bluuebunny/crossref_metadata_2025_split huggingface dataset:
The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues
Authors: Cerdán-Vélez Daniel , Tress Michael Liam 
Published: February 2024

AbstractSummaryThe 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 implementationNone.
Trackplot: a fast and lightweight R script for epigenomic enrichment plots
Authors: Mayakonda Anand , Westermann Frank 
Published: February 2024

Abstract

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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

Abstract

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

Abstract
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.