bluuebunny/crossref_metadata_2025 huggingface dataset:
Hazardous Earth
Authors: McGuire Bill
Published: February 2024

The Earth has always been a dangerous place. During its early history, it was—on various occasions—battered by incoming asteroids, covered by a magma ocean, and even transformed into an ice ball. Over time the planet developed a tripartite structure, comprising a core, enclosing mantle, and outer crust. The crust and the uppermost part of the mantle formed the brittle lithosphere that makes up the tectonic plates. Formed at Mid-Ocean Ridges and consumed in subduction zones, such as those making up the circum-Pacific Ring of Fire, the plates drift across the surface of our world at the same rate as fingernails grow. The movements of the tectonic plates, combined with a constantly restless atmosphere, continue to ensure that earthquakes, volcanic blasts, storms, floods, and other geophysical hazards pose a major threat to society and its economy. Despite action to build resilience, a conspiracy of climate breakdown due to global heating, and the explosive growth of vulnerable mega-cities in some of our planet’s most dangerous locations, means that our world is becoming a more—not less—perilous place.
What was the Gulag?
Authors: Barenberg Alan
Published: February 2024

This chapter offers a multifaceted and comprehensive definition of the Gulag. The Gulag was a system of mass incarceration meant to isolate and punish those considered to be socially or politically dangerous, to rehabilitate criminals, and to provide a compliant labor force to fill undesirable jobs in remote locations. While it bore resemblance to the Imperial Russian exile/prison systems that preceded it, the modern concentration camp common in the nineteenth and twentieth centuries, and modern prison systems in general, this chapter argues that it was unique in important respects. This chapter also examines the variety of different institutions that were part of the Gulag, including prisons, “colonies,” camps, and exile settlements, arguing that the Gulag was more than simply a system of labor camps.
Economics and labor in the Gulag
Authors: Barenberg Alan
Published: February 2024

This chapter examines the place of the Gulag in the Stalinist economy and how economics shaped everyday life in camps and exile settlements. Although forced labor was enormously wasteful, it was frequently deployed to build infrastructure and exploit natural resources in remote locations, giving it an important role in the national economy. This chapter also demonstrates how forced labor structured everyday life for inmates. Labor assignments determined with whom prisoners lived and interacted, and labor output determined the size of the rations that they received. Yet the economics of the Gulag also had an important informal side. The falsification of prisoner productivity data was widespread: brigade leaders attempted to inflate output numbers, and camp bosses repeated these falsifications in reports to their superiors. The workplace was also a location of frequent interaction between prisoners, exiles, and “free” workers, and this undermined efforts to isolate the Gulag from the “outside.”
Status and trends of biological control research, extension, and education in the United States
Authors: Leppla Norman C , LeBeck Lynn M , Johnson Marshall W
Published: February 2024

The number of public-sector biological control scientists and practitioners in the United States was determined by a survey conducted in 2019. A total of 344 personnel were identified in 49 states and Washington DC; 218 employed by universities, 86 by the federal government and 36 by state departments of agriculture. There were 10-34 personnel in eight states, 6-9 in 11, and 0-5 in 31, overall averaging less than 50% of their combined effort on biological control. Applications for biological control agents included about 30% for row crops and vegetables; 12% each for orchards, urban landscapes, outdoor ornamentals, and forests; and 22% for the remainder. The federal government provided an average of 42% of the funding for university, federal, and state biological control research and extension. The states contributed 29-35%, commodity groups supplied 19-24%, and the remaining funds were from private sources. Of 54 universities in the United States, 18 conducted in-person classroom education and training in biological control, with seven offering courses via distance. However, another 18 universities had discontinued their comprehensive courses. Biological control instruction was incorporated into courses and workshops on integrated pest management and sustainable agriculture at 50 universities. Correspondingly, during the past 24 years, biological control has gradually developed from primarily an independent discipline to increasingly being part of integrated pest management. Classical, augmentative and conservation biological control have nevertheless remained distinguishable high priority subdisciplines. Funding continues to be essential for advancing biological control, requiring societal understanding and acceptance. Advancement of biological control in the United States will require increased investment in personnel and their education and training, along with delivery of effective pest management technologies.
New horizons in frailty identification via electronic frailty indices: early implementation lessons from experiences in England and the United States
Authors: Orkaby Ariela R , Callahan Kathryn E , Driver Jane A , Hudson Kristian , Clegg Andrew J , Pajewski Nicholas M
Published: February 2024

Frailty represents an integrative prognostic marker of risk that associates with a myriad of age-related adverse outcomes in older adults. As a concept, frailty can help to target scarce resources and identify subgroups of vulnerable older adults that may benefit from interventions or changes in medical management, such as pursing less aggressive glycaemic targets for frail older adults with diabetes. In practice, however, there are several operational challenges to implementing frailty screening outside the confines of geriatric medicine. Electronic frailty indices (eFIs) based on the theory of deficit accumulation, derived from routine data housed in the electronic health record, have emerged as a rapid, feasible and valid approach to screen for frailty at scale. The goal of this paper is to describe the early experience of three diverse groups in developing, implementing and adopting eFIs (The English National Health Service, US Department of Veterans Affairs and Atrium Health—Wake Forest Baptist). These groups span different countries and organisational complexity, using eFIs for both research and clinical care, and represent different levels of progress with clinical implementation. Using an implementation science framework, we describe common elements of successful implementation in these settings and set an agenda for future research and expansion of eFI-informed initiatives.
The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues
Authors: Cerdán-Vélez Daniel , Tress Michael Liam
Published: February 2024

The recently published T2T-CHM13 reference assembly completed the annotation of the final 8% of the human genome. It introduced 1956 genes, close to 100 of which are predicted to be coding because they have a protein coding parent gene. Here, we confirm the coding status and functional relevance of two of these genes, paralogues of WASHC1 and GPRIN2. We find that LOC124908094, one of four novel subtelomeric WASH1 genes uncovered in the new assembly, produces the WASH1 protein that forms part of the vital actin-regulatory WASH complex. Its coding status is supported by abundant proteomics, conservation, and cDNA evidence. It was previously assumed that gene WASHC1 produced the functional WASH1 protein, but new evidence shows that WASHC1 is a human-derived duplication and likely to be one of 12 WASH1 pseudogenes in the human gene set. We also find that the T2T-CHM13 assembly has added a functionally important copy of GPRIN2 to the human gene set. We demonstrate that uniquely mapping peptides from proteomics databases support the novel LOC124900631 rather than the GRCh38 assembly GPRIN2 gene. These new additions to the set of human coding genes underlines the importance of the new T2T-CHM13 assembly.

Availability and implementation

None.
Trackplot: a fast and lightweight R script for epigenomic enrichment plots
Authors: Mayakonda Anand , Westermann Frank
Published: February 2024

Motivation

BigWig files serve as essential inputs in epigenomic data visualization. However, current R packages for visualizing these files are limited, slow, and burdened by numerous dependencies.

Results

We introduce trackplot, a minimal R script designed for the rapid generation of integrative genomics viewer (IGV) style track plots, profile plots, and heatmaps from bigWig files. This script offers speed, owing to its reliance on bwtool, resulting in performance gains of several magnitudes compared to equivalent packages. The script is lightweight, requiring only the data.table and bwtool packages as primary dependencies. Notably, the plots are generated in base R graphics, eliminating the need for additional packages. trackplot queries the University of California Santa Cruz (UCSC) genome browser for gene models thereby enhancing the reproducibility of analyses. The script extends its support to general transfer format (GTF) further enhancing its versatility. This tool addresses the gaps in existing bigWig visualization approaches by offering speed, simplicity, and minimal dependencies, thereby presenting a valuable asset to researchers in the fields of epigenomics.

Availability and implementation

trackplot is implemented in R is made available under MIT license at https://github.com/PoisonAlien/trackplot.
A dual-rule encoding DNA storage system using chaotic mapping to control GC content
Authors: Zhang Xuncai , Qi Baonan , Niu Ying
Published: February 2024

Motivation

DNA as a novel storage medium is considered an effective solution to the world’s growing demand for information due to its high density and long-lasting reliability. However, early coding schemes ignored the biologically constrained nature of DNA sequences in pursuit of high density, leading to DNA synthesis and sequencing difficulties. This article proposes a novel DNA storage coding scheme. The system encodes half of the binary data using each of the two GC-content complementary encoding rules to obtain a DNA sequence.

Results

After simulating the encoding of representative document and image file formats, a DNA sequence strictly conforming to biological constraints was obtained, reaching a coding potential of 1.66 bit/nt. In the decoding process, a mechanism to prevent error propagation was introduced. The simulation results demonstrate that by adding Reed-Solomon code, 90% of the data can still be recovered after introducing a 2% error, proving that the proposed DNA storage scheme has high robustness and reliability.

Availability and implementation: The source code for the codec scheme of this paper is available at https://github.com/Mooreniah/DNA-dual-rule-rotary-encoding-storage-system-DRRC.
Long non-coding RNA KB-1460A1.5 promotes ferroptosis by inhibiting mTOR/SREBP-1/SCD1-mediated polyunsaturated fatty acid desaturation in glioma
Authors: Xu Lixia , Wen Binli , Wu Qiaoli , Lu Shan , Liao Jianwen , Mo Lidong , Li Qingguo , Tong Xiaoguang , Yan Hua
Published: February 2024

Ferroptosis is a new form of regulated cell death caused by the iron-dependent peroxidation of phospholipids and is related to cell metabolism, redox homeostasis and various signalling pathways related to cancer. The long non-coding RNA (lncRNA) KB-1460A1.5 acts as a tumour suppressor gene to regulate tumour growth in gliomas, but its molecular network regulatory mechanism is still unclear. In this study, we found that KB-1460A1.5 can induce ferroptosis in glioma and enhance sensitivity to RSL3, a ferroptosis inducer. Tandem mass tag proteomics and nontargeted metabolomics suggest that KB-1460A1.5 affects polyunsaturated fatty acid metabolic processes. Gas chromatography–mass spectrometry-based medium- and long-chain fatty acid-targeted metabolomics confirmed that upregulation of KB-1460A1.5 decreased the levels of monounsaturated fatty acids, oleic acid (OA) and palmitoleic acid (PO) in glioma cells. The addition of OA and PO restored KB-1460A1.5-induced cellular ferroptosis. Molecularly, KB-1460A1.5 inhibited the mammalian target of rapamycin signalling pathway to suppress the expression of downstream sterol regulatory element-binding protein 1 (SREBP-1), thereby attenuating the stearoyl-CoA desaturase-1 (SCD1)-mediated desaturation of polyunsaturated fatty acids. Finally, an animal model of subcutaneous glioma confirmed that KB-1460A1.5 could inhibit tumour progression, SREBP-1/SCD1 expression and ferroptosis. In conclusion, increasing the expression level of KB-1460A1.5 in glioma can promote the induction of oxidative stress and ferroptosis in cancer cells through SREBP-1/SCD1-mediated adipogenesis, demonstrating therapeutic potential in preclinical models.
Altered white matter functional pathways in Alzheimer’s disease
Authors: Li Yilu , Peng Jinzhong , Yang Zhenzhen , Zhang Fanyu , Liu Lin , Wang Pan , Biswal Bharat B
Published: February 2024

Alzheimer’s disease (AD) is associated with functional disruption in gray matter (GM) and structural damage to white matter (WM), but the relationship to functional signal in WM is unknown. We performed the functional connectivity (FC) and graph theory analysis to investigate abnormalities of WM and GM functional networks and corpus callosum among different stages of AD from a publicly available dataset. Compared to the controls, AD group showed significantly decreased FC between the deep WM functional network (WM-FN) and the splenium of corpus callosum, between the sensorimotor/occipital WM-FN and GM visual network, but increased FC between the deep WM-FN and the GM sensorimotor network. In the clinical groups, the global assortativity, modular interaction between occipital WM-FN and visual network, nodal betweenness centrality, degree centrality, and nodal clustering coefficient in WM- and GM-FNs were reduced. However, modular interaction between deep WM-FN and sensorimotor network, and participation coefficients of deep WM-FN and splenium of corpus callosum were increased. These findings revealed the abnormal integration of functional networks in different stages of AD from a novel WM-FNs perspective. The abnormalities of WM functional pathways connect downward to the corpus callosum and upward to the GM are correlated with AD.
Equilibrium Poaching in Labor Markets
Authors: Zax Ori , Farja Yanay
Published: February 2024

When firms have to employ a high-ability worker at a managerial position, sometimes they have to poach a promoted worker from another firm without observing that worker’s ability. We discuss the implications of this practice for the promotion signaling framework. Our model shows the turnover of workers and the wages paid at such an economy, and how they depend on the worker’s own ability and the ability of other workers in the firm. We show that due to the winner’s curse, firms make a non-positive expected profit from poaching a worker. In that case, non-promoted workers “subsidize” the wage paid to their manager. The need to hire managers without observing their ability is a new barrier to entry for firms (JEL codes: M51, J31).
Enhanced premelting of ice in contact with hydrophilic polymer films
Authors: Pallbo Jon , Hemette Sylvain , Mizukami Masashi , Kurihara Kazue
Published: February 2024

Premelting is an interfacial phenomenon with practical consequences such as the contribution to the slipperiness of ice. In many situations ice is in contact with opposing materials. We have explored the effect of opposing materials on the premelting behavior of ice by using a resonance shear measurement setup. Interestingly, contact with polyvinyl alcohol polymer films caused enhanced premelting. These results provide information about the nature of ice interfaces and can lead to a better understanding of friction on ice.
CFAuditChain: Audit BlockChain Based On Cuckoo Filter
Authors: Liu Kang , Lu Yang , Tan Shiyi , Liang Wei , Sun Huiping , Chen Zhong
Published: February 2024

Log blockchain can be used to ensure the integrity of log data. However, current methods are facing the problems of throughput mismatch and rough audit granularity. Packaging multiple logs to generate integrity proofs improves throughput but reduces audit granularity, and the auditor can only locate the tampering log packet instead of specific records. This paper proposes CFAuditChain, an audit blockchain based on a cuckoo filter, where the proof of existence (PoE) of the single log is calculated while calculating the integrity proof of packet logs. The PoE is saved in the cuckoo filter and stored using blockchain for immutability. Therefore, the auditor can verify the credibility of each log based on the filter when the integrity proof of a log packet does not match. The theoretical analysis and experimental results show that CFAuditChain provides the granularity of audit logs down to the records level at an acceptable cost.
Family-Centered Early Intervention Deaf/Hard of Hearing (FCEI-DHH): Cultural & Global Implications
Authors: Szarkowski Amy , Moeller Mary Pat , Gale Elaine , Smith Trudy , Birdsey Bianca C , Moodie Sheila T F , Carr Gwen , Stredler-Brown Arlene , Yoshinaga-Itano Christine ,   FCEI-DHH International Consensus Panel, Berke Michele , Binder Doris , Carr Gwen , Cloete Natasha , Crace Jodee , Crowe Kathryn , Dauer Frank , DesGeorges Janet , Dirks Evelien , Fellinger Johannes , Ferguson Bridget , Grover Anita , Hofer Johannes , Holten Sonja Myhre , Holzinger Daniel , Hopkins Karen , Laugen Nina Jakhelln , Lillo-Martin Diane , Magongwa Lucas , Martin Amber , McCall Jolanta , McCarthy Melissa , McDonnell Teresa , Movallali Guita , Müllegger-Treciokaite Daiva , Olson Stephanie B , Olusanya Bolajoko O , Pittman Paula , Porter Ann , Russell Jane , Sarkar Snigdha , Seaver Leeanne , Storbeck Claudine , Stredler-Brown Arlene , Thompson Nanette , Windisch Sabine , Yoshinaga-Itano Christine , Young Alys , Zheng Xuan , Holzinger Daniel
Published: February 2024

This article is the third in a series of eight articles that comprise this special issue on family-centered early intervention for children who are deaf or hard of hearing and their families (FCEI-DHH). It highlights the origins of FCEI-DHH in Western contexts and well-resourced locations and emphasizes the role of culture(s) in shaping FCEI-DHH. This article also cautions against the direct application of the 10 FCEI-DHH Principles presented in this issue across the globe without consideration of cultural implications. Cultural perceptions of decision-making processes and persons who can be decision-makers in FCEI-DHH are explored. Deaf culture(s) and the benefits of exposure to DHH adults with diverse backgrounds are introduced. Structural inequities that impact families’ access to FCEI-DHH programs/services and systems, within and among nations and regions, are noted. The need to consider the cultural influences on families is emphasized; this applies to all levels of FCEI, including the development of systems through implementation of supports.
Should we operate on patients with acute type A aortic dissection who present with cardiopulmonary resuscitation?
Authors: Beckmann Erik , Martens Andreas , Krueger Heike , Korte Wilhelm , Shrestha Pamila , Kaufeld Tim , Shrestha Malakh
Published: February 2024

OBJECTIVES

Acute aortic dissection type A (AADA) is a life-threatening medical emergency. Emergent surgical repair is the gold standard but mortality remains high. Mortality is even higher in patients who arrive at the hospital in poor condition, especially after cardiopulmonary resuscitation (CPR). This study was designed to analyse the outcome of patients who underwent surgery for AADA and who require preoperative CPR.

METHODS

Between 2000 and 2023, 810 patients underwent emergent surgery for AADA at our centre. Of these, 63 had preoperative CPR. We performed a retrospective analysis with follow-up.

RESULTS

Mean age was 64 ± 13 years and 37 (59%) patients were male. Further, 50 (79%) patients had preoperative intubation, and 54 (86%) had pericardial effusion. Twenty-four (38%) patients had out-of-hospital CPR, 19 (30%) required CPR in hospital and 20 (32%) needed CPR in the operating room. Successful CPR with return of spontaneous circulation was achieved in 41 (65%) patients, and 22 (35%) underwent emergent surgery under ongoing CPR. The median time of CPR was 10 (interquartile range 12) min, and the median time from onset of symptoms to start of the operation was 5.5 (interquartile range 4.8) h. The majority of patients underwent ascending aortic replacement with hemiarch repair (n = 37, 59%). Further, 26 (41%) patients underwent full root replacement. Another 15 (24%) patients underwent total arch repair with or without (frozen) elephant trunk repair. Postoperative stroke was present in 8 (13%) patients. The 30-day mortality was 29 (46%). The 30-day mortality of patients with preoperative intubation was not significantly higher (n = 15/28, 54%, P = 0.446). The 1-, 5- and 10-year survival rates of the entire group were 42, 39 and 36%.

CONCLUSIONS

Early mortality for patients undergoing surgery for AADA with preoperative CPR is extremely high (almost 50%). However, this means that also ∼50% of patients benefit from surgery despite poor preoperative prognosis. Patients with preoperative intubation after CPR and unknown neurological condition should also undergo surgery. Patients who survive the initial operation for AADA have acceptable long-term survival. Emergent surgery should be offered for all patients with AADA regardless of the preoperative condition, even after CPR.
Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa
Authors: Putzeys Leena , Wicke Laura , Boon Maarten , van Noort Vera , Vogel Jörg , Lavigne Rob
Published: February 2024

The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14–1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.
Effects of composition on the explosive properties of potassium chlorate and oils
Authors: Tagawa Masahiro , Matyáš Robert , Kučera Jindřich , Pachman Jiří
Published: February 2024

Potassium chlorate has long been utilized as an excellent oxidizing agent in pyrotechnics and explosives. As mixtures of potassium chlorate and any type of combustible material can be explosive, there is a potential risk of misuse in homemade explosives. Unlike commercial explosives, homemade chlorate and oil mixtures do not have a constant composition, which limits their understanding. This study reports the effects of two types of oil (motor oil and cooking oil) and their ratios (ranging from 2.5% to 40.0% (w/w)) on the explosive properties of such mixtures. The impact sensitivity was highest at a motor oil ratio of 5%. The friction sensitivity increased with an increasing oil ratio, reaching a maximum at an oil ratio of around 22.5%, and was close to those of primary explosives. The motor oil mixtures exhibited higher sensitivity than the cooking oil mixtures at oil ratios of 25% or less. A 10% oil mixture, which was close to the ratio of oxygen balance equal to zero, detonated in weak confinement, such as a paper cylinder. The highest detonation velocities in a polypropylene tube were around 2300 and 2550 m/s at a 10% ratio of motor oil and cooking oil, respectively. The velocities of the metal case wall, measured by photonic Doppler velocimetry, reached about 1100 m/s near the end of acceleration. These results show that homemade chlorate and oil mixtures are capable of detonation and quite sensitive over a wide range of oil ratios, with sufficient power to cause damage in the vicinity.
Deregulation of circRNA hsa_circ_0009109 promotes tumor growth and initiates autophagy by sponging miR-544a-3p in gastric cancer
Authors: Zhang Weiwei , Yang Qian , Qian Dongchen , Zhao Keli , Tang Chenxue , Ju Shaoqing
Published: February 2024

Background

Autophagy death of cancer cells is detrimental to apoptosis induced by therapeutic drugs, which promotes tumor progression to a certain extent. Increasing reports have demonstrated the regulatory role of circular RNAs (circRNAs) in autophagy. Here, we aimed to determine the role of hsa_circ_0009109 in autophagy in gastric cancer (GC).

Methods

The effects of hsa_circ_0009109 on autophagy were examined using quantitative real-time polymerase chain reaction (qPCR), transmission electron microscopy, Western blot, and immunofluorescence. The mechanism of hsa_circ_0009109 regulating the miR-544a-3p/bcl-2 axis was analysed using fluorescence in situ hybridization, dual-luciferase reporter, and rescue experiments.

Results

Functional testing indicated that hsa_circ_0009109 was significantly down-expressed in GC tissues and cell lines. A reduction in cytoplasmic-derived hsa_circ_0009109 could promote GC progression by accelerating cell proliferation, enhancing migration and invasion, inhibiting apoptosis, and accelerating the cell cycle progression. Besides, hsa_circ_0009109 was found to exert the effect of an autophagy inhibitor such as 3-Methyladenine (3-MA), which was manifested by the weakening of the immunofluorescence of LC3B and the reduction in autophagy-related proteins after overexpression of hsa_circ_0009109, while increased autophagosomes were observed after interference with hsa_circ_0009109. Subsequently, the crosstalk between hsa_circ_0009109 and miR-544a-3p/bcl-2 was verified using dual-luciferase reporter assay. The autophagy status was altered under the regulation of the hsa_circ_0009109-targeted miR-544a-3p/bcl-2 axis.

Conclusions

The hsa_circ_0009109 mediated a novel autophagy regulatory network through targeting the miR-544a-3p/bcl-2 axis, which may shed new light on the exploration of therapeutic targets for the clinical treatment of GC.
Life-History Trade-Offs in Drosophila: Flies Select a Diet to Maximize Reproduction at the Expense of Lifespan
Authors: Strilbytska Olha , Yurkevych Ihor , Semaniuk Uliana , Gospodaryov Dmytro , Simpson Stephen J , Lushchak Oleh
Published: February 2024

Macronutrient intake impacts physiology, behavior, and gene expression in a wide range of organisms. We used the response surface methodology to compare how life history traits, lifespan, and reproduction differ as a function of protein and carbohydrate intakes under choice and no-choice feeding regimens in the fruit fly, Drosophila melanogaster. We found that when offered a choice of nutritionally complementary foods mated female flies regulated toward a protein to carbohydrate ratio (P:C) that was associated with shortened lifespan and maximal egg production when compared to response surfaces derived from flies fed 1 of a range of fixed diets differing in P:C (no-choice regimen). This difference in lifespan between choice and no-choice feeding was not seen in males or virgin flies, reflecting the fact that increased protein intake is triggered by mating to support egg production. However, whereas in mated females a higher P:C intake was associated with greater egg production under both choice and no-choice feeding, contrary to expectations, choice-fed mated flies laid fewer eggs than no-choice flies on equivalent macronutrient intakes, perhaps reflecting that they had to ingest twice the volume of food to attain an equivalent intake of nutrients than no-choice flies on a diet of equivalent P:C ratio.
RNA-seq-based comparative transcriptome analysis reveals the role of CsPrx73 in waterlogging-triggered adventitious root formation in cucumber
Authors: Pan Jiawei , Song Jia , Sohail Hamza , Sharif Rahat , Yan Wenjing , Hu Qiming , Qi Xiaohua , Yang Xiaodong , Xu Xuewen , Chen Xuehao
Published: February 2024

Abiotic stressors like waterlogging are detrimental to cucumber development and growth. However, comprehension of the highly complex molecular mechanism underlying waterlogging can provide an opportunity to enhance cucumber tolerance under waterlogging stress. We examined the hypocotyl and stage-specific transcriptomes of the waterlogging-tolerant YZ026A and the waterlogging-sensitive YZ106A, which had different adventitious rooting ability under waterlogging. YZ026A performed better under waterlogging stress by altering its antioxidative machinery and demonstrated a greater superoxide ion (O 2−) scavenging ability. KEGG pathway enrichment analysis showed that a high number of differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis. By pairwise comparison and weighted gene co-expression network analysis analysis, 2616 DEGs were obtained which were categorized into 11 gene co-expression modules. Amongst the 11 modules, black was identified as the common module and yielded a novel key regulatory gene, CsPrx73. Transgenic cucumber plants overexpressing CsPrx73 enhance adventitious root (AR) formation under waterlogging conditions and increase reactive oxygen species (ROS) scavenging. Silencing of CsPrx73 expression by virus-induced gene silencing adversely affects AR formation under the waterlogging condition. Our results also indicated that CsERF7-3, a waterlogging-responsive ERF transcription factor, can directly bind to the ATCTA-box motif in the CsPrx73 promoter to initiate its expression. Overexpression of CsERF7-3 enhanced CsPrx73 expression and AR formation. On the contrary, CsERF7-3-silenced plants decreased CsPrx73 expression and rooting ability. In conclusion , our study demonstrates a novel CsERF7-3–CsPrx73 module that allows cucumbers to adapt more efficiently to waterlogging stress by promoting AR production and ROS scavenging.
Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis
Authors: Wu Qiuyun , Mao Shuxiang , Huang Huiping , Liu Juan , Chen Xuan , Hou Linghui , Tian Yuxiao , Zhang Jiahui , Wang Junwei , Wang Yunsheng , Huang Ke
Published: February 2024

Broccoli (Brassica oleracea var. italica Plenck) is an important vegetable crop, as it is rich in health-beneficial glucosinolates (GSLs). However, the genetic basis of the GSL diversity in Brassicaceae remains unclear. Here we report a chromosome-level genome assembly of broccoli generated using PacBio HiFi reads and Hi-C technology. The final genome assembly is 613.79 Mb in size, with a contig N50 of 14.70 Mb. The GSL profile and content analysis of different B. oleracea varieties, combined with a phylogenetic tree analysis, sequence alignment, and the construction of a 3D model of the methylthioalkylmalate synthase 1 (MAM1) protein, revealed that the gene copy number and amino acid sequence variation both contributed to the diversity of GSL biosynthesis in B. oleracea. The overexpression of BoMAM1 (BolI0108790) in broccoli resulted in high accumulation and a high ratio of C4-GSLs, demonstrating that BoMAM1 is the key enzyme in C4-GSL biosynthesis. These results provide valuable insights for future genetic studies and nutritive component applications of Brassica crops.
Intangible assets, global value chains, and innovation: evidence from Vietnamese SMEs
Authors: Doan Hung Quang , Masciarelli Francesca , Meliciani Valentina
Published: February 2024

This paper studies the impact of participation in global value chains (GVCs) on innovation in Vietnamese small and medium enterprises (SMEs). We find that the Vietnamese SMEs that participate in GVCs are more likely to introduce product innovation. We also show that the likelihood of introducing product innovation for firms that participate in GVCs increases when they invest in intangible assets. These findings qualify the learning-by-participating model in GVCs by showing that the gains from GVC participation depend on a firm’s internal absorptive capacities.
Rheumatoid arthritis and cancer risk in the Million Women Study
Authors: Yang TienYu Owen , Floud Sarah , Reeves Gillian K ,   Million Women Study Collaborators, Abbott Simon , Alison Rupert , Atkinson Sarah , Baker Krys , Balkwill Angela , Barnes Isobel , Black Judith , Blanks Roger , Brown Anna , Chadwick Andrew , Ewart Dave , Floud Sarah , Gaitskell Kezia , Gathani Toral , Gerrard Laura , Goodill Adrian , Hermon Carol , Kan Sau Wan , Langston Nicky , Papier Keren , Pirie Kirstin , Reeves Gillian , Shaw Keith , Sherman Emma , Smith-Byrne Karl , Strange Helena , Sweetland Sian , Travis Ruth , Trickett Lyndsey , Wotton Clare , Young Owen Yang Heather , Banks Emily , Carpenter Lucy , Dezateux Carol , Floud Sarah , Patnick Julietta , Peto Richard , Reeves Gillian , Sudlow Cathie
Published: February 2024

Background

Most previous studies of rheumatoid arthritis (RA) and cancer risk have lacked information on potential confounding factors. We investigated RA-associated cancer risks in a large cohort of women in the UK, taking account of shared risk factors.

Methods

In 1996–2001, women aged 50–64, who were invited for routine breast screening at 66 National Health Service (NHS) screening centres in England and Scotland, were also invited to take part in the Million Women Study. Participants provided information on sociodemographic, lifestyle and health-related factors, including RA, and were followed up for cancers and deaths. Cox regression yielded RA-associated hazard ratios (HRs) of 20 cancers, adjusted for 10 characteristics including smoking status and adiposity.

Results

Around 1.3 million women (half of those invited) were recruited into the study. In minimally adjusted analyses, RA was associated with the risk of 13 of the 20 cancers. After additional adjustment for lifestyle factors, many of these associations were attenuated but there remained robust evidence of RA-associated increases in the risk of lung (HR 1.21, 95% confidence interval 1.15–1.26), lymphoid (1.25, 1.18–1.33), myeloid (1.12, 1.01–1.25), cervical (1.39, 1.11–1.75) and oropharyngeal (1.40, 1.21–1.61) cancers, and decreases in the risk of endometrial (0.84, 0.77–0.91) and colorectal (0.82, 0.77–0.87) cancers.

Conclusions

After taking account of shared risk factors, RA is positively associated with lung and certain blood and infection-related cancers, and inversely associated with colorectal cancer. These findings are consistent with existing hypotheses around immune response, susceptibility to infections, and chronic inflammation. The inverse association observed for endometrial cancer merits further investigation.
Effective Density of Non-Degenerate Random Walks on Homogeneous Spaces
Authors: Kim Wooyeon , Kogler Constantin
Published: February 2024

We prove effective density of random walks on homogeneous spaces, assuming that the underlying measure is supported on matrices generating a dense subgroup and having algebraic entries. The main novelty is an argument passing from high dimension to effective equidistribution in the setting of random walks on homogeneous spaces, exploiting the spectral gap of the associated convolution operator.
Constant Mean Curvature Hypersurfaces in Anti-de Sitter Space
Authors: Trebeschi Enrico
Published: February 2024

We study entire spacelike constant mean curvature hypersurfaces in Anti-de Sitter space of any dimension. First, we give a classification result with respect to their asymptotic boundary, namely we show that every admissible sphere $\Lambda $ is the boundary of a unique such hypersurface, for any given value $H$ of the mean curvature. We also demonstrate that, as $H$ varies in $\mathbb {R}$, these hypersurfaces analytically foliate the invisible domain of $\Lambda $. Finally, we extend Cheng-Yau Theorem to the Anti-de Sitter space, which establishes the completeness of any entire constant mean curvature hypersurface.
Type I Interferon Autoantibodies Correlate With Cellular Immune Alterations in Severe COVID-19
Authors: Strunz Benedikt , Maucourant Christopher , Mehta Adi , Wan Hui , Du Likun , Sun Dan , Chen Puran , Nordlander Anna , Gao Yu , Cornillet Martin , Bister Jonna , Kvedaraite Egle , Christ Wanda , Klingström Jonas , Geanon Daniel , Parke Åsa , Ekwall-Larson Anna , Rivino Laura , MacAry Paul A , Aleman Soo , Buggert Marcus , Ljunggren Hans-Gustaf , Pan-Hammarström Qiang , Lund-Johansen Fridtjof , Strålin Kristoffer , Björkström Niklas K ,   the Karolinska KI/K COVID-19 Study Group, Sönnerborg Anders , Dillner Lena , Glans Hedvig , Nauclér Pontus , Rooyackers Olav , Mårtensson Johan , Eriksson Lars I , Persson Björn P , Grip Jonathan , Unge Christian , Djärv Therese , Religa Dorota , Sandberg John Tyler , Bergsten Helena , Brighenti Susanna , Butrym Marta , Chambers Benedict J , Cuapio Angelica , Lozano Isabel Diaz , Dzidic Majda , Emgård Johanna , Flodström-Tullberg Malin , Gorin Jean-Baptiste , Haroun-Izquierdo Alvaro , Hertwig Laura , Kalsum Sadaf , Kokkinou Efthymia , Marquardt Nicole , Lourda Magdalini , Maleki Kimia T , Malmberg Karl-Johan , Michaëlsson Jakob , Mjösberg Jenny , Moll Kirsten , Muvva Jagadeeswara Rao , Norrby-Teglund Anna , Medina Laura M Palma , Parrot Tiphaine , Radler Lena , Ringqvist Emma , Sandberg Johan K , Sekine Takuya , Soini Tea , Svensson Mattias , Tynell Janne , von Kries Andreas , Wullimann David , Perez-Potti André , Rivera-Ballesteros Olga , Varnaite Renata , Akber Mira , Berglin Lena , Brownlie Demi , Loreti Marco Giulio , Sohlberg Ebba , Kammann Tobias , Henriksson Elisabeth , Hammer Quirin
Published: February 2024

Background

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to severe disease with increased morbidity and mortality among certain risk groups. The presence of autoantibodies against type I interferons (aIFN-Abs) is one mechanism that contributes to severe coronavirus disease 2019 (COVID-19).

Methods

This study aimed to investigate the presence of aIFN-Abs in relation to the soluble proteome, circulating immune cell numbers, and cellular phenotypes, as well as development of adaptive immunity.

Results

aIFN-Abs were more prevalent in critical compared to severe COVID-19 but largely absent in the other viral and bacterial infections studied here. The antibody and T-cell response to SARS-CoV-2 remained largely unaffected by the presence aIFN-Abs. Similarly, the inflammatory response in COVID-19 was comparable in individuals with and without aIFN-Abs. Instead, presence of aIFN-Abs had an impact on cellular immune system composition and skewing of cellular immune pathways.

Conclusions

Our data suggest that aIFN-Abs do not significantly influence development of adaptive immunity but covary with alterations in immune cell numbers.
Association of Dynamics of Anellovirus Loads With Hospital-Acquired Pneumonia in Patients With Brain Injury During the Intensive Care Unit Stay
Authors: Castain Louise , Petrier Mélanie , Bulteau Simon , Peltier Cécile , Poulain Cécile , Bouras Marwan , Imbert-Marcille Berthe-Marie , Poschmann Jérémie , Roquilly Antoine , Bressollette-Bodin Céline
Published: February 2024

Background

Critical illness induces immune disorders associated with an increased risk of hospital-acquired pneumonia (HAP) and acute respiratory distress syndrome (ARDS). Torque teno virus (TTV), from the Anelloviridae family, is proposed as a biomarker to measure the level of immunosuppression. Our objective was to describe the kinetics of TTV DNA loads and their association with critical illness–related complications.

Methods

We performed a longitudinal study in 115 patients with brain injury from a prospective cohort, collected endotracheal and blood samples at 3 successive time points after admission in the intensive care unit (ICU) (T1, 0–4 days post ICU admission; T2, 5–10; T3, 11–18), and measured viral DNA loads using the TTV R-GENE kit (BioMérieux) and a pan-Anelloviridae in-house quantitative real-time polymerase chain reaction.

Results

TTV DNA was detected in the blood of 69%, 71%, and 64% of patients with brain injury at T1, T2, and T3, respectively. Time-associated variations of TTV and anellovirus DNA loads were observed. Using a linear mixed-effects model, we found that HAP and ARDS were associated with lower blood anellovirus DNA loads.

Conclusions

Our results show that HAP or ARDS in patients who are critically ill is associated with changes in anellovirus DNA loads and should be evaluated further as a biomarker of immune disorders leading to these complications.
Endophytic Streptomyces sp. MSARE05 isolated from roots of Peanut plant produces a novel antimicrobial compound
Authors: Islam Md Majharul , Saha Shrabani , Sahoo Prithidipa , Mandal Sukhendu
Published: February 2024

Aim

This study aimed to isolate, endophytic Streptomyces sp. MSARE05 isolated from root of a peanut (Arachis hypogaea) inhibits the growth of other bacteria. The research focused on characterizing the strain and the antimicrobial compound.

Methods and Results

The surface-sterilized peanut roots were used to isolate the endophytic bacterium Streptomyces sp. MSARE05. A small-scale fermentation was done to get the antimicrobial compound SM05 produced in highest amount in ISP-2 medium (pH 7) for 7 days at 30°C in shaking (180 rpm) condition. Extraction, purification, and chemical analysis of the antibacterial component revealed a novel class of antibiotics with a 485.54 Dalton molecular weight. The MIC was 0.4–0.8 µg ml−1 against the tested pathogens. It also inhibits multidrug-resistant (MDR) pathogens and Mycobacterium with 0.8–3.2 µg ml−1 MIC. SM05 was found to disrupt cell membrane of target pathogen as evident by significant leakage of intracellular proteins and nucleic acids. It showed synergistic activity with ampicillin, chloramphenicol, streptomycin, and kanamycin.

Conclusions

The new-class antimicrobial SM05 consisting naphthalene core moiety was effective against drug-resistant pathogens but non-cytotoxic to human cells. This study underscores the significance of endophytic Streptomyces as a source of innovative antibiotics, contributing to the ongoing efforts to combat antibiotic resistance.
Whither security? The concept of ‘essential security interests’ in investment treaties’ security exceptions
Authors: Henckels Caroline
Published: February 2024

Unlike the WTO agreements, most investment treaties’ security exceptions do not further define the concept of ‘essential security interests’, creating significant uncertainty. Securitization theory illuminates conceptual problems associated with an expansive approach to security, security’s role in justifying extraordinary deontic powers, and securitization’s contingency on intersubjective agreement. As securitizing actors, states have put forward four paradigms of security, each significantly expanding the concept beyond its traditional contours. Investors have resisted with two counter-securitizing moves, each involving several tactics. Reacting to these moves and countermoves, tribunals have functioned as either empowering audiences or as nullifying audiences. The ambiguity of essentiality has also generated incongruent interpretations. States’, investors’, and tribunals’ approaches operate on three different planes, each with potential to significantly constrain security’s scope or even negate a successful securitization. Expansive and restrictive interpretations of security present competing implications that make defining it an invidious task, but some interpretations of essentiality are more tenable than others. Overall, tribunals’ narrow interpretations of the concept have operated to considerably limit states’ securitization attempts. While investors should keep a close eye on pending cases involving potentially self-judging security exceptions, they need not be overly concerned that security exceptions pose a significant threat to their interests.
Efficacy and safety of streptozocin-based chemotherapy for gastroenteropancreatic neuroendocrine tumors in Japanese clinical practice
Authors: Murakami Masatoshi , Fujimori Nao , Takamatsu Yu , Ito Tetsuhide , Matsumoto Kazuhide , Kakehashi Shotaro , Ohno Akihisa , Teramatsu Katsuhito , Ueda Keijiro , Ishigami Kousei , Ogawa Yoshihiro
Published: February 2024

Background

Streptozocin has been used to treat neuroendocrine tumors in Europe and the USA; however, its actual status in Japan has not been fully clarified owing to the rarity of this disease and the relatively recent approval of streptozocin in Japan.

Methods

We retrospectively analyzed 53 patients with gastroenteropancreatic neuroendocrine tumors who were treated with streptozocin-based chemotherapy at two Japanese hospitals between January 2004 and June 2023.

Results

The overall response and disease control rates were 27.7 and 74.5%, respectively, and the median progression-free survival and overall survival were 7.1 and 20.3 months, respectively. Performance status ≥1 showed a significant negative correlation with progression-free survival, and performance status ≥1 and liver tumor burden ≥25% showed a significant negative correlation with overall survival. No significant differences were observed in the treatment response between pancreatic and gastrointestinal neuroendocrine tumors. No treatment-related serious adverse events were observed; however, 87.7% of patients expressed a decrease in the estimated glomerular filtration rate, which negatively correlated with the duration of streptozocin treatment (r = 0.43, P = 0.0020). In the streptozocin re-administration group (n = 5), no differences were found in efficacy between the initial and second streptozocin treatments.

Conclusions

Although streptozocin is a safe, streptozocin-induced renal dysfunction is a dilemma in streptozocin responders. Streptozocin may benefit patients with gastroenteropancreatic neuroendocrine tumors, especially those with a good performance status; however, in some cases, planned streptozocin withdrawal or switching to other drugs should be considered.