bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fifty years after deep‐ploughing: Effects on yield, roots, nutrient stocks and soil structure
Authors: Burger Dymphie J. , Schneider Florian , Bauke Sara L. , Kautz Timo , Don Axel , Amelung Wulf 
Published: October 2023

AbstractDeep‐ploughing far beyond the common depth of 30 cm was used more than 50 years ago in Northern Germany with the aim to break root‐restricting layers and thereby improve access to subsoil water and nutrient resources. We hypothesized that effects of this earlier intervention on soil properties and yields prevailed after 50 years. Hence, we sampled two sandy soils and one silty soil (Cambisols and a Luvisol) of which half of the field had been deep‐ploughed 50 years ago (soils then re‐classified as Treposols). The adjacent other half was not deep‐ploughed and thus served as the control. At all the three sites, both deep‐ploughed and control parts were then conventionally managed over the last 50 years. We assessed yields during the dry year 2019 and additionally in 2020, and rooting intensity at the year of sampling (2019), as well as changes in soil structure, carbon and nutrient stocks in that year. We found that deep‐ploughing improved yields in the dry spell of 2019 at the sandy sites, which was supported by a more general pattern of higher NDVI indices in deep‐ploughed parts for the period from 2016 to 2021 across varying weather conditions. Subsoil stocks of soil organic carbon and total plant‐available phosphorus were enhanced by 21%–199% in the different sites. Root biomass in the subsoil was reduced due to deep‐ploughing at the silty site and was increased or unaffected at the sandy sites. Overall, the effects of deep‐ploughing were site‐specific, with reduced bulk density in the buried topsoil stripes in the subsoil of the sandy sites, but with elevated subsoil density in the silty site. Hence, even 50 years after deep‐ploughing, changes in soil properties are still detectable, although effect size differed among sites.
Incorporating ecology into gene drive modelling
Authors: Kim Jaehee , Harris Keith D. , Kim Isabel K. , Shemesh Shahar , Messer Philipp W. , Greenbaum Gili 
Published: October 2023

AbstractGene drive technology, in which fast‐spreading engineered drive alleles are introduced into wild populations, represents a promising new tool in the fight against vector‐borne diseases, agricultural pests and invasive species. Due to the risks involved, gene drives have so far only been tested in laboratory settings while their population‐level behaviour is mainly studied using mathematical and computational models. The spread of a gene drive is a rapid evolutionary process that occurs over timescales similar to many ecological processes. This can potentially generate strong eco‐evolutionary feedback that could profoundly affect the dynamics and outcome of a gene drive release. We, therefore, argue for the importance of incorporating ecological features into gene drive models. We describe the key ecological features that could affect gene drive behaviour, such as population structure, life‐history, environmental variation and mode of selection. We review previous gene drive modelling efforts and identify areas where further research is needed. As gene drive technology approaches the level of field experimentation, it is crucial to evaluate gene drive dynamics, potential outcomes, and risks realistically by including ecological processes.
MONETARY ASYMMETRIES WITHOUT (AND WITH) PRICE STICKINESS
Authors: JACCARD IVAN 
Published: October 2023

AbstractThe evidence suggests that monetary policy transmission is asymmetric over the business cycle. Interacting financing frictions with a preference for liquidity provides an explanation for this fact. Our model reproduces a set of asset market and business cycle facts. Accounting for the joint dynamics of asset prices and business cycle fluctuations is key; in a variant of the model that is unable to produce realistic macrofinance implications, monetary asymmetries disappear. Resorting to nonlinear techniques is therefore not sufficient to detect monetary asymmetries. Nonlinearities in the transmission mechanism also critically depend on the macrofinance implications of monetary policy models.
REGULARIZED GMM FOR TIME‐VARYING MODELS WITH APPLICATIONS TO ASSET PRICING
Authors: Cui Liyuan , Feng Guanhao , Hong Yongmiao 
Published: October 2023

AbstractWe propose a regularized generalized method of moments (RegGMM) approach to estimating time‐varying coefficient models via a ridge fusion penalty with a high‐dimensional set of moment conditions. RegGMM only requires a mild condition on the oscillations between consecutive parameter values, accommodating abrupt structural breaks and smooth changes throughout the sample period. RegGMM offers an alternative solution for estimating the time‐varying stochastic discount factor model when pricing U.S. equity cross‐sectional returns. Our time‐varying estimate paths for factor risk prices capture changing performance across multiple risk factors and depict potential regime‐switching scenarios. Finally, RegGMM demonstrates superior asset pricing and investment performance gains compared to alternative methods.
Linking flexural strength and strength‐limiting flaws in additively manufactured alumina with print parameter variations
Authors: Boardman Sarah , Packard Corinne E. 
Published: October 2023

AbstractAdvancing the adoption of lithography‐based ceramic manufacturing (LCM) for structural applications requires understanding how processing parameters impact the printed material's flaw population and failure behavior. Exploratory studies on LCM alumina have mixed results regarding print parameter influence on strength and past fractography is insufficiently complete to guide process engineering for better performance. We perform four‐point flexural strength characterization and comprehensive fractography of LCM alumina to evaluate the impact of processing parameters including orientation, layer height, and curing energy on strength‐limiting defects. Characteristic strengths for fully dense, high‐purity LCM alumina are near or above conventionally processed alumina within the manufacturable range of print parameters studied in this work. Conversely, the Weibull modulus varies greatly (m = 3.8–19.5) depending on print parameters. The dominant strength‐controlling defects all have a printing‐based origin, but vary between delamination, surface texture, and bubbles depending on print orientation. Lowest performance results from alignment of the print axis along the bar length, yielding a low Weibull modulus associated with weak delamination flaws that are not appreciably improved by varying print layer height or curing energy.
Migration patterns and navigation cues of Atlantic salmon post‐smolts migrating from 12 rivers through the coastal zones around the Irish Sea
Authors: Lilly Jessie , Honkanen Hannele H. , Rodger Jessica R. , del Villar Diego , Boylan Patrick , Green Amy , Pereiro Diego , Wilkie Lorna , Kennedy Richard , Barkley Andrea , Rosell Robert , Maoiléidigh Niall Ó. , O'Neill Ross , Waters Catherine , Cotter Deirdre , Bailey David , Roche William , McGill Ross , Barry James , Beck Samantha V. , Henderson Jim , Parke Debbie , Whoriskey Frederick G. , Shields Brian , Ramsden Philip , Walton Silas , Fletcher Melanie , Whelan Ken , Bean Colin W. , Elliott Sophie , Bowman Adrian , Adams Colin E. 
Published: October 2023

AbstractThe freshwater phase of the first seaward migration of juvenile Atlantic salmon (Salmo salar) is relatively well understood when compared with our understanding of the marine phase of their migration. In 2021, 1008 wild and 60 ranched Atlantic salmon smolts were tagged with acoustic transmitters in 12 rivers in England, Scotland, Northern Ireland and Ireland. Large marine receiver arrays were deployed in the Irish Sea at two locations: at the transition of the Irish Sea into the North Atlantic between Ireland and Scotland, and between southern Scotland and Northern Ireland, to examine the early phase of the marine migration of Atlantic salmon smolts. After leaving their natal rivers' post‐smolt migration through the Irish Sea was rapid with minimum speeds ranging from 14.03 to 38.56 km.day−1 for Atlantic salmon smolts that entered the Irish Sea directly from their natal river, to 9.69–39.94 km.day−1 for Atlantic salmon smolts that entered the Irish Sea directly from their natal estuary. Population minimum migration success through the study area was strongly correlated with the distance of travel, populations further away from the point of entry to the open North Atlantic exhibited lower migration success. Post‐smolts from different populations experienced different water temperatures on entering the North Atlantic. This was largely driven by the timing of their migration and may have significant consequences for feeding and ultimately survivorship. The influence of water currents on post‐smolt movement was investigated using data from previously constructed numerical hydrodynamic models. Modeled water current data in the northern Irish Sea showed that post‐smolts had a strong preference for migrating when the current direction was at around 283° (west‐north‐west) but did not migrate when exposed to strong currents in other directions. This is the most favorable direction for onward passage from the Irish Sea to the continental shelf edge current, a known accumulation point for migrating post‐smolts. These results strongly indicate that post‐smolts migrating through the coastal marine environment are: (1) not simply migrating by current following (2) engage in active directional swimming (3) have an intrinsic sense of their migration direction and (4) can use cues other than water current direction to orientate during this part of their migration.
Nationwide multicenter study on adverse events associated with a patency capsule: Additional survey of appropriate use of patency capsule study
Authors: Omori Teppei , Ohmiya Naoki , Watanabe Kenji , Hirai Fumihito , Nakamura Masanao , Kitamura Kazuya , Ozeki Keiji , Oka Shiro , Kawano Seiji , Handa Osamu , Kawai Mikio , Ninomiya Kazeo , Sagawa Tamotsu , Wakamatsu Takahiro , Araki Akihiro , Koike Yuji , Kato Shingo , Hashimoto Shinichi , Mannami Tomohiko , Nakaji Konosuke , Tanaka Shinji , Matsui Toshiyuki ,   the J‐POP study group
Published: October 2023

AbstractBackground and AimThe PillCam patency capsule (PC) without a radio frequency identification tag was released to preclude retention of the small bowel capsule endoscope (CE) in Japan in 2012. We conducted a multicenter study to determine tag‐less PC‐related adverse events (AEs).MethodsWe first conducted a retrospective survey using a standardized data collection sheet for the clinical characteristics of PC‐related AEs among 1096 patients collected in a prospective survey conducted between January 2013 and May 2014 (Cohort 1). Next, we retrospectively investigated additional AEs that occurred before and after Cohort 1 within the period June 2012 and December 2014 among 1482 patients (Cohort 2).ResultsOf the 2578 patients who underwent PC examinations from both cohorts, 74 AEs occurred among 61 patients (2.37%). The main AEs were residual parylene coating in 25 events (0.97%), PC‐induced small bowel obstruction, suspicious of impaction, in 23 events (0.89%), and CE retention even after patency confirmation in 10 events (0.39%). Residual parylene coating was significantly associated with Crohn's disease (P < 0.01). Small bowel obstruction was significantly associated with physicians with less than 1 year of experience handling the PC and previous history of postprandial abdominal pain (P < 0.01 and P < 0.03, respectively). CE retention was ascribed to erroneous judgment of PC localization in all cases.ConclusionsThis large‐scale multicenter study provides evidence supporting the safety and efficiency of a PC to preclude CE retention. Accurate PC localization in patients without excretion and confirmation of previous history of postprandial abdominal pain before PC examinations is warranted (UMIN000010513).
The governance of policy integration and policy coordination through joined‐up government: How subnational levels counteract siloism and fragmentation within Swedish migration policy
Authors: Lidén Gustav , Nyhlén Jon 
Published: October 2023

AbstractModern welfare states struggle with fragmented policies and siloed governments, as well as with the need to deal with wicked problems. We argue that addressing such problems from the perspective of central government can be facilitated by notions of joined‐up government that, combined with vertical aspects of modern governance, provide a basis for analysis. To embark upon such challenges, we examine policy integration and policy coordination within the complex area of Swedish migration policies in light of the European migrant crisis. Through a content analysis of an extensive qualitative material (interviews and documents), we show that policy integration is weakly associated with joint objectives and decision‐making. As a contribution to prior knowledge in the field, we emphasize the unintuitive finding that counteracting siloism and fragmentation in Swedish migration policy is not achieved through coherent governance ranging across tiers, functions, and sectors but mainly at subnational levels through policy coordination relying on a bottom‐up approach.
A novel protein encoded by circVPS13D attenuates antiviral innate immunity by targeting MAVS in teleost fish
Authors: Wang Linchao , Song Yanhong , Yan Xiaolong , Xu Tianjun 
Published: October 2023

ABSTRACT

The signaling adaptor MAVS is a vital adaptor protein in retinoic acid-inducible gene I-like receptors (RLRs) signaling; thus, its expression and responses must be tightly regulated to avoid uncontrolled production of type I IFN by various mechanisms, including ubiquitination. The protein-coding ability of circRNAs has recently been a hot topic, but the roles of protein-coding circRNAs in antiviral innate immunity of teleost have rarely been reported. In this study, we identify that a novel circRNA derived from vacuolar protein sorting-associated protein 13D (
VPS13D
) gene, named circVPS13D, was a suppressor of RLR signaling pathways during poly(I:C) stimulation or
Siniperca chuatsi rhabdovirus
(SCRV) infection. Mechanistically, circVPS13D contains a 513-nucleotide (nt) open reading frame (ORF) and a sequence that is −174 nt as an internal ribosome entry site (IRES), which is required for translation initiation in 5’-cap-independent coding RNAs. SCRV infection promoted the expression of circVPS13D and circVPS13D encodes a novel peptide, termed VPS13D-170 amino acid (aa), which directly interacted with MAVS and inhibited IFN-I production. VPS13D-170aa targeted the K172 residue of MAVS through K48-linked polyubiquitination, leading to proteasomal degradation of MAVS.

IMPORTANCE
The expression of circVPS13D was upregulated with SCRV invasion, which proved that circVPS13D was involved in the regulation of the antiviral immune response. Our study revealed that the existence of circVPS13D promoted the replication of SCRV. Functionally, circVPS13D negatively regulates the antiviral responses of fish. Mechanistically, we confirmed that circVPS13D inhibited RLRs antiviral signaling pathway via the encoded protein VPS13D-170aa by targeting MAVS. Our study provided novel insights into the roles of protein-coding circRNAs and supported VPS13D-170aa as a negative regulator in the antiviral immune responses of teleost fish.
Characterization and biodistribution of under-employed gene therapy vector AAV7
Authors: Yost Samantha A. , Firlar Emre , Glenn Justin D. , Carroll Hayley B. , Foltz Steven , Giles April R. , Egley Jenny M. , Firnberg Elad , Cho Sungyeon , Nguyen Trang , Henry William M. , Janczura Karolina J. , Bruder Joseph , Liu Ye , Danos Olivier , Karumuthil-Melethil Subha , Pannem Sanjana , Yost Valerie , Engelson Yelena , Kaelber Jason T. , Dimant Hemi , Smith Jared B. , Mercer Andrew C. 
Published: October 2023

ABSTRACT
AAV7 is a clade D adeno-associated virus (AAV) whose potential as a gene therapy vector has not been fully evaluated. We show here that high-titer AAV7 vectors can be produced in HEK293 cells and used to transduce cultured cells in an AAV receptor (AAVR)-dependent manner. In contrast with AAV9, AAV7 did not significantly interact with glycans when assayed on a panel of three hundred biologically relevant species. The structure of the AAV7 capsid was obtained by single particle cryo-electron microscopy at 2.7 Å, showing the expected AAV scaffold as well as unique features in variable surface loops. The biodistribution profiles of AAV7 and AAV9 vectors were compared in mice following intravenous administration and quantification of vector genomes and mRNA in tissues, as well as cryofluorescence tomography (CFT) and immunofluorescence (IF). AAV7 displayed a strong cardiac tropism and did not efficiently cross the blood-brain barrier. Surprisingly, strong transgene expression was observed throughout the head as shown by CFT, including regions of the cranial sinuses, teeth, and mandible for both AAV7 and AAV9, an attribute that has not been previously evaluated via traditional biodistribution methods.

IMPORTANCE
The use of adeno-associated viruses (AAVs) as gene delivery vectors has vast potential for the treatment of many severe human diseases. Over one hundred naturally existing AAV capsid variants have been described and classified into phylogenetic clades based on their sequences. AAV8, AAV9, AAVrh.10, and other intensively studied capsids have been propelled into pre-clinical and clinical use, and more recently, marketed products; however, less-studied capsids may also have desirable properties (e.g., potency differences, tissue tropism, reduced immunogenicity, etc.) that have yet to be thoroughly described. These data will help build a broader structure-function knowledge base in the field, present capsid engineering opportunities, and enable the use of novel capsids with unique properties.
Glycerophosphocholine provision rescues
Candida albicans
growth and signaling phenotypes associated with phosphate limitation
Authors: King William R. , Acosta-Zaldívar Maikel , Qi Wanjun , Cherico Nicholas , Cooke Lauren , Köhler Julia R. , Patton-Vogt Jana 
Published: October 2023

ABSTRACT

The fungal pathogen
Candida albicans
must acquire phosphate to colonize, infect, and proliferate in the human host.
C. albicans
has four inorganic phosphate (P
i
) transporters, Pho84 being the major high-affinity transporter; its cells can also use glycerophosphocholine (GPC) as their sole phosphate source. GPC is a lipid metabolite derived from deacylation of the lipid phosphatidylcholine. GPC is found in multiple human tissues, including the renal medulla, where it acts as an osmolyte.
C. albicans
imports GPC into the cell via the Git3 and Git4 transporters. Internalized GPC can be hydrolyzed to release P
i
. To determine if GPC import and subsequent metabolism affect phosphate homeostasis upon P
i
limitation, we monitored growth and phenotypic outputs in cells provided with either P
i
or GPC. In
pho84
∆
/
∆ mutant cells that exhibit phenotypes associated with P
i
limitation, GPC provision rescued sensitivity to osmotic and cell wall stresses. The glycerophosphodiesterase Gde1 was required for phenotypic rescue of osmotic stress by GPC provision. GPC provision, like P
i
provision, resulted in repression of the PHO regulon and activation of TORC1 signaling. P
i
uptake was similar to GPC uptake when phosphate availability was low (200 µM). While available at lower concentrations than P
i
in the human host, GPC is an advantageous P
i
source for the fungus because it simultaneously serves as a choline source. In summary, we find GPC is capable of substituting for P
i
in
C. albicans
by many though not all criteria and may contribute to phosphate availability for the fungus in the human host.

IMPORTANCE

Candida albicans
is the most commonly isolated species from patients suffering from invasive fungal disease.
C. albicans
is most commonly a commensal organism colonizing a variety of niches in the human host. The fungus must compete for resources with the host flora to acquire essential nutrients such as phosphate. Phosphate acquisition and homeostasis have been shown to play a key role in
C. albicans
virulence, with several genes involved in these processes being required for normal virulence and several being upregulated during infection. In addition to inorganic phosphate (P
i
),
C. albicans
can utilize the lipid-derived metabolite glycerophosphocholine (GPC) as a phosphate source. As GPC is available within the human host, we examined the role of GPC in phosphate homeostasis in
C. albicans
. We find that GPC can substitute for P
i
by many though not all criteria and is likely a relevant physiological phosphate source for
C. albicans
.
The impact of global warming on the signature virulence gene, thermolabile hemolysin, of
Vibrio parahaemolyticus
Authors: Zhang Weishan , Chen Keyu , Zhang Lin , Zhang Ximeng , Zhu Baoli , Lv Na , Mi Kaixia 
Published: October 2023

ABSTRACT

Global warming is increasing human exposure to pathogens and has already had an impact on human health.
Vibrio parahaemolyticus
, a major pathogen causing foodborne illness, accumulates in numerous aquatic organisms and can be affected by environmental stressors such as increased replication errors or DNA damage resulting in point mutations. This could lead to an elevation in the mutation rate, which influences the expansion of
Vibrio
spp. habitats and the spread of associated diseases. In this study, a total of 241 strains were isolated from aquatic products imported or exported through China Customs between 2005 and 2010. The whole genomes of those strains were sequenced, revealing a highly significant level of genetic diversity. Our analysis identified 27 new sequence types (STs) ranging from ST2950 to ST2976. The global temperature trend since 1950 affects the thermolabile hemolysin gene (
tlh
) found in all
Vibrio parahaemolyticus
leading to mutant sites exhibiting similar trends as temperatures rise; seven high-frequency mutation hotspots (A180G, T552G, G657T, T858C, C1062T, A1137G, and T1179C) were identified along with two clinically specific sites (T259C and A951T) that may indicate adaptation over time due to climate change, leading to increased virulence potential for this bacterial species. These results provide insight into the genetics of
Vibrio parahaemolyticus
and provide a reference for subsequent research, identification, and monitoring efforts related to its spread.

IMPORTANCE

In this study,
Vibrio parahaemolyticus
strains were collected from a large number of aquatic products globally and found that temperature has an impact on the virulence of these bacteria. As global temperatures rise, mutations in a gene marker called thermolabile hemolysin (
tlh
) also increase. This suggests that environmental isolates adapt to the warming environment and become more pathogenic. The findings can help in developing tools to analyze and monitor these bacteria as well as assess any link between climate change and vibrio-associated diseases, which could be used for forecasting outbreaks associated with them.
The Lithium Boom: Lithium Sources and Prospects for the Russian Lithium Industry
Authors: Tsivadze A. Yu. , Bezdomnikov A. A. , Kostikova G. V. 
Published: October 2023

Abstract
The explosive development of renewable energy in recent years is reshaping the geopolitical picture of the world. Solar panels and wind turbines have become the symbol of the new energy transition, while lithium-ion batteries have become its basis and the driver of development. It was lithium-ion batteries that made it possible to overcome the main problem of renewable energy – inconstancy and uncontrollability. The article highlights the lithium problem, the reasons for the volatility of lithium prices, the main sources of lithium and the difficulties of its production. In addition, the prospects of development of lithium industry in Russia and current domestic developments in lithium mining technology are considered.