increased over time in southern midlatitude highlands, where lakes became proportionally as small as in modern Nevada. Meanwhile, intermittently wetter climates persisted in equatorial and northern‐midlatitude lowlands. This is consistent with a change in Mars' greenhouse effect that left highlands too cold for liquid water except during a brief melt season, or alternatively with a fall in Mars' groundwater table. The data are consistent with a switch of unknown cause in the dependence of AI on elevation, from high‐and‐wet early on, to high‐and‐dry later. These results sharpen our view of Mars' climate as surface conditions became increasingly stressing for life.
East Asian Monsoonal Climate Sensitivity Changed in the Late Pliocene in Response to Northern Hemisphere Glaciations
Authors: Zhang Ze , Licht Alexis , De Vleeschouwer David , Wang Zhixiang , Li Yanzhen , Kemp David B. , Tan Liangcheng , Zhang Rui , Qiang Xiaoke , Huang Chunju
Published: December 2022

Mio‐Pliocene sedimentary archives of the East Asian summer monsoon (EASM) in NE Tibet record a monotonic response to orbital forcing, dominated by eccentricity. By contrast, Pleistocene archives display a more stochastic response that varies regionally and temporally. When and why this response changed is poorly understood. Here, we present a new high‐resolution Rb/Sr ratio data set of EASM intensity from the Sanmenxia Basin, North China, that spans the Plio‐Pleistocene transition. Our results indicate decreased monsoonal rainfall in the late Pliocene, dated at 2.75–2.6 Ma, associated with an intensified response to obliquity and enhanced climate stochasticity. This transition is attributed to the increase of Northern Hemisphere ice volume. Quaternary monsoons display a sensitivity unique to the modern icehouse with large bipolar ice sheets, while pre‐Quaternary monsoons were solely impacted by Antarctic ice sheet dynamics on orbital time‐scales.
Plume‐Induced Rifting of Thickened Crust: 2D Numerical Model and Implications for N–S Rifts in Southern Tibet
Authors: Pang Yajin , Zhang Huai , Shi Yaolin , Gerya Taras
Published: December 2022

N–S rifting is one of the most typical tectonics in southern Tibet, but its formation mechanism remains controversial. Geophysical observations indicated spatial correlations between rifts and lithospheric mantle anomalies, presumably caused by asthenospheric upwelling. Here, we investigate possible plume‐induced rifting via a series of 2‐D thermomechanical models of plume interactions with a heterogeneous lithosphere. The numerical results indicate that a small‐scale mantle plume could promote the formation of a single giant rift throughout the whole thickened crust. In addition, presence of a weak mid‐crustal zone facilitates the rifting development in the upper crust while inhibiting the formation of a giant crustal rift. Instead, multiple rifts develop in the upper crust and thickened crust, jointly controlled by a heterogeneous weak crustal zone and mantle plume. Our numerical results thus emphasize the distinct roles of the weak mid‐crustal zone and small‐scale mantle plume in promoting N‒S rifting in southern Tibet.
Relationships of the Hygroscopicity of HULIS With Their Degrees of Oxygenation and Sources in the Urban Atmosphere
Authors: Zhou Ruichen , Deng Yange , Kunwar Bhagawati , Chen Qingcai , Chen Jing , Ren Lujie , Kawamura Kimitaka , Fu Pingqing , Mochida Michihiro
Published: December 2022

Humic‐like substances (HULIS) are unresolved compounds isolated from organic matter in atmospheric aerosols. Understanding the chemical structures and sources that control the hygroscopicity of HULIS is important for predicting its environmental impacts and possibly useful for parameterization of the hygroscopicity of organic aerosol (OA). Here, the hygroscopic growth of HULIS from total suspended particles samples in Beijing was analyzed using a hygroscopicity tandem differential mobility analyzer. The hygroscopicity parameter of HULIS (κHULIS) was determined to be 0.06 ± 0.03, and was found to correlate positively with O:C and f44 from offline aerosol mass spectrometry. Additionally, κHULIS was correlated positively with oxygenated organic aerosol (OOA) and correlated negatively with cooking OA and biomass burning OA, for which the source‐related OA types were from mass‐spectral‐based positive matrix factorization analyses. Further analysis resolved substantial κ values of 0.09 and 0.22, respectively, for less‐oxidized and more‐oxidized OOA, in contrast to the low κ values for cooking OA and biomass burning OA. Extensions of O:C‐ and source‐based parameterizations reasonably estimated the hygroscopicity of total OA with a moderate contribution from HULIS. This result and the fact that the obtained OOA contributions to κ of OA were similar to those from different environments suggest the applicability of parameterizing the hygroscopicity for a wide range of OA in particular based on source‐related structural characteristics.
Seasonal Cycles of High Mountain Asia Glacier Surface Elevation Detected by ICESat‐2
Authors: Wang Qiuyu , Sun Wenke
Published: December 2022

High Mountain Asia (HMA) glaciers are a key component of mountain hydrology and their seasonal ablation contributes significantly to the annual runoff of several large river systems that protect large populations from water stress. However, the seasonal cycle of glacial change remains unclear. Recent NASA's Ice, Cloud, and Land Elevation Satellite (ICESat‐2) provides an opportunity to survey changes in the glacier surface elevation in unprecedented detail. Here, we used a new approach—which is based on a developed elevation bin cluster with a sliding filter and an iterative recovery method—to obtain the complete seasonal cycle of glacier thickness changes in HMA. We generally identified three types of glaciers: (a) glaciers in the westerly dominant area (WDA) (b) glaciers in the Indian monsoon area (IMA), and (c) glaciers in the transition area (TA). The peak thickness values for the IMA, WDA, and TA glaciers occur in February, May, and June, respectively. Most glaciers in WDA and IMA show a strong seasonal cycle with variations of more than 2 m, while the TA glaciers are mainly characterized by weak changes of up to 1 m. Overall, our results show that the glaciers can provide 67–138 Gt of meltwater per year to downstream. These results provide crucial information for the calibration of models that project glacier response to climate change and simulate the downstream water availability. Our methodology facilitates the application of ICESat‐2 to seasonal tracking of glacier variability in global alpine areas.
Clarifying the Role of ENSO on Easter Island Precipitation Changes: Potential Environmental Implications for the Last Millennium
Authors: Delcroix T. , Michel S. L. L. , Swingedouw D. , Malaizé B. , Daniau A.‐L. , Abarca‐del‐Rio R. , Caley T. , Sémah A.‐M.
Published: December 2022

El Niño Southern Oscillation (ENSO) events yield precipitation deficits and ensuing droughts, often damaging regional forests, in many parts of the world. The relative roles of ENSO, other natural climate changes, and anthropogenic factors on the forest clearing of Easter Island over the last millennium are still debated. Here, we analyze Easter Island precipitation changes using in situ, satellite‐derived and reanalysis products spanning the last 4–7 decades, and 46 monthly 156‐year‐long (1850–2014) simulations derived from 25 CMIP5 and 21 CMIP6 (Coupled Model Intercomparison Project phases 5 and 6) General Circulation Models. Our analysis shows that La Niña events, the cold phases of ENSO, cause precipitation deficits of −0.2 to −0.3 standard deviation (relative to long‐term mean) in all analyzed data types. ENSO‐like events are further examined over the last millennium (850–1981). A new multiproxy reconstruction of the NINO3.4 index based on proxy records from the Past Global Changes 2k database and Random Forest method is produced. Our reconstruction reveals unusual high recurrences of La Niña‐like situations during the fifteenth to seventeenth centuries, which likely induced significant precipitation deficits on the island. These situations are compared to published vegetation reconstructions based on pollen analyses derived from sedimentary cores collected in three island sites. We conclude the environmental consequences of cumulative precipitation deficits over long‐lasting La Niña‐like situations reconstructed here over the fifteenth to seventeenth centuries were likely favoring drought and forest flammability. La Niña events should be better accounted for among the causes of forest clearing on Easter Island.
Gut microbiome-wide association study of depressive symptoms
Authors: Radjabzadeh Djawad , Bosch Jos A. , Uitterlinden André G. , Zwinderman Aeilko H. , Ikram M. Arfan , van Meurs Joyce B. J. , Luik Annemarie I. , Nieuwdorp Max , Lok Anja , van Duijn Cornelia M. , Kraaij Robert , Amin Najaf
Published: December 2022

Depression is one of the most poorly understood diseases due to its elusive pathogenesis. There is an urgency to identify molecular and biological mechanisms underlying depression and the gut microbiome is a novel area of interest. Here we investigate the relation of fecal microbiome diversity and composition with depressive symptoms in 1,054 participants from the Rotterdam Study cohort and validate these findings in the Amsterdam HELIUS cohort in 1,539 subjects. We identify association of thirteen microbial taxa, including genera Eggerthella, Subdoligranulum, Coprococcus, Sellimonas, Lachnoclostridium, Hungatella, Ruminococcaceae (UCG002, UCG003 and UCG005), LachnospiraceaeUCG001, Eubacterium ventriosum and Ruminococcusgauvreauiigroup, and family Ruminococcaceae with depressive symptoms. These bacteria are known to be involved in the synthesis of glutamate, butyrate, serotonin and gamma amino butyric acid (GABA), which are key neurotransmitters for depression. Our study suggests that the gut microbiome composition may play a key role in depression.
Anti-Zeno purification of spin baths by quantum probe measurements
Authors: Dasari Durga Bhaktavatsala Rao , Yang Sen , Chakrabarti Arnab , Finkler Amit , Kurizki Gershon , Wrachtrup Jörg
Published: December 2022

The quantum Zeno and anti-Zeno paradigms have thus far addressed the evolution control of a quantum system coupled to an immutable bath via non-selective measurements performed at appropriate intervals. We fundamentally modify these paradigms by introducing, theoretically and experimentally, the concept of controlling the bath state via selective measurements of the system (a qubit). We show that at intervals corresponding to the anti-Zeno regime of the system-bath exchange, a sequence of measurements has strongly correlated outcomes. These correlations can dramatically enhance the bath-state purity and yield a low-entropy steady state of the bath. The purified bath state persists long after the measurements are completed. Such purification enables the exploitation of spin baths as long-lived quantum memories or as quantum-enhanced sensors. The experiment involved a repeatedly probed defect center dephased by a nuclear spin bath in a diamond at low-temperature.
Dynamic morphological transformations in soft architected materials via buckling instability encoded heterogeneous magnetization
Authors: Xia Neng , Jin Dongdong , Pan Chengfeng , Zhang Jiachen , Yang Zhengxin , Su Lin , Zhao Jinsheng , Wang Liu , Zhang Li
Published: December 2022

The geometric reconfigurations in three-dimensional morphable structures have a wide range of applications in flexible electronic devices and smart systems with unusual mechanical, acoustic, and thermal properties. However, achieving the highly controllable anisotropic transformation and dynamic regulation of architected materials crossing different scales remains challenging. Herein, we develop a magnetic regulation approach that provides an enabling technology to achieve the controllable transformation of morphable structures and unveil their dynamic modulation mechanism as well as potential applications. With buckling instability encoded heterogeneous magnetization profiles inside soft architected materials, spatially and temporally programmed magnetic inputs drive the formation of a variety of anisotropic morphological transformations and dynamic geometric reconfiguration. The introduction of magnetic stimulation could help to predetermine the buckling states of soft architected materials, and enable the formation of definite and controllable buckling states without prolonged magnetic stimulation input. The dynamic modulations can be exploited to build systems with switchable fluidic properties and are demonstrated to achieve capabilities of fluidic manipulation, selective particle trapping, sensitivity-enhanced biomedical analysis, and soft robotics. The work provides new insights to harness the programmable and dynamic morphological transformation of soft architected materials and promises benefits in microfluidics, programmable metamaterials, and biomedical applications.
Food abundance in men before puberty predicts a range of cancers in grandsons
Authors: Vågerö Denny , Cederström Agneta , van den Berg Gerard J.
Published: December 2022

Nutritional conditions early in human life may influence phenotypic characteristics in later generations. A male-line transgenerational pathway, triggered by the early environment, has been postulated with support from animal and a small number of human studies. Here we analyse individuals born in Uppsala Sweden 1915–29 with linked data from their children and parents, which enables us to explore the hypothesis that pre-pubertal food abundance may trigger a transgenerational effect on cancer events. We used cancer registry and cause-of-death data to analyse 3422 cancer events in grandchildren (G2) by grandparental (G0) food access. We show that variation in harvests and food access in G0 predicts cancer occurrence in G2 in a specific way: abundance among paternal grandfathers, but not any other grandparent, predicts cancer occurrence in grandsons but not in granddaughters. This male-line response is observed for several groups of cancers, suggesting a general susceptibility, possibly acquired in early embryonic development. We observed no transgenerational influence in the middle generation.
Increases in reef size, habitat and metacommunity complexity associated with Cambrian radiation oxygenation pulses
Authors: Zhuravlev Andrey Yu. , Mitchell Emily G. , Bowyer Fred , Wood Rachel , Penny Amelia
Published: December 2022

Oxygenation during the Cambrian Radiation progressed via a series of short-lived pulses. However, the metazoan biotic response to this episodic oxygenation has not been quantified, nor have the causal evolutionary processes been constrained. Here we present ecological analyses of Cambrian archaeocyath sponge reef communities on the Siberian Platform (525–514 Ma). During the oxic pulse at ~521–519 Ma, we quantify reef habitat expansion coupled to an increase in reef size and metacommunity complexity, from individual within-community reactions to their local environment, to ecologically complex synchronous community-wide response, accompanied by an increase in rates of origination. Subsequently, reef and archaeocyath body size are reduced in association with increased rates of extinction due to inferred expanded marine anoxia (~519–516.5 Ma). A later oxic pulse at ~515 Ma shows further reef habitat expansion, increased archaeocyath body size and diversity, but weaker community-wide environmental responses. These metrics confirm that oxygenation events created temporary pulses of evolutionary diversification and enhanced ecosystem complexity, potentially via the expansion of habitable space, and increased archaeocyath individual and reef longevity in turn leading to niche differentiation. Most notably, we show that progression towards increasing biodiversity and ecosystem complexity was episodic and discontinuous, rather than linear, during the Cambrian Radiation.
Multiple drivers and lineage-specific insect extinctions during the Permo–Triassic
Authors: Jouault Corentin , Nel André , Perrichot Vincent , Legendre Frédéric , Condamine Fabien L.
Published: December 2022

The Permo–Triassic interval encompasses three extinction events including the most dramatic biological crisis of the Phanerozoic, the latest Permian mass extinction. However, their drivers and outcomes are poorly quantified and understood for terrestrial invertebrates, which we assess here for insects. We find a pattern with three extinctions: the Roadian/Wordian (≈266.9 Ma; extinction of 64.5% insect genera), the Permian/Triassic (≈252 Ma; extinction of 82.6% insect genera), and the Ladinian/Carnian boundaries (≈237 Ma; extinction of 74.8% insect genera). We also unveil a heterogeneous effect of these extinction events across the major insect clades. Because extinction events have impacted Permo–Triassic ecosystems, we investigate the influence of abiotic and biotic factors on insect diversification dynamics and find that changes in floral assemblages are likely the strongest drivers of insects’ responses throughout the Permo–Triassic. We also assess the effect of diversity dependence between three insect guilds; an effect ubiquitously found in current ecosystems. We find that herbivores held a central position in the Permo–Triassic interaction network. Our study reveals high levels of insect extinction that profoundly shaped the evolutionary history of the most diverse non-microbial lineage.
The PhanSST global database of Phanerozoic sea surface temperature proxy data
Authors: Judd Emily J. , Tierney Jessica E. , Huber Brian T. , Wing Scott L. , Lunt Daniel J. , Ford Heather L. , Inglis Gordon N. , McClymont Erin L. , O’Brien Charlotte L. , Rattanasriampaipong Ronnakrit , Si Weimin , Staitis Matthew L. , Thirumalai Kaustubh , Anagnostou Eleni , Cramwinckel Marlow Julius , Dawson Robin R. , Evans David , Gray William R. , Grossman Ethan L. , Henehan Michael J. , Hupp Brittany N. , MacLeod Kenneth G. , O’Connor Lauren K. , Sánchez Montes Maria Luisa , Song Haijun , Zhang Yi Ge
Published: December 2022

Paleotemperature proxy data form the cornerstone of paleoclimate research and are integral to understanding the evolution of the Earth system across the Phanerozoic Eon. Here, we present PhanSST, a database containing over 150,000 data points from five proxy systems that can be used to estimate past sea surface temperature. The geochemical data have a near-global spatial distribution and temporally span most of the Phanerozoic. Each proxy value is associated with consistent and queryable metadata fields, including information about the location, age, and taxonomy of the organism from which the data derive. To promote transparency and reproducibility, we include all available published data, regardless of interpreted preservation state or vital effects. However, we also provide expert-assigned diagenetic assessments, ecological and environmental flags, and other proxy-specific fields, which facilitate informed and responsible reuse of the database. The data are quality control checked and the foraminiferal taxonomy has been updated. PhanSST will serve as a valuable resource to the paleoclimate community and has myriad applications, including evolutionary, geochemical, diagenetic, and proxy calibration studies.
COVID-BEHAVE dataset: measuring human behaviour during the COVID-19 pandemic
Authors: Konsolakis Kostas , Banos Oresti , Cabrita Miriam , Hermens Hermie
Published: December 2022

Aiming to illuminate the effects of enforced confinements on people’s lives, this paper presents a novel dataset that measures human behaviour holistically and longitudinally during the COVID-19 outbreak. In particular, we conducted a study during the first wave of the lockdown, where 21 healthy subjects from the Netherlands and Greece participated, collecting multimodal raw and processed data from smartphone sensors, activity trackers, and users’ responses to digital questionnaires. The study lasted more than two months, although the duration of the data collection varies per participant. The data are publicly available and can be used to model human behaviour in a broad sense as the dataset explores physical, social, emotional, and cognitive domains. The dataset offers an exemplary perspective on a given group of people that could be considered to build new models for investigating behaviour changes as a consequence of the lockdown. Importantly, to our knowledge, this is the first dataset combining passive sensing, experience sampling, and virtual assistants to study human behaviour dynamics in a prolonged lockdown situation.
Containment of SARS-CoV-2 Delta strain in Guangzhou, China by quarantine and social distancing: a modelling study
Authors: Zeng Zhiqi , Wu Tong , Lin Zhijie , Luo Lei , Lin Zhengshi , Guan Wenda , Liang Jingyi , Yu Minfei , Guan Peikun , He Wei , Liu Zige , Lu Guibin , Xie Peifang , Chen Canxiong , Lau Eric H. Y. , Yang Zifeng , Hon Chitin , He Jianxing
Published: December 2022

China detected the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with Delta variant in May 2021. We assessed control strategies against this variant of concern. We constructed a robust transmission model to assess the effectiveness of interventions against the Delta variant in Guangzhou with initial quarantine/isolation, followed by social distancing. We also assessed the effectiveness of alternative strategies and that against potentially more infectious variants. The effective reproduction number (Rt) fell below 1 when the average daily number of close contacts was reduced to ≤ 7 and quarantine/isolation was implemented on average at the same day of symptom onset in Guangzhou. Simulations showed that the outbreak could still be contained when quarantine is implemented on average 1 day after symptom onset while the average daily number of close contacts was reduced to ≤ 9 per person one week after the outbreak's beginning. Early quarantine and reduction of close contacts were found to be important for containment of the outbreaks. Early implementation of quarantine/isolation along with social distancing measures could effectively suppress spread of the Delta and more infectious variants.
Palliative care reduces emergency room visits and total hospital days among patients with metastatic HPB and GI cancers
Authors: Billiot Angelle A. , Danos Denise M. , Stevens Jenny , Vance Katie M. , Raven Mary C. , Lyons John M.
Published: December 2022

Palliative care services (PCS) have improved quality of life for patients across various cancer subtypes. Minimal data exists regarding PCSfor metastatic hepatopancreaticobiliary (HPB) and gastrointestinal (GI) cancers. We assessed the impact of PCS on emergency department visits, hospital admissions, and survival among these patients. Patients with metastatic HPB and GI cancer referred to outpatient PCS between 2014 and 2018 at a single institution were included. We compared the demographics, outcomes, and end-of-life indicators between those who did and did not receive PCS. The study included 183 patients, with 118 (64.5%) having received PCS. There were no significant differences in age, gender, race, marital status, or insurance. Those receiving PCS were more likely to have colorectal cancer (p = 0.0082) and receive chemotherapy (p = 0.0098). On multivariate analysis, PCS was associated with fewer ED visits (p = 0.0319), hospital admissions (p = 0.0002), and total inpatient hospital days (p < 0.0001) per 30 days of life. Overall survival was greater among patients receiving PCS (HR: 0.65 (0.46–0.92)). Outpatient PCS for patients with metastatic HPB and GI cancer is associated with fewer emergency department visits, hospital admissions, and inpatient hospital days, and improved overall survival.
Lithospheric double shear zone unveiled by microseismicity in a region of slow deformation
Authors: de Nardis Rita , Pandolfi Claudia , Cattaneo Marco , Monachesi Giancarlo , Cirillo Daniele , Ferrarini Federica , Bello Simone , Brozzetti Francesco , Lavecchia Giusy
Published: December 2022

The deformation style of the continental lithosphere is a relevant issue for geodynamics and seismic hazard perspectives. Here we show the first evidence of two well-distinct low-angle and SW-dipping individual reverse shear zones of the Italian Outer Thrust System in Central Italy. One corresponds to the down-dip prosecution of the Adriatic Basal Thrust with its major splay and the other to a hidden independent structure, illuminated at a depth between 25 and 60 km, for an along-strike extent of ~ 150 km. Combining geological information with high-quality seismological data, we unveil this novel configuration and reconstruct a detailed 3D geometric and kinematic fault model of the compressional system, active at upper crust to upper mantle depths. In addition, we report evidence of coexisting deformation volumes undergoing well-distinguished stress fields at different lithospheric depths. These results provide fundamental constraints for a forthcoming discussion on the Apennine fold-and-thrust system's geodynamic context as a shallow subduction zone or an intra-continental lithosphere shear zone.
Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community
Authors: Goodarzi Zahra , Asad Sedigheh , Mehrshad Maliheh
Published: December 2022

Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.
Efficacy of a novel self-expandable metal stent with dumbbell-shaped flare ends for distal biliary obstruction due to unresectable pancreatic cancer
Authors: Miyazawa Masaki , Takatori Hajime , Okafuji Hirofumi , Hayashi Tomoyuki , Toyama Tadashi , Yamada Shinya , Kitamura Kazuya , Arai Kuniaki , Sakai Yoshio , Yamashita Taro , Yamashita Tatsuya , Mizukoshi Eishiro , Honda Masao , Kaneko Shuichi
Published: December 2022

This study aimed to evaluate the efficacy of a novel fully covered self-expandable metal stent (SEMS) with dumbbell-shaped flare ends for the palliation of distal biliary obstruction (DBO) due to unresectable pancreatic cancer (UPC). Patients with DBO due to UPC who received the novel HILZO fully covered stent (HFS), the WALLFLEX partially covered stent (WPS) or fully covered stent (WFS) were analyzed. The incidence of recurrent biliary obstruction (RBO), time to RBO (TRBO), and the incidence of complications were compared among the three SEMS groups. Eighty-four patients (HFS, n = 36; WPS, n = 20; WFS, n = 28) were included. The incidence of RBO was low in the HFS group (versus the WPS and WFS group, p = 0.033 and 0.023, respectively). TRBO in the HFS group was longer than that in the WFS group (p = 0.049). Placement of the HFS was an independent factor for long TRBO in multivariable analysis (p = 0.040). The incidence of pancreatitis and cholecystitis in the HFS group was low (one for each). It is recommended to use the HFS for the palliation of DBO due to UPC from the viewpoint of the low incidence of RBO and complications.
Novel expression cassettes for increasing apolipoprotein AI transgene expression in vascular endothelial cells
Authors: Sethuraman Meena , Dronadula Nagadhara , Bi Lianxiang , Wacker Bradley K. , Knight Ethan , De Bleser Pieter , Dichek David A.
Published: December 2022

Transduction of endothelial cells (EC) with a vector that expresses apolipoprotein A-I (APOAI) reduces atherosclerosis in arteries of fat-fed rabbits. However, the effects on atherosclerosis are partial and might be enhanced if APOAI expression could be increased. With a goal of developing an expression cassette that generates higher levels of APOAI mRNA in EC, we tested 4 strategies, largely in vitro: addition of 2 types of enhancers, addition of computationally identified EC-specific cis-regulatory modules (CRM), and insertion of the rabbit APOAI gene at the transcription start site (TSS) of sequences cloned from genes that are highly expressed in cultured EC. Addition of a shear stress-responsive enhancer did not increase APOAI expression. Addition of 2 copies of a Mef2c enhancer increased APOAI expression from a moderately active promoter/enhancer but decreased APOAI expression from a highly active promoter/enhancer. Of the 11 CRMs, 3 increased APOAI expression from a moderately active promoter (2–7-fold; P < 0.05); none increased expression from a highly active promoter/enhancer. Insertion of the APOAI gene into the TSS of highly expressed EC genes did not increase expression above levels obtained with a moderately active promoter/enhancer. New strategies are needed to further increase APOAI transgene expression in EC.
Desloratadine, an FDA-approved cationic amphiphilic drug, inhibits SARS-CoV-2 infection in cell culture and primary human nasal epithelial cells by blocking viral entry
Authors: Morin-Dewaele Margot , Bartier Sophie , Berry François , Brillet Rozenn , López-Molina Dennis Salomón , Nguyễn Công Trung , Maille Pascale , Sereno Kevin , Nevers Quentin , Softic Laurent , Vaugeois Jean-Marie , Louis Bruno , Bequignon Emilie , Bruscella Patrice , Coste André , Pawlotsky Jean-Michel , Jamain Stéphane , Ahmed-Belkacem Abdelhakim
Published: December 2022

The 2019 global coronavirus (COVID-19) pandemic has brought the world to a grinding halt, highlighting the urgent need for therapeutic and preventive solutions to slow the spread of emerging viruses. The objective of this study was to assess the anti-SARS-CoV-2 effectiveness of 8 FDA-approved cationic amphiphilic drugs (CADs). SARS-CoV-2-infected Vero cells, Calu-3 cells and primary Human Nasal Epithelial Cells (HNEC) were used to investigate the effects of CADs and revealed their antiviral mode of action. Among the CADs tested, desloratadine, a commonly used antiallergic, well-tolerated with no major side effects, potently reduced the production of SARS-CoV-2 RNA in Vero-E6 cells. Interestingly, desloratadine was also effective against HCoV-229E and HCoV-OC43 showing that it possessed broad-spectrum anti-coronavirus activity. Investigation of its mode of action revealed that it targeted an early step of virus lifecycle and blocked SARS-CoV-2 entry through the endosomal pathway. Finally, the ex vivo kinetic of the antiviral effect of desloratadine was evaluated on primary Human Nasal Epithelial Cells (HNEC), showing a significant delay of viral RNA production with a maximal reduction reached after 72 h of treatment. Thus, this treatment could provide a substantial contribution to prophylaxis and systemic therapy of COVID-19 or other coronaviruses infections and requires further studies.
Atraumatic spinal needle indicates correct CSF opening pressure
Authors: Woo Marcel S. , Kessner Simon S. , Schlemm Eckhard , Gerloff Christian
Published: December 2022

The accurate assessment of cerebrospinal fluid opening pressure during spinal puncture provides important medical information in diagnosis, prognosis and therapy of several neurological conditions. However, purpose-specific spinal needle choice is debated. While atraumatic needles are associated with lower incidence of post-puncture headache and re-hospitalisation, some clinicians believe that they lack in accuracy of CSF opening pressure assessment. Our primary objective was to investigate different needle types on correctly assessing CSF opening pressure. We compared typical clinically utilised traumatic (0.9 mm outer diameter) and atraumatic (0.7 mm; 0.45 mm) spinal needles with regards to the assessment of the opening pressure in an experimental spinal puncture model testing experimental and cerebrospinal fluids in predefined pressures. Our goal was to measure the time until indicated pressure levels were correctly shown. Atraumatic needles of at least 0.7 mm diameter had a similar accuracy as traumatic needles without significant differences in time-to-equilibrium. These results were independent of protein and glucose concentration and the presence of haemoglobin. This study demonstrates that atraumatic needles can be used to accurately measure CSF opening pressure. This knowledge might guide clinicians in their choice of needle and help to reduce post-puncture headaches and re-hospitalisation.
Blood monocyte levels predict the risk of acute exacerbations of chronic obstructive pulmonary disease: a retrospective case–control study
Authors: Lin Ching-Hsiung , Li Yi-Rong , Lin Pei Ru , Wang Bing-Yen , Lin Sheng-Hao , Huang Kuo-Yang , Kor Chew-Teng
Published: December 2022

Monocytes were critical cells in the innate immune system. Monocyte recruitment to the lungs is a crucial process of pathophysiology in chronic obstructive pulmonary disease (COPD). Current evidence on the association between the occurrence of acute exacerbations of COPD (AECOPD) and monocytes was unclear. This study aimed to examine whether blood monocytes are associated with the occurrence of AECOPD and to determine the specific blood monocyte level to predict AECOPD. A retrospective case–control study was conducted at Changhua Christian Hospital. A total of 444 eligible patients with COPD were included between January 2017 and December 2019. Restricted cubic splines were used to analyze the nonlinear relationships between continuous white blood cell values and the occurrence of AECOPD. The association between monocytes and the occurrence of AECOPD was assessed using the logistic, lasso, and ridge regression models. Restricted cubic splines revealed nonlinear associations among the monocyte level, the continuous value of the eosinophil-to-lymphocyte ratio, and the occurrence of AECOPD. The lowest risk of occurrence of AECOPD ranged from 7.4 to 10%; < 7.4% with an absolute count < 0.62 or > 10% indicated significant risk. No significant association was noted between the eosinophil-to-lymphocyte ratio categories in the tertiles (< 0.049, 0.049 to < 0.122, and ≥ 0.122) and the risk of AECOPD. A significantly higher risk was noted in the association of the occurrence of AECOPD with the CAT score; mMRC score; wheezing cough; preexisting chronic pulmonary disease; hypertension and malignancy; use of dual- and triple, and oral long-acting bronchodilators for COPD treatment; and WBC count. We reported a nonlinear relationship between monocytes and the occurrence of AECOPD. Patients with monocyte percentage of > 10% or < 7.4% with an absolute count < 0.62 had higher risk of occurrence of AECOPD. Overall, our study demonstrated the specific value of monocytes in identifying high risks of the occurrence of AECOPD; this value is an easy-to-obtain, inexpensive biomarker in patients with AECOPD and should be further investigated in future prospective clinical studies.
The evolutionary process of invasion in the fall armyworm (Spodoptera frugiperda)
Authors: Yainna Sudeeptha , Tay Wee Tek , Durand Karine , Fiteni Estelle , Hilliou Frédérique , Legeai Fabrice , Clamens Anne-Laure , Gimenez Sylvie , Asokan R. , Kalleshwaraswamy C. M. , Deshmukh Sharanabasappa S. , Meagher Robert L. , Blanco Carlos A. , Silvie Pierre , Brévault Thierry , Dassou Anicet , Kergoat Gael J. , Walsh Thomas , Gordon Karl , Nègre Nicolas , d’Alençon Emmanuelle , Nam Kiwoong
Published: December 2022

The fall armyworm (FAW; Spodoptera frugiperda) is one of the major agricultural pest insects. FAW is native to the Americas, and its invasion was first reported in West Africa in 2016. Then it quickly spread through Africa, Asia, and Oceania, becoming one of the main threats to corn production. We analyzed whole genome sequences of 177 FAW individuals from 12 locations on four continents to infer evolutionary processes of invasion. Principal component analysis from the TPI gene and whole genome sequences shows that invasive FAW populations originated from the corn strain. Ancestry coefficient and phylogenetic analyses from the nuclear genome indicate that invasive populations are derived from a single ancestry, distinct from native populations, while the mitochondrial phylogenetic tree supports the hypothesis of multiple introductions. Adaptive evolution specific to invasive populations was observed in detoxification, chemosensory, and digestion genes. We concluded that extant invasive FAW populations originated from the corn strain with potential contributions of adaptive evolution.
Exploring the response of a key Mediterranean gorgonian to heat stress across biological and spatial scales
Authors: Gómez-Gras D. , Bensoussan N. , Ledoux J. B. , López-Sendino P. , Cerrano C. , Ferretti E. , Kipson S. , Bakran-Petricioli T. , Serrao E. A. , Paulo D. , Coelho M. A. G. , Pearson G. A. , Boavida J. , Montero-Serra I. , Pagès-Escolà M. , Medrano A. , López-Sanz A. , Milanese M. , Linares C. , Garrabou J.
Published: December 2022

Understanding the factors and processes that shape intra-specific sensitivity to heat stress is fundamental to better predicting the vulnerability of benthic species to climate change. Here, we investigate the response of a habitat-forming Mediterranean octocoral, the red gorgonianParamuricea clavata(Risso, 1826) to thermal stress at multiple biological and geographical scales. Samples from elevenP. clavatapopulations inhabiting four localities separated by hundreds to more than 1500 km of coast and with contrasting thermal histories were exposed to a critical temperature threshold (25 °C) in a common garden experiment in aquaria. Ten of the 11 populations lacked thermotolerance to the experimental conditions provided (25 days at 25 °C), with 100% or almost 100% colony mortality by the end of the experiment. Furthermore, we found no significant association between local average thermal regimes nor recent thermal history (i.e., local water temperatures in the 3 months prior to the experiment) and population thermotolerance. Overall, our results suggest that local adaptation and/or acclimation to warmer conditions have a limited role in the response ofP. clavatato thermal stress. The study also confirms the sensitivity of this species to warm temperatures across its distributional range and questions its adaptive capacity under ocean warming conditions. However, important inter-individual variation in thermotolerance was found within populations, particularly those exposed to the most severe prior marine heatwaves. These observations suggest thatP. clavatacould harbor adaptive potential to future warming acting on standing genetic variation (i.e., divergent selection) and/or environmentally-induced phenotypic variation (i.e., intra- and/or intergenerational plasticity).
A perceptual glitch in serial perception generates temporal distortions
Authors: Sierra Franklenin , Muralikrishnan R. , Poeppel David , Tavano Alessandro
Published: December 2022

Precisely estimating event timing is essential for survival, yet temporal distortions are ubiquitous in our daily sensory experience. Here, we tested whether the relative position, duration, and distance in time of two sequentially-organized events—standard S, with constant duration, and comparison C, with duration varying trial-by-trial—are causal factors in generating temporal distortions. We found that temporal distortions emerge when the first event is shorter than the second event. Importantly, a significant interaction suggests that a longer inter-stimulus interval (ISI) helps to counteract such serial distortion effect only when the constant S is in the first position, but not if the unpredictable C is in the first position. These results imply the existence of a perceptual bias in perceiving ordered event durations, mechanistically contributing to distortion in time perception. We simulated our behavioral results with a Bayesian model and replicated the finding that participants disproportionately expand first-position dynamic (unpredictable) short events. Our results clarify the mechanisms generating time distortions by identifying a hitherto unknown duration-dependent encoding inefficiency in human serial temporal perception, something akin to a strong prior that can be overridden for highly predictable sensory events but unfolds for unpredictable ones.
Impact of SNPs, off-targets, and passive permeability on efficacy of BCL6 degrading drugs assigned by virtual screening and 3D-QSAR approach
Authors: Karimi Solmaz , Shahabi Farzaneh , Mubarak Shaden M. H. , Arjmandi Hanie , Hashemi Zahra Sadat , Pourzardosht Navid , Zakeri Alireza , Mahboobi Mahdieh , Jahangiri Abolfazl , Rahbar Mohammad Reza , Khalili Saeed
Published: December 2022

B-cell lymphoma 6 (BCL6) regulates various genes and is reported to be overexpressed in lymphomas and other malignancies. Thus, BCL6 inhibition or its tagging for degradation would be an amenable therapeutic approach. A library of 2500 approved drugs was employed to find BCL6 inhibitory molecules via virtual screening. Moreover, the 3D core structure of 170 BCL6 inhibitors was used to build a 3D QSAR model and predict the biological activity. The SNP database was analyzed to study the impact on the destabilization of BCL6/drug interactions. Structural similarity search and molecular docking analyses were used to assess the interaction between possible off-targets and BCL6 inhibitors. The tendency of drugs for passive membrane permeability was also analyzed. Lifitegrast (DB11611) had favorable binding properties and biological activity compared to the BI-3802. Missense SNPs were located at the essential interaction sites of the BCL6. Structural similarity search resulted in five BTB-domain containing off-target proteins. BI-3802 and Lifitegrast had similar chemical behavior and binding properties against off-target candidates. More interestingly, the binding affinity of BI-3802 (against off-targets) was higher than Lifitegrast. Energetically, Lifitegrast was less favorable for passive membrane permeability. The interaction between BCL6 and BI-3802 is more prone to SNP-derived variations. On the other hand, higher nonspecific binding of BI-3802 to off-target proteins could bring about higher undesirable properties. It should also be noted that energetically less desirable passive membrane translocation of Lifitegrast would demand drug delivery vehicles. However, further empirical evaluation of Lifitegrast would unveil its true potential.
N7-methylguanosine methylation-related regulator genes as biological markers in predicting prognosis for melanoma
Authors: Deng Jiehua , Lin Jiahua , Liu Chang , Li Jiasong , Cai Jun , Zhou Xiyu , Li Xiong
Published: December 2022

The aim of this study is to find those N7-methylguanosine (m7G) methylation-related regulator genes (m7GMRRGs) which were associated with melanoma prognosis and use them to develop a prognostic prediction model. Clinical information was retrieved online from The Cancer Gene Atlas (TCGA) and the Gene Expression Omnibus (GEO). R software was used to extract m7GMRRGs by differential expression analysis. To create a prognostic risk model, univariate and multivariate Cox regression analyses were employed for the evaluation of the prognostic significance of m7G methylation modifiers. Internal validation using cohort from TCGA (training set) and external validation using cohort from GEO (validation set) of the model were carried out. The model’s predictive performance was confirmed by using the Kaplan–Meier, univariate, and multivariate Cox regression, and receiver operating characteristic curve (ROC) by constructing column line plots incorporating clinical factor characteristics. Immune infiltration analyses were performed to assess the immune function of m7GMRRGs. Drug sensitivity analysis was conducted to study chemotherapeutic drug treatment cues. Prognostic models using four m7GMRRGs (EIF4E3, LARP1, NCBP3, and IFIT5) showed good prognostic power in training and validation sets. The area under the curve (AUC) at 1, 3, and 5 years for GEO-melanoma were 0.689, 0.704, and 0.726, respectively. The prediction model could distinctly classify patients with melanoma into different risk subgroups (P < 0.001 for TCGA-melanoma and P < 0.05 for GEO-melanoma). Clinical characteristics were taken into account in Cox regression and AUC analysis, which highlighted that the risk score served as an independent risk factor determining the prognosis of patients with melanoma. Immuno-infiltration analysis showed that m7GMRRGs could potentially regulate CD8+ T cells as well as regulatory T cells (Treg cells). Results of our study indicate a association between m7GMRRGs and melanoma prognosis, and the prognostic prediction model using m7GMRRGs may predict the prognosis of patients with melanoma well. Nevertheless, these results may provide a clue for potential better options of melanoma treatment but need further validation in futural studies.