bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated sand management: modeling of sand erosion in a mature oil field in Malaysia
Authors: Mohammadian Erfan , Haron Amir Syakib , Jafari Mehdi , Liu Bo , Azdarpour Amin , Ostadhassan Mehdi
Published: January 2024

Sand production can lead to various problems, including erosion in production flow lines that may lead to total production loss for extended periods and costly workover operations. The extent of erosive damage is determined by many factors, among which the flow and sand rates are the most significant. Three main issues must be addressed to ensure an efficient production operation: Sand erosion estimation, Sand monitoring (settling and deposition), and maintaining optimum production rates. If sand production exceeds certain levels, i.e., allowable sand rate, the erosion in the production network becomes problematic. Sand production has been problematic in some wells in Reservoir X. Core, and historical production data was used to build a comprehensive model using Schlumberger PIPESIM™ hydraulic modelling. The software allows for detailed modelling of the production network by which erosion rate, erosion hotspots, and deposition of the produced sand can be quantitatively analyzed. Considering an allowable erosion rate of 0.3 mm/year, the model outcomes indicate that sand erosion is critical in wells J-1, J-2, and L-2. The next step was identifying the hotspots where the produced sand is deposited in the abovementioned wells. The modelling results indicated that sand deposition is primarily severe in the teeline between the platforms. Moreover, the gas-oil ratio was identified as the most influential factor in the sand deposition. Lastly, a sensitivity analysis was conducted on the allowable flow rates and maximum (technical) allowable sand production and erosion rates to find optimum production rates from reservoir X.
The structure and development of Loess Critical Zone and its soil carbon cycle
Authors: Yang Yang , Zhang Ping-ping , Song Yi , Li Zi-min , Zhou Yuan-yuan , Sun Hui , Qiao Jiangbo , Wang Yun-qiang , An Shao-shan
Published: January 2024

The Loess Critical Zone (LCZ) is located in the intersection of bedrock, groundwater, pedosphere, atmosphere and biosphere. It is a key issue to understand the structural characteristics and soil carbon (C) cycle of the LCZ. We summarized the mechanisms of C exchange between rocks and the atmosphere, and discussed the mechanisms of C stabilization and persistence of the LCZ. Due to the deep layer, C stocks of the CLZ could be underestimated. In light of the recent theory of microbial C pump, soil microorganisms play an important role in C cycle, however, the microbial function is not widely considered in C cycling model of the LCZ. For future studies, it is suggested to systematically study the C cycling process from plant canopy to bedrock by the framework system of the LCZ. A variety of techniques and methods are integrated to combine short-term and high-frequency observations with long-term positioning observations, and pay attention to the response and feedback mechanisms of soil organic C (SOC) cycling to global changes and human activities, especially the migration and transformation of SOC in each circle and interface of the LCZ. We also recommend the necessity for intensive and long-term C monitoring in LCZ over broad geographic scale, to improve microbial C model for accurately evaluating terrestrial C budget and its dynamics. Altogether, this is the first review of C cycling, spanning from the land surface down to the bedrock in the LCZ, which is significant implications for biogeochemical cycling of C in surface and deep layers down to the bedrock.
Investigation of the first reported outbreak of New Delhi metallo-β-lactamase-1-producing Pseudomonas aeruginosa in Texas
Authors: Sopirala Madhuri M. , Hartless Kathleen , Reid Sherry , Christie-Smith Angela , Fiveash Jeanette , Badejogbin Aderonke , Psenicka Andrew Otto
Published: January 2024

We describe an epidemiologic investigation and successful control measures for the first reported outbreak of blaNDM-1-carrying Pseudomonas aeruginosa in Texas occurring in a veteran with transmission of the same organism and a blaNDM-5-carrying Escherichia coli, respectively, to two roommates and blaNDM-carrying organism/s to a patient cared for by common staff.
Canada and Comparative Territorial Politics
Authors: Lecours André
Published: January 2024

This presidential address on Canada and the study of territorial politics makes four main arguments. The first is that territory is a central component of politics, especially of Canadian politics, and that it should remain a focal point of specialists of Canadian and comparative politics. The second is that territory matters in contemporary politics because it serves as grounding for political communities, their claims, and their politics. The third is that not “identifying” parts of Canadian politics as “territorial politics” risks overlooking the importance of territory in the theorizing of federalism, nationalism and regionalism. The fourth is that, through the case of Canada, political scientists have made significant contributions to the study of comparative territorial politics.
Effect of physically effective fibre on chewing behaviour, ruminal fermentation, digesta passage and protein metabolism of dairy cows
Authors: Heering R. , Baumont R. , Selje-Aßmann N. , Dickhoefer U.
Published: January 2024

Dietary fibre concentration and particle size influence chewing behaviour, ruminal fermentation and digesta passage in dairy cows and through this, may impact nitrogen (N) use and excretion by the animals. The aim was thus to evaluate the effects of physically effective neutral detergent fibre (peNDF) concentration on chewing behaviour, ruminal fermentation, passage rate and protein metabolism in four lactating, rumen-cannulated Holstein cows in a 4 × 4 latin square design. Four total mixed rations with identical ingredients, chemical composition and a negative ruminal N balance (–2.1 g/kg dry matter) were tested. They varied in peNDF concentration, adjusted by feed mixing time: low (L), medium-low (ML), medium-high (MH) and high (H) peNDF. Nutrient intakes, number of total chews, organic matter digestibility and yield and efficiency of ruminal microbial protein synthesis responded quadratically to increasing peNDF concentration, with greater values for MH and ML diets. While rumination and total chewing intensity (min/kg dry matter) increased with increasing peNDF concentration, milk yield and composition, digesta passage rates and concentrations of ammonium-N and volatile fatty acids in rumen fluid were similar across diets. Energy-corrected milk yield and partitioning of N between milk and urine responded quadratically to increased peNDF concentration. Energy-corrected milk yield and the percentage of ingested N secreted via milk were lower, but the percentage of N intake excreted via urine was greater for MH and ML diets. Hence, feeding dairy cows a low-protein diet with varying peNDF concentrations affects their chewing behaviour, nutrient digestion and protein metabolism.
Outcomes and characteristics in term infants with necrotising enterocolitis and CHD
Authors: Kelleher Sean T. , Coleman John , McMahon Colin J. , James Adam
Published: January 2024

Background:

CHD is a significant risk factor for the development of necrotising enterocolitis. Existing literature does not differentiate between term and preterm populations. Long-term outcomes of these patients are not well understood. The aim was to investigate the baseline characteristics and outcomes of term normal birth weight infants with CHD who developed necrotising enterocolitis.

Methods:

A retrospective review was performed of infants from a single tertiary centre with CHD who developed necrotising enterocolitis of Bell’s Stage 1–3, over a ten-year period. Inclusion criteria was those born greater than 36 weeks’ gestation and birth weight over 2500g. Exclusion criteria included congenital gastro-intestinal abnormalities. Sub-group analysis was performed using Fisher’s exact test.

Results:

Twenty-five patients were identified, with a median gestational age of 38 weeks. Patients with univentricular physiology accounted for 32% (n = 8) and 52% of patients (n = 13) had a duct-dependent lesion. Atrioventricular septal defect was the most common cardiac diagnosis (n = 6, 24%). Patients with trisomy 21 accounted for 20% of cases. Mortality within 30 days of necrotising enterocolitis was 20%. Long-term mortality was 40%, which increased with increasing Bell’s Stage. In total, 36% (n = 9) required surgical management of necrotising enterocolitis, the rate of which was significantly higher in trisomy 21 cases (p < 0.05).

Conclusion:

Not previously described in term infants is the high rate of trisomy 21 and atrioventricular septal defect. This may reflect higher baseline incidence in our population. Infants with trisomy 21 were more likely to develop surgical necrotising enterocolitis. Mortality at long-term follow-up was high in patients with Bell’s Stage 2–3.
Neurodevelopmental outcomes at 18 months of children diagnosed with CHD compared to children born very preterm
Authors: Roberts Samantha D. , Sananes Renee , Wojtowicz Magdalena , Seed Michael , Miller Steven P. , Chau Vann , Au-Young Stephanie H. , Guo Ting , Ly Linh , Kazazian Vanna , Grunau Ruth E. , Williams Tricia S.
Published: January 2024

Children with CHD or born very preterm are at risk for brain dysmaturation and poor neurodevelopmental outcomes. Yet, studies have primarily investigated neurodevelopmental outcomes of these groups separately.

Objective:

To compare neurodevelopmental outcomes and parent behaviour ratings of children born term with CHD to children born very preterm.

Methods:

A clinical research sample of 181 children (CHD [n = 81]; very preterm [≤32 weeks; n = 100]) was assessed at 18 months.

Results:

Children with CHD and born very preterm did not differ on Bayley-III cognitive, language, or motor composite scores, or on expressive or receptive language, or on fine motor scaled scores. Children with CHD had lower ross motor scaled scores compared to children born very preterm (p = 0.047). More children with CHD had impaired scores (<70 SS) on language composite (17%), expressive language (16%), and gross motor (14%) indices compared to children born very preterm (6%; 7%; 3%; ps < 0.05). No group differences were found on behaviours rated by parents on the Child Behaviour Checklist (1.5–5 years) or the proportion of children with scores above the clinical cutoff. English as a first language was associated with higher cognitive (p = 0.004) and language composite scores (p < 0.001). Lower median household income and English as a second language were associated with higher total behaviour problems (ps < 0.05).

Conclusions:

Children with CHD were more likely to display language and motor impairment compared to children born very preterm at 18 months. Outcomes were associated with language spoken in the home and household income.
Development and application of a 2-step methodology to select a reference society providing Dietary Reference Values for national implementation
Authors: Jotterand Chaparro Corinne , Moullet Clémence , Bertoni Maluf Valeria A. , Parel Nicolas , Tume Lyvonne , Chatelan Angéline , Benzi Schmid Clara , Reinert Raphaël , Bucher Della Torre Sophie
Published: January 2024

Objective:

To describe and discuss a 2-step methodology developed to select a reference society that provides Dietary Reference Values (DRVs) for national implementation and to illustrate its application in Switzerland with one macronutrient and one micronutrient.

Design:

During Step 1, we searched and compared DRVs and methodologies used to define DRVs from eight European societies for seven selected nutrients. We repeated this procedure during Step 2 for DRVs from two preselected societies for 44 nutrients.

Setting:

The 2-step methodology applied here for Switzerland may be used in other countries.

Participants:

The research team commissioned six external experts from three linguistic regions of Switzerland, who provided their opinions through two online surveys, individual interviews, and a focus group.

Results:

After Step 1, we excluded five societies because of old publication dates, irrelevant publication languages for Switzerland, difficulty in accessing documents, or because their DRVs were mainly based on another society. After Step 2, the two societies were qualified based on the analysis of the values and methodologies used. The need for free and easily accessible scientific background information favored the European Food Safety Authority (EFSA). We chose alternative societies for nine nutrients for the overall population or subgroups, and for elderly.

Conclusions:

To manage heterogeneous and complex data from several societies, adopting a 2-step methodology including fewer nutrients and more societies during Step 1, and fewer societies but all nutrients in Step 2, was very helpful. With some exceptions, we selected EFSA as the main society to provide DRVs for Switzerland.
Implementation and effectiveness of a school-based intervention to increase adherence to national school meal guidelines: a non-randomised controlled trial
Authors: Randby Jorunn Sofie , Ogden Terje , Lien Nanna
Published: January 2024

Objective:

Implementation of school meal guidelines is often inadequate, and evidence for effective implementation strategies for school-based nutrition interventions is limited. The aim of the present study was to examine the implementation and effectiveness of a multi-strategy implementation intervention to increase adherence to the Norwegian national school meal guideline.

Design:

The study was a school-based hybrid implementation effectiveness trial with a pre–post non-equivalent control group design, testing three implementation strategies: internal facilitation, training and an educational meeting.

Setting:

Primary schools and after-school services in two counties in south-east Norway.

Participants:

School principals, after-school leaders and class teachers from thirty-three schools in the intervention county and principals and after-school leaders from thirty-four schools in a comparison county.

Results:

There was a significant difference of 4 percentage points in change scores between the intervention and the comparison groups at follow-up, after adjusting for baseline adherence (B = 0·04, seB = 0·01, t = 3·10, P = 0·003). The intervention effect was not associated with the school’s socio-economic profile. School-level fidelity was the implementation dimension that was most strongly correlated (r
s
= 0·48) with the change scores in the intervention group, indicating that principals’ support is important for gaining the largest intervention effects.

Conclusions:

A school-based intervention with low intensity, based on trained teachers as internal facilitators, can increase adherence to the national school meal guideline among Norwegian primary schools, irrespective of local socio-economic conditions. Implementation fidelity, at an organisational level, may be a useful predictor for intervention outcomes in schools.
FORMALLY REGULAR RINGS AND DESCENT OF REGULARITY
Authors: Majadas Javier , Alvite Samuel , Barral Nerea G.
Published: January 2024

Valuation rings and perfectoid rings are examples of (usually non-Noetherian) rings that behave in some sense like regular rings. We give and study an extension of the concept of regular local rings to non-Noetherian rings so that it includes valuation and perfectoid rings and it is related to Grothendieck’s definition of formal smoothness as in the Noetherian case. For that, we have to take into account the topologies. We prove a descent theorem for regularity along flat homomorphisms (in fact for homomorphisms of finite flat dimension), extending some known results from the Noetherian to the non-Noetherian case, as well as generalizing some recent results in the non-Noetherian case, such as the descent of regularity from perfectoid rings by B. Bhatt, S. Iyengar and L. Ma.
Religious Experience and the Philosophy of Perception
Authors: Chen Cheryl K.
Published: January 2024

Do we need justification in order to know God exists? Must we infer God exists, if we are to know that he is there? How might religious experience ground belief in God?
God and the Problem of Evil: Why Soul-Making Won't Suffice
Authors: Earp Brian D.
Published: January 2024

If you believe in the existence of an infinitely good, all-knowing, and all-powerful deity (‘God’), how do you explain the reality of evil – including the inexpressible suffering and death of innocents? Wouldn't God be forced to vanquish such suffering due to God's very nature? Alvin Plantinga has argued, convincingly, that if the possibility of ultimate goodness somehow necessarily required that evil be allowed to exist, God, being omnibenevolent, would have to allow it. But as John Hick has noted, the mere logical possibility of such a situation might not be enough to console the doubting theist. We need a positive reason to believe that evil as we know it is compatible with God's existence. So, Hick offers a ‘soul-making’ theodicy – or vindication – of God, suggesting that the human soul cannot fully progress to spiritual maturity (a kind of ultimate good on his account) without grappling with evil. In this short piece I argue that, if we accept Hick's premises about souls and soul-making, we can indeed make sense of evil to some extent. But, I suggest, his account cannot justify the type or amount of evil we see in the world, so his theodicy does not succeed
Philosophy for Coming Through: Review of Read's Why Climate Breakdown Matters
Authors: Foster John
Published: January 2024

Philosophy has overwhelmingly approached climate breakdown in terms of the ethical obligations to the future which it is supposed to involve. This review of a recent book by Rupert Read shows him bringing philosophy to bear on why and how it matters in the first place – as an already present disaster which could reconnect us deeply with ourselves.
Measurement and Construct-Level Invariance of the Revised Child	Anxiety and Depression Scale (RCADS)
Authors: Buil J. Marieke , Kösters Mia P. , Koot Hans M.
Published: January 2024

Abstract: Measurement and construct-level invariance of the Dutch Revised Child Anxiety and Depression Scale’s test scores (RCADS) across gender and ethnic (minority) backgrounds of the four largest ethnic groups of children living in the Netherlands (i.e., native Dutch; Moroccan; Turkish; or Surinamese/Antillean) was evaluated. Symptoms of generalized anxiety disorder, social phobia, separation anxiety disorder, panic disorder, obsessive-compulsive disorder, and major depressive disorder were rated by 2,679 mainstream elementary schoolchildren ( Mage = 10.61). Results from discrete multiple-group confirmatory factor analyses showed that factor means were generally insensitive to gender bias. However, moderate violations of measurement invariance between native Dutch and the three ethnic minority groups were found for social phobia, panic disorder, and separation anxiety disorder symptoms. Girls had higher mean levels on all RCADS subscales compared to boys. Furthermore, with a few exceptions, children from ethnic minority groups reported higher levels of symptoms of panic disorder, generalized anxiety disorder, and obsessive-compulsive disorder compared to native Dutch children. Scores derived from the RCADS are largely comparable between elementary school boys and girls, but for three out of six subscales, caution is warranted when comparing mean level differences of native Dutch children with children of Turkish, Moroccan, and Surinamese/Antillean ethnic backgrounds.
An Improved 3D Numerical Ray‐Tracing Method for Solving the Spitze Effects Based on Poeverlein's Diagram
Authors: Song Huan , Qing Haiyin , Xu Jiyao
Published: January 2024

The Spitze phenomenon is closely related to the Earth's magnetic field, and characterizes high‐frequency (HF) rays propagating in the ionosphere. Specifically, when the reflection conditions are satisfied, HF rays are reflected perpendicular to the Earth's magnetic field. Studying the HF rays reflected from the Spitze region is important to indirectly learn about the ionosphere magnetic properties. The 3D numerical ray‐tracing method is a widely used HF rays inversion technique. However, the conventional 3D Haselegrove numerical ray‐tracing method can not trace the ordinary rays in the Spitze region back to the ground. Therefore, we improved the conventional ray‐tracing method based on Poeverlein's diagram. The improved method can change the ordinary rays' propagation directions when they travel very close to the Spitze reflection point. In this way, the ordinary rays' propagation interruption caused by the Spitze can be eliminated. An example showing the ordinary and extraordinary rays traced by the conventional and improved ray‐tracing methods under the quiet ionosphere is provided to validate the improvement. In addition, three disturbed ionospheric backgrounds with large‐scale, medium‐scale, and small‐scale TIDs are designed to simulate various HF rays for further validation. The simulation results show that the Spitze exists in the quiet and disturbed ionosphere, and the improved ray‐tracing method can properly solve the Spitze effects on the traced ordinary rays.
Premature Deaths Due To Heat Exposure: The Potential Effects of Neighborhood‐Level Versus City‐Level Acclimatization Within US Cities
Authors: Shindell D. , Hunter R. , Faluvegi G. , Parsons L.
Published: January 2024

For the population of a given US city, the risk of premature death associated with heat exposure increases as temperatures rise, but risks in hotter cities are generally lower than in cooler cities at equivalent temperatures due to factors such as acclimatization. Those living in especially hot neighborhoods within cities might therefore suffer much more than average if such adaptation is only at the city‐wide level, whereas they might not experience greatly increased risk if adjustment is at the neighborhood level. To compare these possibilities, we use high spatial resolution temperature data to evaluated heat‐related deaths assuming either adjustment at the city‐wide or at the neighborhood scale in 10 large US cities. On average, we find that if inhabitants are adjusted to their local conditions, a neighborhood that was 10°C hotter than a cooler one would experience only about 1.0–1.5 excess heat deaths per year per 100,000 persons. By contrast, if inhabitants are acclimatized to city‐wide temperatures, the hotter neighborhood would experience about 15 excess deaths per year per 100,000 persons. Using idealized analyses, we demonstrate that current city‐wide epidemiological data do not differentiate between these differing adjustments. Given the very large effects of assumptions about neighborhood‐level acclimatization found here, as well as the fact that current literature is conflicting on the spatial scale of acclimatization, more neighborhood‐level epidemiological data are urgently needed to determine the health impacts of variations in heat exposure within urban areas, better constrain projected changes, and inform mitigation efforts.
Unraveling the Tectonic History of the Tharsis Rise on Mars: Plume Migration and Critical Taper Dome
Authors: Karagoz Oguzcan , Kenkmann Thomas , Hergarten Stefan
Published: January 2024

Wrinkle ridges are widespread tectonic landforms that serve as paleo‐strain and paleo‐stress indicators of the compressional history and thermal evolution of Mars. To reconstruct the center of the Tharsis rise and its migration with time, we mapped wrinkle ridges in the periphery of the dome and analyzed 34,741 wrinkle ridge segments with a total length of 77,294 km. We determined the deviation of each wrinkle ridge segment from a concentric strike direction for systematically changing centers. A fitting procedure indicates that all wrinkle ridge segments can be allocated with good precision to five different stress centers (C1‐5) within the Tharsis rise: the southern edge of the Alba Mons caldera (C1), Ceraunius Fossae (C2), between Ulysses Patera and Pavonis Chasma (C3), Phoenicis Lacus (C4), and Claritas Rupes (C5). We performed a morphometric analysis of each wrinkle ridge and calculated the amount of shortening and depth of detachment, making use of methods for constructing balanced cross‐sections. The amount of horizontal shortening varies from 1.5 to 3.8 km and the range of the detachment depth was found to be between 2.9 and 8.8 km, with significant variance forming an acute wedge of 1.2°–2.2°. Based on the critical taper theory, we inferred a very low basal friction coefficient ranging from 0.077 to 0.093 across the detachments for the five centers (C1–C5). Our findings suggest that these detachments are either localized along salt or clay layers or occur where liquid water is dominant below an impermeable permafrost layer.
Detecting Paleoclimate Transitions With Laplacian Eigenmaps of Recurrence Matrices (LERM)
Authors: James Alexander , Emile‐Geay Julien , Malik Nishant , Khider Deborah
Published: January 2024

Paleoclimate records can be considered low‐dimensional projections of the climate system that generated them. Understanding what these projections tell us about past climates, and changes in their dynamics, is a main goal of time series analysis on such records. Laplacian eigenmaps of recurrence matrices (LERM) is a novel technique using univariate paleoclimate time series data to indicate when notable shifts in dynamics have occurred. LERM leverages time delay embedding to construct a manifold that is mappable to the attractor of the climate system; this manifold can then be analyzed for significant dynamical transitions. Through numerical experiments with observed and synthetic data, LERM is applied to detect both gradual and abrupt regime transitions. Our paragon for gradual transitions is the Mid‐Pleistocene Transition (MPT). We show that LERM can robustly detect gradual MPT‐like transitions for sufficiently high signal‐to‐noise (S/N) ratios, though with a time lag related to the embedding process. Our paragon of abrupt transitions is the “8.2 ka” event; we find that LERM is generally robust at detecting 8.2 ka‐like transitions for sufficiently high S/N ratios, though edge effects become more influential. We conclude that LERM can usefully detect dynamical transitions in paleogeoscientific time series, with the caveat that false positive rates are high when dynamical transitions are not present, suggesting the importance of using multiple records to confirm the robustness of transitions. We share an open‐source Python package to facilitate the use of LERM in paleoclimatology and paleoceanography.
Hypoxia induces mitochondrial protein lactylation to limit oxidative phosphorylation
Authors: Mao Yunzi , Zhang Jiaojiao , Zhou Qian , He Xiadi , Zheng Zhifang , Wei Yun , Zhou Kaiqiang , Lin Yan , Yu Haowen , Zhang Haihui , Zhou Yineng , Lin Pengcheng , Wu Baixing , Yuan Yiyuan , Zhao Jianyuan , Xu Wei , Zhao Shimin
Published: January 2024

Oxidative phosphorylation (OXPHOS) consumes oxygen to produce ATP. However, the mechanism that balances OXPHOS activity and intracellular oxygen availability remains elusive. Here, we report that mitochondrial protein lactylation is induced by intracellular hypoxia to constrain OXPHOS. We show that mitochondrial alanyl-tRNA synthetase (AARS2) is a protein lysine lactyltransferase, whose proteasomal degradation is enhanced by proline 377 hydroxylation catalyzed by the oxygen-sensing hydroxylase PHD2. Hypoxia induces AARS2 accumulation to lactylate PDHA1 lysine 336 in the pyruvate dehydrogenase complex and carnitine palmitoyltransferase 2 (CPT2) lysine 457/8, inactivating both enzymes and inhibiting OXPHOS by limiting acetyl-CoA influx from pyruvate and fatty acid oxidation, respectively. PDHA1 and CPT2 lactylation can be reversed by SIRT3 to activate OXPHOS. In mouse muscle cells, lactylation is induced by lactate oxidation-induced intracellular hypoxia during exercise to constrain high-intensity endurance running exhaustion time, which can be increased or decreased by decreasing or increasing lactylation levels, respectively. Our results reveal that mitochondrial protein lactylation integrates intracellular hypoxia and lactate signals to regulate OXPHOS.
Efficient genomics-based ‘end-to-end’ selective tree breeding framework
Authors: El-Kassaby Yousry A. , Cappa Eduardo P. , Chen Charles , Ratcliffe Blaise , Porth Ilga M.
Published: January 2024

Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method’s superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.
How spin relaxes and dephases in bulk halide perovskites
Authors: Xu Junqing , Li Kejun , Huynh Uyen N. , Fadel Mayada , Huang Jinsong , Sundararaman Ravishankar , Vardeny Valy , Ping Yuan
Published: January 2024

Spintronics in halide perovskites has drawn significant attention in recent years, due to their highly tunable spin-orbit fields and intriguing interplay with lattice symmetry. Here, we perform first-principles calculations to determine the spin relaxation time (T1) and ensemble spin dephasing time ($${T}_{2}^{*}$$

T

2

*

) in a prototype halide perovskite, CsPbBr3. To accurately capture spin dephasing in external magnetic fields we determine the Landé g-factor from first principles and take it into account in our calculations. These allow us to predict intrinsic spin lifetimes as an upper bound for experiments, identify the dominant spin relaxation pathways, and evaluate the dependence on temperature, external fields, carrier density, and impurities. We find that the Fröhlich interaction that dominates carrier relaxation contributes negligibly to spin relaxation, consistent with the spin-conserving nature of this interaction. Our theoretical approach may lead to new strategies to optimize spin and carrier transport properties.
Leafhopper salivary vitellogenin mediates virus transmission to plant phloem
Authors: Wang Yanfei , Lu Chengcong , Guo Shude , Guo Yuxin , Wei Taiyun , Chen Qian
Published: January 2024

Salivary effectors of piercing-sucking insects can suppress plant defense to promote insect feeding, but it remains largely elusive how they facilitate plant virus transmission. Leafhopper Nephotettix cincticeps transmits important rice reovirus via virus-packaging exosomes released from salivary glands and then entering the rice phloem. Here, we report that intact salivary vitellogenin of N. cincticeps (NcVg) is associated with the GTPase Rab5 of N. cincticeps (NcRab5) for release from salivary glands. In virus-infected salivary glands, NcVg is upregulated and packaged into exosomes mediated by virus-induced NcRab5, subsequently entering the rice phloem. The released NcVg inherently suppresses H2O2 burst of rice plants by interacting with rice glutathione S-transferase F12, an enzyme catalyzing glutathione-dependent oxidation, thus facilitating leafhoppers feeding. When leafhoppers transmit virus, virus-upregulated NcVg thus promotes leafhoppers feeding and enhances viral transmission. Taken together, the findings provide evidence that viruses exploit insect exosomes to deliver virus-hijacked effectors for efficient transmission.
Selective blockade of Cav1.2 (α1C) versus Cav1.3 (α1D) L-type calcium channels by the black mamba toxin calciseptine
Authors: Mesirca Pietro , Chemin Jean , Barrère Christian , Torre Eleonora , Gallot Laura , Monteil Arnaud , Bidaud Isabelle , Diochot Sylvie , Lazdunski Michel , Soong Tuck Wah , Barrère-Lemaire Stéphanie , Mangoni Matteo E. , Nargeot Joël
Published: January 2024

L-type voltage-gated calcium channels are involved in multiple physiological functions. Currently available antagonists do not discriminate between L-type channel isoforms. Importantly, no selective blocker is available to dissect the role of L-type isoforms Cav1.2 and Cav1.3 that are concomitantly co-expressed in the heart, neuroendocrine and neuronal cells. Here we show that calciseptine, a snake toxin purified from mamba venom, selectively blocks Cav1.2 -mediated L-type calcium currents (ICaL) at concentrations leaving Cav1.3-mediated ICaL unaffected in both native cardiac myocytes and HEK-293T cells expressing recombinant Cav1.2 and Cav1.3 channels. Functionally, calciseptine potently inhibits cardiac contraction without altering the pacemaker activity in sino-atrial node cells, underscoring differential roles of Cav1.2− and Cav1.3 in cardiac contractility and automaticity. In summary, calciseptine is a selective L-type Cav1.2 Ca2+ channel blocker and should be a valuable tool to dissect the role of these L-channel isoforms.
Midbrain node for context-specific vocalisation in fish
Authors: Schuppe Eric R. , Ballagh Irene , Akbari Najva , Fang Wenxuan , Perelmuter Jonathan T. , Radtke Caleb H. , Marchaterre Margaret A. , Bass Andrew H.
Published: January 2024

Vocalizations communicate information indicative of behavioural state across divergent social contexts. Yet, how brain regions actively pattern the acoustic features of context-specific vocal signals remains largely unexplored. The midbrain periaqueductal gray (PAG) is a major site for initiating vocalization among mammals, including primates. We show that PAG neurons in a highly vocal fish species (Porichthys notatus) are activated in distinct patterns during agonistic versus courtship calling by males, with few co-activated during a non-vocal behaviour, foraging. Pharmacological manipulations within vocally active PAG, but not hindbrain, sites evoke vocal network output to sonic muscles matching the temporal features of courtship and agonistic calls, showing that a balance of inhibitory and excitatory dynamics is likely necessary for patterning different call types. Collectively, these findings support the hypothesis that vocal species of fish and mammals share functionally comparable PAG nodes that in some species can influence the acoustic structure of social context-specific vocal signals.
Derivation of human primordial germ cell-like cells in an embryonic-like culture
Authors: Esfahani Sajedeh Nasr , Zheng Yi , Arabpour Auriana , Irizarry Agnes M. Resto , Kobayashi Norio , Xue Xufeng , Shao Yue , Zhao Cheng , Agranonik Nicole L. , Sparrow Megan , Hunt Timothy J. , Faith Jared , Lara Mary Jasmine , Wu Qiu Ya , Silber Sherman , Petropoulos Sophie , Yang Ran , Chien Kenneth R. , Clark Amander T. , Fu Jianping
Published: January 2024

Primordial germ cells (PGCs) are the embryonic precursors of sperm and eggs. They transmit genetic and epigenetic information across generations. Given the prominent role of germline defects in diseases such as infertility, detailed understanding of human PGC (hPGC) development has important implications in reproductive medicine and studying human evolution. Yet, hPGC specification remains an elusive process. Here, we report the induction of hPGC-like cells (hPGCLCs) in a bioengineered human pluripotent stem cell (hPSC) culture that mimics peri-implantation human development. In this culture, amniotic ectoderm-like cells (AMLCs), derived from hPSCs, induce hPGCLC specification from hPSCs through paracrine signaling downstream of ISL1. Our data further show functional roles of NODAL, WNT, and BMP signaling in hPGCLC induction. hPGCLCs are successfully derived from eight non-obstructive azoospermia (NOA) participant-derived hPSC lines using this biomimetic platform, demonstrating its promise for screening applications.
Metallopolymer strategy to explore hypoxic active narrow-bandgap photosensitizers for effective cancer photodynamic therapy
Authors: Zhang Zhao , Wei Zixiang , Guo Jintong , Lyu Jinxiao , Wang Bingzhe , Wang Gang , Wang Chunfei , Zhou Liqiang , Yuan Zhen , Xing Guichuan , Wu Changfeng , Zhang Xuanjun
Published: January 2024

Practical photodynamic therapy calls for high-performance, less O2-dependent, long-wavelength-light-activated photosensitizers to suit the hypoxic tumor microenvironment. Iridium-based photosensitizers exhibit excellent photocatalytic performance, but the in vivo applications are hindered by conventional O2-dependent Type-II photochemistry and poor absorption. Here we show a general metallopolymerization strategy for engineering iridium complexes exhibiting Type-I photochemistry and enhancing absorption intensity in the blue to near-infrared region. Reactive oxygen species generation of metallopolymer Ir-P1, where the iridium atom is covalently coupled to the polymer backbone, is over 80 times higher than that of its mother polymer without iridium under 680 nm irradiation. This strategy also works effectively when the iridium atom is directly included (Ir-P2) in the polymer backbones, exhibiting wide generality. The metallopolymer nanoparticles exhibiting efficient O2•− generation are conjugated with integrin αvβ3 binding cRGD to achieve targeted photodynamic therapy.
A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand
Authors: Power Jean F. , Carere Carlo R. , Welford Holly E. , Hudson Daniel T. , Lee Kevin C. , Moreau John W. , Ettema Thijs J. G. , Reysenbach Anna-Louise , Lee Charles K. , Colman Daniel R. , Boyd Eric S. , Morgan Xochitl C. , McDonald Ian R. , Craig Cary S. , Stott Matthew B.
Published: January 2024

Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
Anomalous temperature dependence of elastic limit in metallic glasses
Authors: Wang Yifan , Liu Jing , Jiang Jian-Zhong , Cai Wei
Published: January 2024

Understanding the atomistic mechanisms of inelastic deformation in metallic glasses (MGs) remains challenging due to their amorphous structure, where local carriers of plasticity cannot be easily defined. Using molecular dynamics (MD) simulations, we analyzed the onset of inelastic deformation in CuZr MGs, specifically the temperature dependence of the elastic limit, in terms of localized shear transformation (ST) events. We find that although the ST events initiate at lower strain with increasing temperature, the elastic limit increases with temperature in certain temperature ranges. We explain this anomalous behavior through the framework of an energy-strain landscape (ESL) constructed from high-throughput strain-dependent energy barrier calculations for the ST events identified in the MD simulations. The ESL reveals that the anomalous behavior is caused by the transition of ST events from irreversible to reversible with increasing temperature. An analytical formulation is developed to predict this transition and the temperature dependence of the elastic limit.
Mic19 depletion impairs endoplasmic reticulum-mitochondrial contacts and mitochondrial lipid metabolism and triggers liver disease
Authors: Dong Jun , Chen Li , Ye Fei , Tang Junhui , Liu Bing , Lin Jiacheng , Zhou Pang-Hu , Lu Bin , Wu Min , Lu Jia-Hong , He Jing-Jing , Engelender Simone , Meng Qingtao , Song Zhiyin , He He
Published: January 2024

Endoplasmic reticulum (ER)-mitochondria contacts are critical for the regulation of lipid transport, synthesis, and metabolism. However, the molecular mechanism and physiological function of endoplasmic reticulum-mitochondrial contacts remain unclear. Here, we show that Mic19, a key subunit of MICOS (mitochondrial contact site and cristae organizing system) complex, regulates ER-mitochondria contacts by the EMC2-SLC25A46-Mic19 axis. Mic19 liver specific knockout (LKO) leads to the reduction of ER-mitochondrial contacts, mitochondrial lipid metabolism disorder, disorganization of mitochondrial cristae and mitochondrial unfolded protein stress response in mouse hepatocytes, impairing liver mitochondrial fatty acid β-oxidation and lipid metabolism, which may spontaneously trigger nonalcoholic steatohepatitis (NASH) and liver fibrosis in mice. Whereas, the re-expression of Mic19 in Mic19 LKO hepatocytes blocks the development of liver disease in mice. In addition, Mic19 overexpression suppresses MCD-induced fatty liver disease. Thus, our findings uncover the EMC2-SLC25A46-Mic19 axis as a pathway regulating ER-mitochondria contacts, and reveal that impairment of ER-mitochondria contacts may be a mechanism associated with the development of NASH and liver fibrosis.
Microbial co-occurrences on catheters from long-term catheterized patients
Authors: Nye Taylor M. , Zou Zongsen , Obernuefemann Chloe L. P. , Pinkner Jerome S. , Lowry Erin , Kleinschmidt Kent , Bergeron Karla , Klim Aleksandra , Dodson Karen W. , Flores-Mireles Ana L. , Walker Jennifer N. , Wong Daniel Garrett , Desai Alana , Caparon Michael G. , Hultgren Scott J.
Published: January 2024

Catheter-associated urinary tract infections (CAUTIs), a common cause of healthcare-associated infections, are caused by a diverse array of pathogens that are increasingly becoming antibiotic resistant. We analyze the microbial occurrences in catheter and urine samples from 55 human long-term catheterized patients collected over one year. Although most of these patients were prescribed antibiotics over several collection periods, their catheter samples remain colonized by one or more bacterial species. Examination of a total of 366 catheter and urine samples identify 13 positive and 13 negative genus co-occurrences over 12 collection periods, representing associations that occur more or less frequently than expected by chance. We find that for many patients, the microbial species composition between collection periods is similar. In a subset of patients, we find that the most frequently sampled bacteria, Escherichia coli and Enterococcus faecalis, co-localize on catheter samples. Further, co-culture of paired isolates recovered from the same patients reveals that E. coli significantly augments E. faecalis growth in an artificial urine medium, where E. faecalis monoculture grows poorly. These findings suggest novel strategies to collapse polymicrobial CAUTI in long-term catheterized patients by targeting mechanisms that promote positive co-associations.
ECOLE: Learning to call copy number variants on whole exome sequencing data
Authors: Mandiracioglu Berk , Ozden Furkan , Kaynar Gun , Yilmaz Mehmet Alper , Alkan Can , Cicek A. Ercument
Published: January 2024

Copy number variants (CNV) are shown to contribute to the etiology of several genetic disorders. Accurate detection of CNVs on whole exome sequencing (WES) data has been a long sought-after goal for use in clinics. This was not possible despite recent improvements in performance because algorithms mostly suffer from low precision and even lower recall on expert-curated gold standard call sets. Here, we present a deep learning-based somatic and germline CNV caller for WES data, named ECOLE. Based on a variant of the transformer architecture, the model learns to call CNVs per exon, using high-confidence calls made on matched WGS samples. We further train and fine-tune the model with a small set of expert calls via transfer learning. We show that ECOLE achieves high performance on human expert labelled data for the first time with 68.7% precision and 49.6% recall. This corresponds to precision and recall improvements of 18.7% and 30.8% over the next best-performing methods, respectively. We also show that the same fine-tuning strategy using tumor samples enables ECOLE to detect RT-qPCR-validated variations in bladder cancer samples without the need for a control sample. ECOLE is available at https://github.com/ciceklab/ECOLE.
Histone lactylation couples cellular metabolism with developmental gene regulatory networks
Authors: Merkuri Fjodor , Rothstein Megan , Simoes-Costa Marcos
Published: January 2024

Embryonic cells exhibit diverse metabolic states. Recent studies have demonstrated that metabolic reprogramming drives changes in cell identity by affecting gene expression. However, the connection between cellular metabolism and gene expression remains poorly understood. Here we report that glycolysis-regulated histone lactylation couples the metabolic state of embryonic cells with chromatin organization and gene regulatory network (GRN) activation. We found that lactylation marks genomic regions of glycolytic embryonic tissues, like the neural crest (NC) and pre-somitic mesoderm. Histone lactylation occurs in the loci of NC genes as these cells upregulate glycolysis. This process promotes the accessibility of active enhancers and the deployment of the NC GRN. Reducing the deposition of the mark by targeting LDHA/B leads to the downregulation of NC genes and the impairment of cell migration. The deposition of lactyl-CoA on histones at NC enhancers is supported by a mechanism that involves transcription factors SOX9 and YAP/TEAD. These findings define an epigenetic mechanism that integrates cellular metabolism with the GRNs that orchestrate embryonic development.