bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction
Authors: Baum Robert M 
Published: July 2024

Abstract
This chapter studies the representation of African history and African religions from Herodotus to contemporary scholars, many of which described Africa as a place without history and without religion. It provides a critical perspective on various evolutionary theories of religion which share a tendency to place Africa toward the bottom of their stages of religion. It demonstrates the pervasive theism and this-worldly focus of African religious traditions. It analyzes the sources available for the study of the history of ancient African religions, including written texts, oral traditions, archaeological evidence, and linguistic sources. The chapter also examines theories about African religions, including debates about the nature of African religious traditions.
Egypt and the Nile Valley before the Roman Occupation
Authors: Baum Robert M 
Published: July 2024

Abstract
This chapter examines the history of religions in the Nile valley from the Ramesside Dynasty to the fall of the Ptolemies. This period covers the peak of the Egyptian empire followed by Libyan and Nubian dynasties, followed by a series of foreign rulers—Assyrians, Persians, and Greeks, each introducing new religious ideas and practices. Both the Nubians and Alexander the Great sought the support of Amun-Re to legitimate their rule. The Ptolemies created a Hellenistic-Egyptian god, Serapis, in an effort to unite the two peoples. Egyptian religion increasingly emphasized the importance of dreams in their religious practice. Nubians retained many of their own deities, while incorporating Amun-Re as the supreme god, but with a Nubian birthplace.
Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints
Authors: Dou Chang , Yang Yijie , Zhu Fei , Li BingZhi , Duan Yuping 
Published: July 2024

Abstract
With the exponential growth of digital data, there is a pressing need for innovative storage media and techniques. DNA molecules, due to their stability, storage capacity, and density, offer a promising solution for information storage. However, DNA storage also faces numerous challenges, such as complex biochemical constraints and encoding efficiency. This paper presents Explorer, a high-efficiency DNA coding algorithm based on the De Bruijn graph, which leverages its capability to characterize local sequences. Explorer enables coding under various biochemical constraints, such as homopolymers, GC content, and undesired motifs. This paper also introduces Codeformer, a fast decoding algorithm based on the transformer architecture, to further enhance decoding efficiency. Numerical experiments indicate that, compared with other advanced algorithms, Explorer not only achieves stable encoding and decoding under various biochemical constraints but also increases the encoding efficiency and bit rate by ¿10%. Additionally, Codeformer demonstrates the ability to efficiently decode large quantities of DNA sequences. Under different parameter settings, its decoding efficiency exceeds that of traditional algorithms by more than two-fold. When Codeformer is combined with Reed–Solomon code, its decoding accuracy exceeds 99%, making it a good choice for high-speed decoding applications. These advancements are expected to contribute to the development of DNA-based data storage systems and the broader exploration of DNA as a novel information storage medium.
Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation
Authors: Lin Yuefan , Pan Zixiang , Zeng Yuansong , Yang Yuedong , Dai Zhiming 
Published: July 2024

Abstract
Recent advances in single-cell technologies enable the rapid growth of multi-omics data. Cell type annotation is one common task in analyzing single-cell data. It is a challenge that some cell types in the testing set are not present in the training set (i.e. unknown cell types). Most scATAC-seq cell type annotation methods generally assign each cell in the testing set to one known type in the training set but neglect unknown cell types. Here, we present OVAAnno, an automatic cell types annotation method which utilizes open-set domain adaptation to detect unknown cell types in scATAC-seq data. Comprehensive experiments show that OVAAnno successfully identifies known and unknown cell types. Further experiments demonstrate that OVAAnno also performs well on scRNA-seq data. Our codes are available online at https://github.com/lisaber/OVAAnno/tree/master.
Phylogeography of Père David’s red-backed vole, Eothenomys melanogaster (Rodentia: Cricetidae), in Taiwan
Authors: Oshida Tatsuo , Chang Yu-Cheng , Harada Masashi , Iwasa Masahiro A , Chang Shih-Wei , Ando Akiro , Koyasu Kazuhiro , Lin Liang-Kong 
Published: July 2024

Abstract
Sympatrically distributed mammal species do not always show congruent phylogeographical traits. In Taiwan, montane mammals show two different phylogeographical patterns: some species have no clear genetic diversification, whereas others show clear north–south genetic divergence. The ecological characteristics of each species might be important factors determining each pattern. The former species group is adapted to rich forest habitats, whereas the latter species group requires more complicated habitats consisting of both forested and non-forested areas. If the latter group has experienced similar historical processes, we might find a congruent zoogeographical pattern that separates its northern and southern populations. To test this hypothesis, we examined the phylogeographical characteristics of Eothenomys melanogaster found in the habitat of the latter species group, based on mitochondrial and nuclear DNA sequences and chromosomes. All genetic markers demonstrated clear north–south divergence. The boundary between the two populations was in the mountainous areas, including Mount Houhuan. Our results suggested that the southern population was the first to immigrate from the Asian continent to the south of the boundary, followed by the immigration of the northern population to the north of the boundary. Both populations could have been isolated from each other by a boundary in Taiwan during the Pleistocene.
Remimazolam vs. propofol for general anaesthesia in elderly patients: a meta-analysis with trial sequential analysis
Authors: Pereira Eduardo Maia , Moraes Vitor Ryuiti , Gaya da Costa Mariana , Nascimento Tatiana Souza do , Slawka Eric , Júnior Carlos Galhardo , Struys Michel MRF 
Published: July 2024

BACKGROUNDElderly patients comprise an increasing proportion of patients undergoing surgery, and they require special attention due to age-related physiological changes. Propofol is the traditional agent for anaesthesia, and recently, remimazolam, a novel ultra-short-acting benzodiazepine, has emerged as an alternative to propofol in general anaesthesia.OBJECTIVESWe aim to compare remimazolamvs. propofol for general anaesthesia in elderly patients regarding hypotension, induction characteristics, haemodynamics and recovery outcomes.DESIGNMeta-analysis with sensitivity and trial sequential analyses (TSA) to assess inconsistencies. Risk ratios and mean differences with 95% confidence intervals (95% CIs) were computed using a random effects model. Subgroups and meta-regression according to anaesthesia methods were also performed.DATA SOURCESWe systematically searched MEDLINE, Embase and Cochrane for randomised controlled trials (RCTs) up to January 1, 2024.ELIGIBILITY CRITERIAPatients at least 60 years old, comparing remimazolamvs. propofol for general anaesthesia.RESULTSEleven RCTs (947 patients) were included. Compared with propofol, remimazolam was associated with lower postinduction and intra-operative hypotension (RR 0.41, 95% CI 0.27 to 0.62,P < 0.001) and incidence of bradycardia (risk ratio 0.58, 95% CI 0.34 to 0.98,P = 0.04), with a higher heart rate (P = 0.01). The incidence of injection pain was lower (P < 0.001), but remimazolam was associated with a longer time to loss of consciousness (P < 0.001) and a higher bispectral index at loss of consciousness (P = 0.04). No differences were found for mean arterial pressure, emergence time, extubation time and incidence of emergence agitation. The TSA was consistent and achieved the required information size for hypotension.CONCLUSIONSRemimazolam significantly reduced the risk of hypotension, bradycardia and injection pain, despite an increase in the time to loss of consciousness. Remimazolam appears to be an effective and well tolerated alternative to propofol in elderly patients undergoing general anaesthesia.
Diversity of microglial transcriptional responses during opioid exposure and neuropathic pain
Authors: Sypek Elizabeth I. , Tassou Adrien , Collins Hannah Y. , Huang Karen , McCallum William M. , Bourdillon Alexandra T. , Barres Ben A. , Bohlen Christopher J. , Scherrer Grégory 
Published: July 2024

Abstract
Microglia take on an altered morphology during chronic opioid treatment. This morphological change is broadly used to identify the activated microglial state associated with opioid side effects, including tolerance and opioid-induced hyperalgesia (OIH). Microglia display similar morphological responses in the spinal cord after peripheral nerve injury (PNI). Consistent with this observation, functional studies have suggested that microglia activated by opioids or PNI engage common molecular mechanisms to induce hypersensitivity. In this article, we conducted deep RNA sequencing (RNA-seq) and morphological analysis of spinal cord microglia in male mice to comprehensively interrogate transcriptional states and mechanistic commonality between multiple models of OIH and PNI. After PNI, we identify an early proliferative transcriptional event across models that precedes the upregulation of histological markers of microglial activation. However, we found no proliferative transcriptional response associated with opioid-induced microglial activation, consistent with histological data, indicating that the number of microglia remains stable during morphine treatment, whereas their morphological response differs from PNI models. Collectively, these results establish the diversity of pain-associated microglial transcriptomic responses and point towards the targeting of distinct insult-specific microglial responses to treat OIH, PNI, or other central nervous system pathologies.
Noninvasive targeted modulation of pain circuits with focused ultrasonic waves
Authors: Riis Thomas S. , Feldman Daniel A. , Losser Adam J. , Okifuji Akiko , Kubanek Jan 
Published: July 2024

Abstract
Direct interventions into deep brain circuits constitute promising treatment modalities for chronic pain. Cingulotomy and deep brain stimulation targeting the anterior cingulate cortex have shown notable improvements in the unpleasantness of pain, but these interventions require brain surgeries. In this study, we have developed an approach that can modulate this deep brain affective hub entirely noninvasively, using low-intensity transcranial-focused ultrasound. Twenty patients with chronic pain received two 40-minute active or sham stimulation protocols and were monitored for one week in a randomized crossover trial. Sixty percent of subjects experienced a clinically meaningful reduction of pain on day 1 and on day 7 following the active stimulation, while sham stimulation provided such benefits only to 15% and 20% of subjects, respectively. On average, active stimulation reduced pain by 60.0% immediately following the intervention and by 43.0% and 33.0% on days 1 and 7 following the intervention. The corresponding sham levels were 14.4%, 12.3%, and 6.6%. The stimulation was well tolerated, and no adverse events were detected. Side effects were generally mild and resolved within 24 hours. Together, the direct, ultrasonic stimulation of the anterior cingulate cortex offers rapid, clinically meaningful, and durable improvements in pain severity.
Impact of the 2022 Infant Formula Shortage on Self-Reported Rates of Anxiety and Depression
Authors: DuBois Dominique , Sundell Joe , Thomsen Michael R. , Brown Clare C. 
Published: July 2024

Purpose:
To evaluate the impact of the 2022 infant formula shortage on self-reported anxiety and depression.

Background:
The US national infant formula shortage of 2022 originated from supply chain disruptions triggered by the COVID-19 pandemic, and the shortage was further compounded by a recall of tainted formula products.

Methods:
We used survey-weighted data from the Household Pulse Survey (HPS) to measure self-reported anxiety and depression among individuals with formula-fed infants less than 1 year of age. We evaluated the association between 2 formula disruption variables (being impacted by the infant formula shortage or having difficulty obtaining formula in the last 7 days) with 2 mental health outcomes (anxiety and depression) using multivariable logistic regressions.

Results:
We found increased odds of self-reported anxiety (aOR: 3.13; P < .001) and depression (aOR: 3.05; P = .005) for respondents affected by the infant formula shortage. There were no adjusted associations between having difficulty obtaining formula in the last 7 days and anxiety and depression.

Conclusions:
Individuals affected by the infant formula shortage had increased odds of both anxiety and depression. Continued efforts to improve food security for low-income infants is critical for ensuring equitable nutritional and health outcomes across infant populations.

Implications for practice and research:
Continued efforts to reduce food insecurity for low-income infants are critically needed, as infant nutrition impacts caregiver mental health and infant health. Efforts to improve lactation support and breastfeeding initiation are needed in addition to improvements in access to formula.
Ex-Vivo 3D Cellular Models of Pancreatic Ductal Adenocarcinoma
Authors: Acimovic Ivana , Gabrielová Viktorie , Martínková Stanislava , Eid Michal , Vlažný Jakub , Moravčík Petr , Hlavsa Jan , Moráň Lukáš , Cakmakci Riza Can , Staňo Peter , Procházka Vladimír , Kala Zdeněk , Trnka Jan , Vaňhara Petr 
Published: July 2024

Abstract
Pancreas is a vital gland of gastrointestinal system with exocrine and endocrine secretory functions, interweaved into essential metabolic circuitries of the human body. Pancreatic ductal adenocarcinoma (PDAC) represents one of the most lethal malignancies, with a 5-year survival rate of 11%. This poor prognosis is primarily attributed to the absence of early symptoms, rapid metastatic dissemination, and the limited efficacy of current therapeutic interventions. Despite recent advancements in understanding the etiopathogenesis and treatment of PDAC, there remains a pressing need for improved individualized models, identification of novel molecular targets, and development of unbiased predictors of disease progression. Here we aim to explore the concept of precision medicine utilizing 3-dimensional, patient-specific cellular models of pancreatic tumors and discuss their potential applications in uncovering novel druggable molecular targets and predicting clinical parameters for individual patients.
Dynamic continualization of mechanical metamaterials with quasi-periodic microstructure
Authors: Del Toro Rosaria , De Bellis Maria Laura , Bacigalupo Andrea 
Published: July 2024

This article focuses on characterizing a class of quasi-periodic metamaterials created through the repeated arrangement of an elementary cell in a fixed direction. The elementary cell consists of two building blocks made of elastic materials and arranged according to the generalized Fibonacci sequence, giving rise to a quasi-periodic finite microstructure, also called Fibonacci generation. By exploiting the transfer matrix method, the frequency band structure of selected periodic approximants associated with the Fibonacci superlattice, i.e. the layered quasi-periodic metamaterial, is determined. The self-similarity of the frequency band structure is analysed by means of the invariants of the symplectic transfer matrix as well as the transmission coefficients of the finite clusters of Fibonacci generations. A high-frequency continualization scheme is then proposed to identify integral-type or gradient-type non-local continua. The frequency band structures obtained from the continualization scheme are compared with those derived from the Floquet–Bloch theory to validate the proposed scheme.
This article is part of the theme issue ‘Current developments in elastic and acoustic metamaterials science (Part 1).’
RNA recognition by minimal ProQ fromNeisseria meningitidis
Authors: Basczok Maciej , Olejniczak Mikołaj 
Published: July 2024

ABSTRACTNeisseria meningitidisminimal ProQ is a global RNA binding protein belonging to the family of FinO-domain proteins. TheN. meningitidisProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions. To better understand how this minimal FinO-domain protein recognizes RNAs, we compared its binding to seven different natural RNA ligands of this protein. Next, two of these RNAs,rpmG-3’ and AniS, were subject to further mutational studies. The data showed thatN. meningitidisProQ binds the lower part of the intrinsic transcription terminator hairpin, and that the single-stranded sequences on the 5’ and 3ʹ side of terminator stem are required for tight binding. However, the specific lengths of 5’ and 3ʹ RNA sequences required for optimal binding differed between the two RNAs. Additionally, our data show that the 2ʹ-OH and 3ʹ-OH groups of the 3ʹ terminal ribose contribute to RNA binding byN. meningitidisProQ. In summary, the minimal ProQ protein fromN. meningitidishas generally similar requirements for RNA binding as the isolated FinO domains of other proteins of this family, but differs from them in detailed RNA features that are optimal for specific RNA recognition.
Early life psychosocial stress increases binge-like ethanol consumption and CSF1R inhibition prevents stress-induced alterations in microglia and brain macrophage population density
Authors: Gironda Stephen C. , Centanni Samuel W. , Weiner Jeffrey L. 
Published: July 2024

AbstractEarly life stress (ELS) has lasting consequences on microglia and brain macrophage function. During ELS, microglia and brain macrophages alter their engagement with synapses leading to changes in neuronal excitability. Further, ELS can induce innate immune memory formation in microglia and brain macrophages resulting in altered responsivity to future environmental stimuli. These alterations can result in lasting adaptations in circuit function and may mediate the relationship between ELS and the risk to develop alcohol use disorder (AUD). Whether microglia and brain macrophages truly mediate this relationship remains elusive. Here, we report: 1) an ELS model, psychosocial stress (PSS), increases binge-like ethanol consumption in early adulthood. 2) Repeated binge-like ethanol consumption increases microglia and brain macrophage population densities across the brain. 3) PSS may elicit innate immune memory formation in microglia and brain macrophages leading to altered population densities following repeated binge-like ethanol consumption. 4) Microglia and brain macrophage inhibition trended towards preventing PSS-evoked changes in binge-like ethanol consumption and normalized microglia and brain macrophage population densities. Therefore, our study suggests that acutely inhibiting microglia and brain macrophage function during periods of early life PSS may prevent innate immune memory formation and assist in reducing the risk to develop AUD.HighlightsAn early life psychosocial stress (PSS) exposure increases ethanol consumptionMicroglial inhibition during PSS trends towards reducing ethanol consumptionBinge ethanol consumption increases microglial count and alters cell proximityEarly life PSS alters microglial responsivity to binge ethanol consumptionMicroglial inhibition may prevent microglial innate immune memory formation
Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models
Authors: Roche Rahmatullah , Tarafder Sumit , Bhattacharya Debswapna 
Published: July 2024

AbstractGround-breaking progress has been made in structure prediction of biomolecular assemblies, including the recent breakthrough of AlphaFold 3. However, it remains challenging for AlphaFold 3 and other state-of-the-art deep learning-based methods to accurately predict protein-RNA complex structures, in part due to the limited availability of evolutionary and structural information related to protein-RNA interactions that are used as inputs to the existing approaches. Here, we introduce ProRNA3D-single, a new deep-learning framework for protein-RNA complex structure prediction with only single-sequence input. Using a novel geometric attention-enabled pairing of biological language models of protein and RNA, a previously unexplored avenue, ProRNA3D-single enables the prediction of interatomic protein-RNA interaction maps, which are then transformed into multi-scale geometric restraints for modeling 3D structures of protein-RNA complexes via geometry optimization. Benchmark tests show that ProRNA3D-single convincingly outperforms current state-of-the-art methods including AlphaFold 3, particularly when evolutionary information is limited; and exhibits remarkable robustness and performance resilience by attaining better accuracy with only single-sequence input than what most methods can achieve even with explicit evolutionary information. Freely available athttps://github.com/Bhattacharya-Lab/ProRNA3D-single, ProRNA3D-single should be broadly useful for modeling 3D structures of protein-RNA complexes at scale, regardless of the availability of evolutionary information.
Maintenance of taste receptor cell presynaptic sites requires gustatory nerve fibers
Authors: Landon Shannon M. , Holder Emily , Ng Amber , Wood Ryan , Gutierrez Kuri Eduardo , Pinto Laura , Humayun Saima , Macpherson Lindsey J. 
Published: July 2024

AbstractThe turnover and re-establishment of peripheral taste synapses is vital to maintain connectivity between the primary taste receptor cells and the gustatory neurons which relay taste information from the tongue to the brain. Despite the importance of neuron-taste cell reconnection, mechanisms governing synapse assembly and the specificity of synaptic connections is largely unknown. Here we use the expression of presynaptic proteins, CALHM1 and Bassoon, to probe whether nerve fiber connectivity is an initiating factor for the recruitment of presynaptic machinery in different populations of taste cells. Under homeostatic conditions, the vast majority (>90%) of presynaptic sites are directly adjacent to nerve fibers. In the days immediately following gustatory nerve transection and complete denervation, Bassoon and CALHM1 puncta are markedly reduced. This suggests that nerve fiber innervation is crucial for the recruitment and maintenance of presynaptic sites. In support of this, we find that expression ofBassoonandCalhm1mRNA transcripts are significantly reduced after denervation. During nerve fiber regeneration into the taste bud, presynaptic sites begin to replenish, but are not as frequently connected to nerve fibers as intact controls (∼50% compared to >90%). This suggests that gustatory neuron proximity, rather than direct contact, likely drives taste receptor cells to express and aggregate presynaptic proteins at the cell membrane. Together, these data support the idea that trophic factors secreted by gustatory nerve fibers prompt taste receptor cells to produce presynaptic specializations at the cell membrane, which in turn may guide neurons to form mature synapses. These findings provide new insights into the mechanisms driving synaptogenesis and synaptic plasticity within the rapidly changing taste bud environment.