bluuebunny/crossref_metadata_2025 huggingface dataset:
Studying the internal structures of the central region of prestellar core L1517B in Taurus molecular cloud using ammonia (NH3) (1,1) and (2,2) lines
Authors: Koley Atanu
Published: November 2023

Measurement of internal structures in the prestellar core is essential for understanding the initial conditions prior to star formation. In this work, we study the ammonia lines (NH

$_{3}$

) (J, K = 1,1 and 2,2) in the central region of the prestellar core L1517B with the Karl G. Jansky Very Large Array (VLA) radio telescope (spatial resolution

$\sim$

3.7′′). Our analysis indicates that the central region of the core is close-to-round in shape obtained both from NH

$_{3}$

(1,1) and (2,2) emissions. Radially averaged kinetic temperature (

$T_{k}$

) is almost constant with a mean value of

$\sim$

9 K. A radially sharp decrease in kinetic temperature (

$T_{k}$

) has not been observed inside the central dense nucleus of this prestellar core. In addition, we also notice that there is an overall velocity gradient from north-east to south-west direction in this region, which may be indicative of the rotational motion of the core. We then calculate the parameter

$\beta$

, which is defined as the ratio of rotational energy to gravitational potential energy and find that

$\beta$

equals to

$\sim$

5

$\times$

10

$^{-3}$

; which indicates that rotation has no effect at least inside the central region of the core. We also perform the viral analysis and observe that the central region may be in a stage of contraction. From this study, we also show that turbulence inside the central region is subsonic in nature (sonic Mach number,

$M_{s}$

$<$

1) and has no prominent length-scale dependence. Furthermore, we notice that the decrement of excitation temperature (

$T_{ex}$

) and column density of NH

$_{3}$

from the centre of the core to the outer side with the peak values of

$\sim$

5.6 K and

$\sim$

10

$^{15}$

cm

$^{-2}$

, respectively. In conclusion, this work examines different physical and kinematical properties of the central region of the L1517B prestellar core.
Judicial Specialization and Deference in Asylum Cases on the U.S. Courts of Appeals
Authors: STOBB MAUREEN , KENNEDY JOSHUA B.
Published: November 2023

Many look to the federal courts as an avenue of control of the growing administrative state. Some advocate the creation of specialized federal courts of appeals in areas such as immigration and social security. Yet, little is known about whether repeat exposure to specific types of cases enables federal judges to overcome doctrines of deference and whether such an effect would be policy-neutral. Gathering a sample of over 4000 cases decided by the U.S. Courts of Appeals between 2002 and 2017, we demonstrate that exposure to asylum cases over time emboldens federal judges to challenge administrative asylum decisions, asserting their personal policy preferences. The effect is particularly strong when the legal issue should prompt deference based on bureaucratic expertise. These findings not only address important questions raised by bureaucracy and court scholars but also inform a salient public debate concerning the proper treatment of those seeking refuge within our borders.
Genesis of the Jinying gold deposit, southern Jilin Province, NE China: Constraints from geochronology and isotope geochemistry
Authors: Zhang Yong , Wu Yushi , Li Huali , Han Jilong , Song Quanheng
Published: November 2023

The Jinying gold deposit is located in southern Jilin Province in northeast China and is representative of the large Early Cretaceous gold deposits in this area. To better understand ore genesis of this deposit, a multi-isotope integrated analysis of U–Pb–Rb–Sr–He–Ar–S has been carried out. Laser ablation inductively coupled plasma–mass spectrometry (LA–ICP–MS) dating of zircons from the granodiorite porphyry and dioritic porphyrite in the study area yields ages of 172.1 ± 1.2 Ma and 122.5 ± 0.8 Ma, suggesting that corresponding intrusion occurred in the Middle Jurassic and the Early Cretaceous. Rb–Sr dating of the pyrite yields an isochron age of 120 ± 3 Ma, suggesting that gold mineralization occurred in the Early Cretaceous. The fluid inclusions in pyrite yield 3He/4He ratios clustered within a small range from 0.08 to 0.13 Ra, 40Ar/36Ar ratios between 331.6 and 351.3, and mantle He in the range of 1.0–1.6%, indicating that the ore-forming fluids originated from a mixed crustal and mantle source. The in situ S isotopic values of pyrite vary between + 0.1 ‰ and + 2.8 ‰, suggesting that the ore-related sulphur came from the deep magmatic source. Combined with the geological history of the study area, it can be concluded that the gold mineralization was possibly related to the extensional setting associated with the rollback of the Palaeo-Pacific Plate.
Gender Equality Provisions in Trade and Investment Agreements: Are They Widening the Negotiation Capacity Gap?
Authors: Bahri Amrita , Amaral Renata
Published: November 2023

In the recent years, there has been an upsurge in the number of countries that are mainstreaming gender equality concerns in their trade and investment agreements. These recent developments challenge the long-standing assumption that trade, investment, and gender equality are not related. They also show that gender mainstreaming in trade and investment agreements is here to stay. However, very few countries – mostly developed countries – have led this mainstreaming approach and have made efforts to incentivize other countries to negotiate gender-responsive trade and investment agreements. The majority of developing countries are yet to take their first steps in negotiating such policy instruments with a gender lens, and their hesitation can be grounded in various reasons including fears of protectionism, lack of data, paucity of understanding and expertise, and, more broadly, constraints relating to their negotiation capacity. Moreover, the inclusion of gender-related concerns in the negotiation of such agreements has deepened and widened the negotiation capacity gap between developed and developing countries. In this article, the authors attempt to assess this widening negotiation capacity gap with the help of empirical research, and how this capacity gap can lead to disproportionate and negative repercussions for developing countries more than developed countries.
CBT for post-traumatic stress disorder and depression in the context of pregnancy loss: a case study reflection
Authors: Hassan Hibah , Holmes Natalie
Published: November 2023

Women who experience pregnancy loss are at increased risk of psychological distress, including post-traumatic stress disorder (PTSD) and depression. Despite the substantial evidence base for trauma-focused cognitive behavioural therapy (CBT) for PTSD, there is limited research on this specific type of trauma, as well as a dearth of research exploring treatment for co-morbid PTSD and depression. This study used a single case experimental design to assess the efficacy of sequential CBT for treating PTSD and depression in a primary care setting in the United Kingdom. Results demonstrate a reduction in scores on the PCL-5 following trauma-focused CBT, but not a clinically significant reduction in depression scores. This write-up reflects on the effectiveness of sequential treatment and suggests alternative approaches. Future directions for research are also given.

Dedication: The authors dedicate this paper to all parents who have experienced pregnancy or baby loss.

Key learning aims

(1)

To gain an understanding of some of the challenges in delivering CBT for trauma related to pregnancy loss.

(2)

To reflect on treatment of co-morbid PTSD and depression through flexible use of evidence-based treatment, and consider alternative approaches to sequential treatment.

(3)

To consider the impact of grief in formulation and treatment.
The impact of smoking and nicotine exposure during pregnancy on fetal nephrogenesis: a systematic review
Authors: Popham Kelsey , Kandasamy Yogavijayan
Published: November 2023

The effect of smoking and nicotine exposure during pregnancy on fetal nephrogenesis is a growing area of research. The objective of this systematic review is to summarise the current evidence in this research field. Our literature search identified a total of 415 articles from PubMed, Embase, Scopus, and Cochrane. After electronic sorting and manual screening, 18 eligible articles were found, 6 being human studies and 12 being animal studies. Articles that did not study nicotine or smoking, did not focus on fetal kidney development, or did not include nicotine or smoking exposure during pregnancy were excluded from the systematic review. The main outcomes of the studies were kidney weight, volume and size, kidney histopathology and morphology, and kidney function. Evidence from human studies identified a reduction in fetal kidney size, volume, and weight in offspring exposed to smoking during pregnancy; and the greatest impact was seen in offspring exposed to >5–10 cigarettes per day. Animal studies investigated kidney histopathology and highlighted kidney injury and microscopic changes in response to nicotine exposure during pregnancy. Further research is required to determine the impact on kidney function. Recreational nicotine use is evolving, and with the increasing use of urine cotinine in the evaluation of nicotine exposure, further research is needed.
The Repetition Period of MeV Electron Microbursts as Measured by SAMPEX/HILT
Authors: Kandar Hamdan , Blum Lauren , Shumko Mykhaylo , Chen Lunjin , Shue Jih‐Hong
Published: November 2023

Here we examine properties of MeV electron microbursts to better understand their generation mechanisms. Using 15 years of data from Solar, Anomalous, Magnetospheric Particles Explorer/Heavy Ion Large Telescope, >1 MeV microburst repetition periods (time spacing between bursts) are examined and clear dependencies on Auroral Electrojet (AE), L shell, and magnetic local time (MLT) are discovered. Microburst repetition periods are shortest around 0–6 hr MLT and 4–5 L shell, and grow longer toward the day and afternoon sectors and larger L shells. Shorter repetition periods (<1 s) are also found to be more common during higher AE, while longer periods (>10 s) more common during quiet times. The microburst repetition period distributions are compared directly to those of rising tone chorus wave elements and found to be similar in the night, dawn and day MLT sectors, suggesting chorus wave repetition periods are likely directly controlling those of microburst precipitation. However, dusk‐side distributions differ, indicating that the dusk‐side microbursts properties may be controlled by other processes.
The Attenuation and Scattering Signature of Fluid Reservoirs and Tectonic Interactions in the Central‐Southern Apennines (Italy)
Authors: Talone D. , De Siena L. , Lavecchia G. , de Nardis R.
Published: November 2023

Despite the high detection level of the Italian seismic network and the risk associated with its fault networks, Central‐Southern Italy has no unique geophysical model of the crust able to illuminate its complex tectonics. Here, we obtain seismic attenuation and scattering tomography models of this area; both reveal high attenuation and scattering anomalies characterizing the entire Apenninic Chain and related to its East‐ and West‐dipping extensional Quaternary tectonic alignments. Fault‐associated fractured zones become preferential ways for circulating and degassing high‐attenuation CO2‐bearing fluids. A previously undetected fluid source area is a high‐attenuation volume below the Matese complex, while a similar smaller anomaly supports a fluid source near L'Aquila. The most prominent low attenuation and scattering volumes reveal a locked aseismic zone corresponding to the Fucino‐Morrone‐Porrara fault systems, representing a zone of significant seismic hazard.
Fine and Coarse Dust Effects on Radiative Forcing, Mass Deposition, and Solar Devices Over the Middle East
Authors: Mostamandi Suleiman , Ukhov Alexander , Engelbrecht Johann , Shevchenko Illia , Osipov Sergey , Stenchikov Georgiy
Published: November 2023

In desert regions like the Middle East, dust has a profound impact on the environment, climate, air quality, and solar devices. The size of dust particles determines the extent of these effects. Dust deposition (DD) measurements show that coarse dust particles with geometric radius r > 10 μm comprise most of the deposited mass. Still, these particles are not represented in the current models that are tuned to fit the observed aerosol optical depth (AOD). As a result, the existing models and reanalysis products underestimate DD and dust emission (DE) almost 3 times. This is the first study to constrain the dust simulations by both AOD and DD measurements to quantify the effect of coarse and fine dust using the WRF‐Chem model. We found that, on average, coarse dust contributes less than 10% to dust shortwave radiative forcing (RF) at the surface but comprises more than 70% of DE. Annual mean net RF over the Arabian Peninsula and regional seas locally reaches −25 W m−2. Airborne fine dust particles with radii r < 3 μm are mainly responsible for the significant dimming (5%–10%) of solar radiation, cooling the surface, and hampering solar energy production. However, dust mass deposition is primarily linked to coarse particles, decreasing the efficiency of photovoltaic panels by 2%–5% per day. Therefore, incorporating coarse dust in model simulations and data assimilation would improve the overall description of the dust mass balance and its impact on environmental systems and solar devices.
Perspectives of current understanding and therapeutics of Diamond-Blackfan anemia
Authors: Liu Yang , Karlsson Stefan
Published: November 2023

Abstact

Diamond-Blackfan anemia (DBA) is a rare congenital bone marrow failure disorder characterized by erythroid hypoplasia. It primarily affects infants and is often caused by heterozygous allelic variations in ribosomal protein (RP) genes. Recent studies also indicated that non-RP genes like GATA1, TSR2, are associated with DBA. P53 activation, translational dysfunction, inflammation, imbalanced globin/heme synthesis, and autophagy dysregulation were shown to contribute to disrupted erythropoiesis and impaired red blood cell production. The main therapeutic option for DBA patients is corticosteroids. However, half of these patients become non-responsive to corticosteroid therapy over prolonged treatment and have to be given blood transfusions. Hematopoietic stem cell transplantation is currently the sole curative option, however, the treatment is limited by the availability of suitable donors and the potential for serious immunological complications. Recent advances in gene therapy using lentiviral vectors have shown promise in treating RPS19-deficient DBA by promoting normal hematopoiesis. With deepening insights into the molecular framework of DBA, emerging therapies like gene therapy hold promise for providing curative solutions and advancing comprehension of the underlying disease mechanisms.
Effectiveness of pre-pregnancy lifestyle in preventing gestational diabetes mellitus—a systematic review and meta-analysis of 257,876 pregnancies
Authors: Sampathkumar Swetha , Parkhi Durga , Ghebremichael-Weldeselassie Yonas , Sukumar Nithya , Saravanan Ponnusamy
Published: November 2023

Background

Gestational Diabetes Mellitus (GDM) is hyperglycaemia first detected during pregnancy. Globally, GDM affects around 1 in 6 live births (up to 1 in 4 in low- and middle-income countries- LMICs), thus, urgent measures are needed to prevent this public health threat.

Objective

To determine the effectiveness of pre-pregnancy lifestyle in preventing GDM.

Methods

We searched MEDLINE, Web of science, Embase and Cochrane central register of controlled trials. Randomized control trials (RCTs), case-control studies, and cohort studies that assessed the effect of pre-pregnancy lifestyle (diet and/or physical activity based) in preventing GDM were included. Random effects model was used to calculate odds ratio (OR) with 95% confidence interval. The Cochrane ROB-2 and the Newcastle-Ottawa Scale were used for assessing the risk of bias. The protocol was registered in PROSPERO (ID: CRD42020189574)

Results

Database search identified 7935 studies, of which 30 studies with 257,876 pregnancies were included. Meta-analysis of the RCTs (N = 5; n = 2471) in women who received pre-pregnancy lifestyle intervention showed non-significant reduction of the risk of developing GDM (OR 0.76, 95% CI: 0.50–1.17, p = 0.21). Meta-analysis of cohort studies showed that women who were physically active pre-pregnancy (N = 4; n = 23263), those who followed a low carbohydrate/low sugar diet (N = 4; n = 25739) and those women with higher quality diet scores were 29%, 14% and 28% less likely to develop GDM respectively (OR 0.71, 95% CI: 0.57, 0.88, p = 0.002, OR 0.86, 95% CI: 0.68, 1.09, p = 0.22 and OR 0.72, 95% CI 0.60–0.87, p = 0.0006).

Conclusion

This study highlights that some components of pre-pregnancy lifestyle interventions/exposures such as diet/physical activity-based preparation/counseling, intake of vegetables, fruits, low carbohydrate/low sugar diet, higher quality diet scores and high physical activity can reduce the risk of developing gestational diabetes. Evidence from RCTs globally and the number of studies in LMICs are limited, highlighting the need for carefully designed RCTs that combine the different aspects of the lifestyle and are personalized to achieve better clinical and cost effectiveness.
NF-κB signaling activation and roles in thyroid cancers: implication of MAP3K14/NIK
Authors: Cormier Françoise , Housni Selma , Dumont Florent , Villard Mélodie , Cochand-Priollet Béatrix , Mercier-Nomé Françoise , Perlemoine Karine , Bertherat Jérôme , Groussin Lionel
Published: November 2023

Among follicular-derived thyroid cancers (TC), those with aggressive behavior and resistance to current treatments display poor prognosis. NF-κB signaling pathways are involved in tumor progression of various cancers. Here, we finely characterize the NF-κB pathways and their involvement in TC. By using immunoblot and gel shift assays, we demonstrated that both classical and alternative NF-κB pathways are activated in ten TC-derived cell lines, leading to activated RelA/p50 and RelB/p50 NF-κB dimers. By analyzing the RNAseq data of the large papillary thyroid carcinoma (PTC) cohort from The Cancer Genome Atlas (TCGA) project, we identified a tumor progression-related NF-κB signature in BRAFV600E mutated-PTCs. That corroborated with the role of RelA and RelB in cell migration and invasion processes that we demonstrated specifically in BRAFV600E mutated-cell lines, together with their role in the control of expression of genes implicated in invasiveness (MMP1, PLAU, LCN2 and LGALS3). We also identified NF-κB-inducing kinase (NIK) as a novel actor of the constitutive activation of the NF-κB pathways in TC-derived cell lines. Finally, its implication in invasiveness and its overexpression in PTC samples make NIK a potential therapeutic target for advanced TC treatment.
Accuracy of HPV E6/E7 oncoprotein tests to detect high-grade cervical lesions: a systematic literature review and meta-analysis
Authors: Downham Laura , Jaafar Iman , Rol Mary Luz , Nyawira Nyaga Victoria , Valls Joan , Baena Armando , Zhang Li , Gunter Marc J. , Arbyn Marc , Almonte Maribel
Published: November 2023

Background

Cervical carcinogenesis is mediated by the HPV-E6 and E7 oncoproteins, considered as biomarkers usable in managing screen-positive women.

Methods

We conducted a systematic review and meta-analysis assessing the accuracy of HPV-E6/E7-oncoprotein tests to detect underlying cervical-precancer and cancer. We included studies reporting data on oncoprotein test accuracy detecting cervical intraepithelial neoplasia grade 3 or worse. Random effects logistic regression models were applied for pooling absolute and relative accuracy.

Results

Twenty-two studies were included. Sensitivity and specificity estimates ranged from 54.2% (95%CI: 45.2–63.0) to 69.5% (95%CI:60.8–76.9) and from 82.8% (95%CI: 50.4–95.8) to 99.1 (95%CI: 98.8–99.3), respectively in the population irrespective of HPV status. Higher sensitivity estimates ranging from 60.8% (95%CI: 49.6–70.9) to 75.5% (95%CI: 71.7–78.9) but lower specificity estimates ranging from 83.7% (95%CI: 76.1–89.3) to 92.1% (95%CI: 88.5–94.6) were observed in studies enrolling high-risk-HPV-positive women. Studies recruiting only HIV-positive women showed a pooled sensitivity of 46.9% (95%CI: 30.6–63.9) with a specificity of 98.0% (95%CI: 96.8–98.7).

Conclusions

The high specificity of oncoprotein tests supports its use for triaging HPV-positive women. However, oncoprotein-negative women would not be recommended to undertake routine screening, requiring further follow-up. Large-scale and longitudinal studies are needed to further investigate the role of E6/E7-oncoprotein detection in predicting the risk of developing cervical pre-cancer and cancer.
Circulating tumour cells and PD-L1-positive small extracellular vesicles: the liquid biopsy combination for prognostic information in patients with metastatic non-small cell lung cancer
Authors: Eslami-S Zahra , Cortés-Hernández Luis Enrique , Sinoquet Léa , Gauthier Ludovic , Vautrot Valentin , Cayrefourcq Laure , Avoscan Laure , Jacot William , Pouderoux Stéphane , Viala Marie , Thomas Quentin Dominique , Lamy Pierre-Jean , Quantin Xavier , Gobbo Jessica , Alix-Panabières Catherine
Published: November 2023

Background

Circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), and extracellular vesicles (EVs) are minimally invasive liquid biopsy biomarkers. This study investigated whether they predict prognosis, alone or in combination, in heterogenous unbiased non-small cell lung cancer (NSCLC) patients.

Methods

Plasma samples of 54 advanced NSCLC patients from a prospective clinical trial. CtDNA mutations were identified using the UltraSEEK™ Lung Panel (MassARRAY® technology). PD-L1 expression was assessed in small EVs (sEVs) using an enzyme-linked immunosorbent assay.

Results

At least one ctDNA mutation was detected in 37% of patients. Mutations were not correlated with overall survival (OS) (HR = 1.1, 95% CI = 0.55; 1.83, P = 0.980) and progression-free survival (PFS) (HR = 1.00, 95% CI = 0.57–1.76, P = 0.991). High PD-L1+ sEV concentration was correlated with OS (HR = 1.14, 95% CI = 1.03–1.26, P = 0.016), but not with PFS (HR = 1.08, 95% CI = 0.99–1.18, P = 0.095). The interaction analysis suggested that PD-L1+ sEV correlation with PFS changed in function of CTC presence/absence (P interaction = 0.036). The combination analysis highlighted worse prognosis for patients with CTCs and high PD-L1+ sEV concentration (HR = 7.65, 95% CI = 3.11–18.83, P < 0.001). The mutational statuses of ctDNA and tumour tissue were significantly correlated (P = 0.0001).

Conclusion

CTCs and high PD-L1+ sEV concentration correlated with PFS and OS, but not ctDNA mutations. Their combined analysis may help to identify patients with worse OS.

Trial registration

NCT02866149, Registered 01 June 2015, https://clinicaltrials.gov/ct2/show/study/NCT02866149.
Online conversion of reconstructed neural morphologies into standardized SWC format
Authors: Mehta Ketan , Ljungquist Bengt , Ogden James , Nanda Sumit , Ascoli Ruben G. , Ng Lydia , Ascoli Giorgio A.
Published: November 2023

Digital reconstructions provide an accurate and reliable way to store, share, model, quantify, and analyze neural morphology. Continuous advances in cellular labeling, tissue processing, microscopic imaging, and automated tracing catalyzed a proliferation of software applications to reconstruct neural morphology. These computer programs typically encode the data in custom file formats. The resulting format heterogeneity severely hampers the interoperability and reusability of these valuable data. Among these many alternatives, the SWC file format has emerged as a popular community choice, coalescing a rich ecosystem of related neuroinformatics resources for tracing, visualization, analysis, and simulation. This report presents a standardized specification of the SWC file format. In addition, we introduce xyz2swc, a free online service that converts all 26 reconstruction formats (and 72 variations) described in the scientific literature into the SWC standard. The xyz2swc service is available open source through a user-friendly browser interface (https://neuromorpho.org/xyz2swc/ui/) and an Application Programming Interface (API).
Phase biasing of a Josephson junction using Rashba–Edelstein effect
Authors: Senapati Tapas , Karnad Ashwin Kumar , Senapati Kartik
Published: November 2023

A charge-current-induced shift in the spin-locked Fermi surface leads to a non-equilibrium spin density at a Rashba interface, commonly known as the Rashba–Edelstein effect. Since this is an intrinsically interfacial property, direct detection of the spin moment is difficult. Here we demonstrate that a planar Josephson Junction, realized by placing two closely spaced superconducting electrodes over a Rashba interface, allows for a direct detection of the spin moment as an additional phase in the junction. Asymmetric Fraunhofer patterns obtained for Nb-(Pt/Cu)-Nb nano-junctions, due to the locking of Rashba–Edelstein spin moment to the flux quantum in the junction, provide clear signatures of this effect. This simple experiment offers a fresh perspective on direct detection of spin polarization induced by various spin-orbit effects. In addition, this platform also offers a magnetic-field-controlled phase biasing mechanism in conjunction with the Rashba–Edelstein spin-orbit effect for superconducting quantum circuits.
Inconsistent shifts in warming and temperature variability are linked to reduced avian fitness
Authors: Taff Conor C. , Shipley J. Ryan.
Published: November 2023

As the climate has warmed, many birds have advanced their breeding timing. However, as climate change also changes temperature distributions, breeding earlier might increase nestling exposure to either extreme heat or cold. Here, we combine >300,000 breeding records from 24 North American birds with historical temperature data to understand how exposure to extreme temperatures has changed. Average spring temperature increased since 1950 but change in timing of extremes was inconsistent in direction and magnitude; thus, populations could not track both average and extreme temperatures. Relative fitness was reduced following heatwaves and cold snaps in 11 and 16 of 24 species, respectively. Latitudinal variation in sensitivity in three widespread species suggests that vulnerability to extremes at range limits may contribute to range shifts. Our results add to evidence demonstrating that understanding individual sensitivity and its links to population level processes is critical for predicting vulnerability to changing climates.
Microbial methane cycling in a landfill on a decadal time scale
Authors: Grégoire Daniel S. , George Nikhil A. , Hug Laura A.
Published: November 2023

Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.
Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding
Authors: Dastidar Sayantani Ghosh , De Kumar Bony , Lauckner Bo , Parrello Damien , Perley Danielle , Vlasenok Maria , Tyagi Antariksh , Koney Nii Koney-Kwaku , Abbas Ata , Nechaev Sergei
Published: November 2023

Responses of cells to stimuli are increasingly discovered to involve the binding of sequence-specific transcription factors outside of known target genes. We wanted to determine to what extent the genome-wide binding and function of a transcription factor are shaped by the cell type versus the stimulus. To do so, we induced the Heat Shock Response pathway in two different cancer cell lines with two different stimuli and related the binding of its master regulator HSF1 to nascent RNA and chromatin accessibility. Here, we show that HSF1 binding patterns retain their identity between basal conditions and under different magnitudes of activation, so that common HSF1 binding is globally associated with distinct transcription outcomes. HSF1-induced increase in DNA accessibility was modest in scale, but occurred predominantly at remote genomic sites. Apart from regulating transcription at existing elements including promoters and enhancers, HSF1 binding amplified during responses to stimuli may engage inactive chromatin.
Enhanced optical conductivity and many-body effects in strongly-driven photo-excited semi-metallic graphite
Authors: Sidiropoulos T. P. H. , Di Palo N. , Rivas D. E. , Summers A. , Severino S. , Reduzzi M. , Biegert J.
Published: November 2023

The excitation of quasi-particles near the extrema of the electronic band structure is a gateway to electronic phase transitions in condensed matter. In a many-body system, quasi-particle dynamics are strongly influenced by the electronic single-particle structure and have been extensively studied in the weak optical excitation regime. Yet, under strong optical excitation, where light fields coherently drive carriers, the dynamics of many-body interactions that can lead to new quantum phases remain largely unresolved. Here, we induce such a highly non-equilibrium many-body state through strong optical excitation of charge carriers near the van Hove singularity in graphite. We investigate the system’s evolution into a strongly-driven photo-excited state with attosecond soft X-ray core-level spectroscopy. We find an enhancement of the optical conductivity of nearly ten times the quantum conductivity and pinpoint it to carrier excitations in flat bands. This interaction regime is robust against carrier-carrier interaction with coherent optical phonons acting as an attractive force reminiscent of superconductivity. The strongly-driven non-equilibrium state is markedly different from the single-particle structure and macroscopic conductivity and is a consequence of the non-adiabatic many-body state.
Fostering temporal crop diversification to reduce pesticide use
Authors: Guinet Maé , Adeux Guillaume , Cordeau Stéphane , Courson Emeric , Nandillon Romain , Zhang Yaoyun , Munier-Jolain Nicolas
Published: November 2023

Temporal crop diversification could reduce pesticide use by increasing the proportion of crops with low pesticide use (dilution effects) or enhancing the regulation of pests, weeds and diseases (regulation effects). Here, we use the French National DEPHY Network to compare pesticide use between 16 main crops (dilution effect) and to assess whether temporal crop taxonomic and functional diversification, as implemented in commercial farms specialized in arable field crops, could explain variability in total pesticide use within 16 main crops (regulation effect). The analyses are based on 14,556 crop observations belonging to 1334 contrasted cropping systems spanning the diversity of French climatic regions. We find that cropping systems with high temporal crop diversity generally include crops with low pesticide use. For several crops, total pesticide use is reduced under higher temporal crop functional diversity, temporal crop taxonomic diversity, or both. Higher cover crop frequency increases total pesticide use through an increase in herbicide use. Further studies are required to identify crop sequences that maximize regulation and dilution effects while achieving other facets of cropping system multiperformance.
SND1 binds to ERG and promotes tumor growth in genetic mouse models of prostate cancer
Authors: Liao Sheng-You , Rudoy Dmytro , Frank Sander B. , Phan Luan T. , Klezovitch Olga , Kwan Julian , Coleman Ilsa , Haffner Michael C. , Li Dapei , Nelson Peter S. , Emili Andrew , Vasioukhin Valeri
Published: November 2023

SND1 and MTDH are known to promote cancer and therapy resistance, but their mechanisms and interactions with other oncogenes remain unclear. Here, we show that oncoprotein ERG interacts with SND1/MTDH complex through SND1’s Tudor domain. ERG, an ETS-domain transcription factor, is overexpressed in many prostate cancers. Knocking down SND1 in human prostate epithelial cells, especially those overexpressing ERG, negatively impacts cell proliferation. Transcriptional analysis shows substantial overlap in genes regulated by ERG and SND1. Mechanistically, we show that ERG promotes nuclear localization of SND1/MTDH. Forced nuclear localization of SND1 prominently increases its growth promoting function irrespective of ERG expression. In mice, prostate-specific Snd1 deletion reduces cancer growth and tumor burden in a prostate cancer model (PB-Cre/Ptenflox/flox/ERG mice), Moreover, we find a significant overlap between prostate transcriptional signatures of ERG and SND1. These findings highlight SND1’s crucial role in prostate tumorigenesis, suggesting SND1 as a potential therapeutic target in prostate cancer.
Maternal vitamin B1 is a determinant for the fate of primordial follicle formation in offspring
Authors: Liu Wen-Xiang , Liu Hai-Ning , Weng Zhan-Ping , Geng Qi , Zhang Yue , Li Ya-Feng , Shen Wei , Zhou Yang , Zhang Teng
Published: November 2023

The mediation of maternal-embryonic cross-talk via nutrition and metabolism impacts greatly on offspring health. However, the underlying key interfaces remain elusive. Here, we determined that maternal high-fat diet during pregnancy in mice impaired preservation of the ovarian primordial follicle pool in female offspring, which was concomitant with mitochondrial dysfunction of germ cells. Furthermore, this occurred through a reduction in maternal gut microbiota-related vitamin B1 while the defects were restored via vitamin B1 supplementation. Intriguingly, vitamin B1 promoted acetyl-CoA metabolism in offspring ovaries, contributing to histone acetylation and chromatin accessibility at the promoters of cell cycle-related genes, enhancement of mitochondrial function, and improvement of granulosa cell proliferation. In humans, vitamin B1 is downregulated in the serum of women with gestational diabetes mellitus. In this work, these findings uncover the role of the non-gamete transmission of maternal high-fat diet in influencing offspring oogenic fate. Vitamin B1 could be a promising therapeutic approach for protecting offspring health.
Fate specification is spatially intermingled across planarian stem cells
Authors: Park Chanyoung , Owusu-Boaitey Kwadwo E. , Valdes Giselle M. , Reddien Peter W.
Published: November 2023

Regeneration requires mechanisms for producing a wide array of cell types. Neoblasts are stem cells in the planarian Schmidtea mediterranea that undergo fate specification to produce over 125 adult cell types. Fate specification in neoblasts can be regulated through expression of fate-specific transcription factors. We utilize multiplexed error-robust fluorescence in situ hybridization (MERFISH) and whole-mount FISH to characterize fate choice distribution of stem cells within planarians. Fate choices are often made distant from target tissues and in a highly intermingled manner, with neighboring neoblasts frequently making divergent fate choices for tissues of different location and function. We propose that pattern formation is driven primarily by the migratory assortment of progenitors from mixed and spatially distributed fate-specified stem cells and that fate choice involves stem-cell intrinsic processes.
CELLULAR, A Cell Autophagy Imaging Dataset
Authors: Al Outa Amani , Hicks Steven , Thambawita Vajira , Andresen Siri , Enserink Jorrit M. , Halvorsen Pål , Riegler Michael A. , Knævelsrud Helene
Published: November 2023

Cells in living organisms are dynamic compartments that continuously respond to changes in their environment to maintain physiological homeostasis. While basal autophagy exists in cells to aid in the regular turnover of intracellular material, autophagy is also a critical cellular response to stress, such as nutritional depletion. Conversely, the deregulation of autophagy is linked to several diseases, such as cancer, and hence, autophagy constitutes a potential therapeutic target. Image analysis to follow autophagy in cells, especially on high-content screens, has proven to be a bottleneck. Machine learning (ML) algorithms have recently emerged as crucial in analyzing images to efficiently extract information, thus contributing to a better understanding of the questions at hand. This paper presents CELLULAR, an open dataset consisting of images of cells expressing the autophagy reporter mRFP-EGFP-Atg8a with cell-specific segmentation masks. Each cell is annotated into either basal autophagy, activated autophagy, or unknown. Furthermore, we introduce some preliminary experiments using the dataset that can be used as a baseline for future research.
Chromosome genome assembly and whole genome sequencing of 110 individuals of Conogethes punctiferalis (Guenée)
Authors: Gao Bojia , Peng Yan , Jin Minghui , Zhang Lei , Han Xiu , Wu Chao , Yuan He , Awawing Andongma , Zheng Fangqiang , Li Xiangdong , Xiao Yutao
Published: November 2023

The yellow peach moth, Conogethes punctiferalis, is a highly polyphagous pest widespread in eastern and southern Asia. It demonstrates a unique ability to adapt to rotten host fruits and displays resistance to pathogenic microorganisms, including fungi. However, the lack of available genomic resources presents a challenge in comprehensively understanding the evolution of its innate immune genes. Here, we report a high-quality chromosome-level reference genome for C. punctiferalis utilizing PacBio HiFi sequencing and Hi-C technology. The genome assembly was 494 Mb in length with a contig N50 of 3.25 Mb. We successfully anchored 1,226 contigs to 31 pseudochromosomes. Our BUSCO analysis further demonstrated a gene coverage completeness of 96.3% in the genome assembly. Approximately 43% repeat sequences and 21,663 protein-coding genes were identified. In addition, we resequenced 110 C. punctiferalis individuals from east China, achieving an average coverage of 18.4 × and identifying 5.8 million high-quality SNPs. This work provides a crucial resource for understanding the evolutionary mechanism of C. punctiferalis’ innate immune system and will help in developing new antibacterial drugs.
Canada Source Watershed Polygons (Can-SWaP): A dataset for the protection of Canada’s municipal water supply
Authors: Robinne François-Nicolas , Lamache Chloé , Thompson Daniel K. , Leach Jason A. , Bladon Kevin D.
Published: November 2023

Over 80% of municipal (i.e., excluding industrial and agricultural) water use in Canada comes from streams, lakes, and reservoirs. These freshwater bodies and their catchments require adequate protection to secure drinking water supply for Canadians. Canada, like most countries, lacks a consolidated national dataset of municipal catchments, arguably due to gaps in data availability. Against this backdrop, we present the Canada Source Watershed Polygons dataset, or Can-SWaP. Can-SWaP was created using point locations of more than 3,300 municipal water licences defining rights to surface water withdrawal. Where possible, the resulting 1,574 catchments were assessed for accuracy in spatial coverage against provincial and local datasets. Each watershed in Can-SWaP has an estimated water volume used for municipal water purposes derived from licencing data, and several variables from RiverATLAS for investigating the integrity of surface drinking water sources in Canada. Furthermore, basing our method on the HydroSHEDS suite of global products offers a robust framework for the production of other national datasets following an established international standard.
Automating weighing of faces and voices based on cue saliency in trustworthiness impressions
Authors: Vives Marc-Lluís , Frances Candice , Baus Cristina
Published: November 2023

When encountering people, their faces are usually paired with their voices. We know that if the face looks familiar, and the voice is high-pitched, the first impression will be positive and trustworthy. But, how do we integrate these two multisensory physical attributes? Here, we explore 1) the automaticity of audiovisual integration in shaping first impressions of trustworthiness, and 2) the relative contribution of each modality in the final judgment. We find that, even though participants can focus their attention on one modality to judge trustworthiness, they fail to completely filter out the other modality for both faces (Experiment 1a) and voices (Experiment 1b). When asked to judge the person as a whole, people rely more on voices (Experiment 2) or faces (Experiment 3). We link this change to the distinctiveness of each cue in the stimulus set rather than a general property of the modality. Overall, we find that people weigh faces and voices automatically based on cue saliency when forming trustworthiness impressions.
Just-in-time deep learning for real-time X-ray computed tomography
Authors: Graas Adriaan , Coban Sophia Bethany , Batenburg K. Joost , Lucka Felix
Published: November 2023

Real-time X-ray tomography pipelines, such as implemented by RECAST3D, compute and visualize tomographic reconstructions in milliseconds, and enable the observation of dynamic experiments in synchrotron beamlines and laboratory scanners. For extending real-time reconstruction by image processing and analysis components, Deep Neural Networks (DNNs) are a promising technology, due to their strong performance and much faster run-times compared to conventional algorithms. DNNs may prevent experiment repetition by simplifying real-time steering and optimization of the ongoing experiment. The main challenge of integrating DNNs into real-time tomography pipelines, however, is that they need to learn their task from representative databeforethe start of the experiment. In scientific environments, such training data may not exist, and other uncertain and variable factors, such as the set-up configuration, reconstruction parameters, or user interaction, cannot easily be anticipated beforehand, either. To overcome these problems, we developedjust-in-time learning, an online DNN training strategy that takes advantage of the spatio-temporal continuity of consecutive reconstructions in the tomographic pipeline. This allows training and deploying comparatively small DNNs during the experiment. We provide software implementations, and study the feasibility and challenges of the approach by training the self-supervised Noise2Inverse denoising task with X-ray data replayed from real-world dynamic experiments.
Morphogenetic identification of a new record Deudorix livia (Lepidoptera: Lycaenidae) in Assiut Governorate of Northern Upper Egypt
Authors: Abdel-Galil Farouk A. , Mousa Sara E. , Abou-Elhagag Gaber H. , Ahmed Ahmed M. M. , Al-Farga Ammar , Allam Mohammad , Mahmoud Mervat A. B.
Published: November 2023

Deudorix livia (Klug, 1834) (Lepidoptera: Lycaenidae) is one of the most serious lepidopteran insect pests attacking pomegranate fruit around the world, including Egypt (Assiut Governorate, Upper Egypt). To create an effective program (IPM) to control such harmful pests, accurate identification of the pest morphology and genetic structure is essential. Studies on the morphogenetics of this pest are scarce. So, the goal of this research is to identify it both morphologically and genetically. Pomegranate butterfly immature stages were collected from infested pomegranate fruits and reared in the laboratory until the adult's emergence. By using light and scanning electron microscopy, some morphological structures of males and females were studied. DNA was extracted from the legs of a pomegranate butterfly adult. Also, PCR was conducted by using the mitochondrial CO1 gene for sequencing and phylogenetic tests. The results show that the body scales are a mixture of dark and light gray on the dorsal side and white on the ventral side in both sexes. The average male body length (BL) was 11.674 ± 0.299 mm and was 11.458 ± 1.001 mm for the females. The wing venation is similar in both sexes. For the first time, a partial sequence of the mitochondrial CO1 gene in D. livia was deposited in GenBank (MW463927).
Hemokinin-1 is a mediator of chronic restraint stress-induced pain
Authors: Borbély Éva , Kecskés Angéla , Kun József , Kepe Eszter , Fülöp Barbara , Kovács-Rozmer Katalin , Scheich Bálint , Renner Éva , Palkovits Miklós , Helyes Zsuzsanna
Published: November 2023

The Tac4 gene-derived hemokinin-1 (HK-1) binds to the NK1 receptor, similarly to Substance P, and plays a role in acute stress reactions and pain transmission in mice. Here we investigated Tac4 mRNA expression in stress and pain-related regions and its involvement in chronic restraint stress-evoked behavioral changes and pain using Tac4 gene-deleted (Tac4-/-) mice compared to C57Bl/6 wildtypes (WT). Tac4 mRNA was detected by in situ hybridization RNAscope technique. Touch sensitivity was assessed by esthesiometry, cold tolerance by paw withdrawal latency from 0°C water. Anxiety was evaluated in the light–dark box (LDB) and open field test (OFT), depression-like behavior in the tail suspension test (TST). Adrenal and thymus weights were measured at the end of the experiment. We found abundant Tac4 expression in the hypothalamic–pituitary–adrenal axis, but Tac4 mRNA was also detected in the hippocampus, amygdala, somatosensory and piriform cortices in mice, and in the frontal regions and the amygdala in humans. In Tac4-/- mice of both sexes, stress-induced mechanical, but not cold hyperalgesia was significantly decreased compared to WTs. Stress-induced behavioral alterations were mild or absent in male WT animals, while significant changes of these parameters could be detected in females. Thymus weight decrease can be observed in both sexes. Higher baseline anxiety and depression-like behaviors were detected in male but not in female HK-1-deficient mice, highlighting the importance of investigating both sexes in preclinical studies. We provided the first evidence for the potent nociceptive and stress regulating effects of HK-1 in chronic restraint stress paradigm. Identification of its targets might open new perspectives for therapy of stress-induced pain.