bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Resolution Geospatial Mapping of Zero-Dose and Underimmunized Children Following Nigeria's 2021 Multiple Indicator Cluster Survey/National Immunization Coverage Survey
Authors: Jean Baptiste Anne Eudes , Wagai John , Hahné Susan , Adeniran Adeyemi , Koko Richard Ipuragboma , de Vos Stijn , Shibeshi Messeret , Sanders E A M , Masresha Balcha , Hak Eelko 
Published: November 2023

Abstract

Background
“Zero-dose” children are those who are without any routine vaccination or are lacking the first dose of the diphtheria, tetanus, and pertussis–containing vaccine. Based on global estimates from the World Health Organization/United Nations Children’s Fund in 2022, Nigeria has the highest number of zero-dose children, with &gt;2.3 million unvaccinated.

Methods
We used data from the 2021 Nigeria Multiple Indicator Cluster Survey/National Immunization Coverage Survey to identify zero-dose and underimmunized children. Geospatial modeling techniques were employed to determine the prevalence of zero-dose children and predict risk areas with underimmunized children at a high resolution (1 × 1 km).

Results
Zero-dose and underimmunized children are more prevalent in socially deprived groups. Univariate and multivariate bayesian analyses showed positive correlations between the prevalence of zero-dose and underimmunized children and factors such as stunting, contraceptive prevalence, and literacy. The prevalence of zero-dose and underimmunized children varies significantly by region and ethnicity, with higher rates observed in the country's northern parts. Significant heterogeneity in the distribution of undervaccinated children was observed.

Conclusions
Nigeria needs to enhance its immunization system and coverage. Geospatial modeling can help deliver vaccines effectively to underserved communities. By adopting this approach, countries can ensure equitable vaccine access and contribute to global vaccination objectives.
Proportion of APOBEC3-induced defective HIV DNA after 1 year of dolutegravir + lamivudine simplification in the ANRS 167 LAMIDOL trial
Authors: Mazouz Fella , Bertine Mélanie , Coppée Romain , Storto Alexandre , Katlama Christine , Landman Roland , Cabié André , Peytavin Gilles , Raffi François , Yazdanpanah Yazdan , Descamps Diane , Joly Véronique , Ghosn Jade , Charpentier Charlotte ,   the LAMIDOL Study Group, Bouchaud Olivier , Goujard Cécile , Phung Bao , Viard Jean Paul , Weiss Laurence , Duvivier Claudine , Katlama Christine , Girard Pierre Marie , Molina Jean Michel , Morlat Philippe , Jacomet Christine , Piroth Lionel , Cabie André , Poizot-Martin Isabelle , Reynes Jacques , Allavena Clotilde , Billaud Eric , Boutoille David , Raffi François , Reliquet Véronique , Rosenthal Eric , Naqvi Alissa , Aumaitre Hughes , Souala Faouzi , Bernard Louis , Biezunski Noémie , Ajana Faiza , Miailhes Patrick , Amat Karine , Benalicherif Aida , Sylla Babacar 
Published: November 2023

Abstract

Background
Hypermutated viruses induced by APOBEC3 (apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3) proteins comprise some of the defective viruses in the HIV reservoir. Here, we assessed the proportion of APOBEC3-induced defective proviruses in HIV-positive patients before and after receiving dolutegravir + lamivudine dual therapy.

Methods
PBMCs of virologically suppressed patients enrolled in the ANRS 167 LAMIDOL trial, evaluating a switch from triple therapy to dolutegravir + lamivudine, were collected 8 weeks before (W-8) and 48 weeks after (W48) dual-therapy initiation. The Vif and RT regions were subject to next-generation sequencing. Bioinformatic algorithms were developed to identify APOBEC3-defective sequences and APOBEC3-related drug resistance mutations (APOMuts). All hypermutated sequences and those containing at least one stop codon were considered as defective.

Results
One hundred and four patients were enrolled (median virological suppression duration: 4.2 years; IQR: 2.0–9.1). Proviral defective reads at W-8 and W48 were detected in Vif in 22% and 29% of patients, respectively, and in RT in 38% and 42% of patients, respectively. At least one APOMut was present in proviruses of 27% and 38% of patients at W-8 and W48, respectively. The ratio of APOMuts/number of potential APOMut sites was significantly higher at W48 (16.5%) than at W-8 (9.8%, P = 0.007). The presence of APOBEC3-defective viruses at W-8 was not associated with HIV total DNA level, nor with the third drug class received prior to switching to dolutegravir + lamivudine, nor with the duration of virological suppression.

Conclusions
Whereas no significant change in the proportion of patients with APOBEC3-defective proviruses was evidenced after 1 year of dolutegravir + lamivudine maintenance, enrichment in APOMuts was observed. Further longer-term studies are needed to assess the other forms of defective viruses with dual-therapy.
Effect of Pseudostellaria heterophylla polysaccharide on the growth and liver metabolism of chicks
Authors: Yu Yange , Zhu Zhaoyan , Ding Mengxia , Wang Bingxin , Guo Yujie , Tian Yadong , Jiang Ruirui , Sun Guirong , Han Ruili , Kang Xiangtao , Yan Fengbin 
Published: November 2023

Abstract
In this study, the effects of Pseudostellaria heterophylla polysaccharide (PHP) on the growth, development, and liver metabolism of chicks were investigated by feeding chicks diets. Four hundred 7-d-old Gushi roosters were selected and randomly divided into four groups, labeled A, B, C, and D. Group A was fed the basal diet, and Groups B, C, and D were fed 100, 200, and 400 mg PHP per kilogram of basal diet, respectively. At 14, 21, 28 and 35 d of age, five chicks were randomly selected from each group to collect samples for index detection. The results showed that compared with Group A, there were significant reduction in average daily feed intake (ADFI) and feed-to-weight ratio (F/G) at 14, 21, and 28 d (P &lt; 0.05), significant increase in average daily gain (ADG) at 21, 28 d (P &lt; 0.05), significantly increased levels of total protein (TP), albumin (ALB), insulin (INS), thyroxine (T3), growth hormone (GH) at 14, 28 d (P &lt; 0.05), significantly decreased levels of glucose (GLU), total cholesterol (TC), glucagon (GC), and triglyceride (TG) at 28 d in Group C (P &lt; 0.05). There were significantly increased levels of TP, ALB at 14, 21 d (P &lt; 0.05), significantly increased level of TP at 35 d (P &lt; 0.05), significantly increased level of GH at 28 d (P &lt; 0.05), significantly decreased levels of GLU, GC at 28 d (P &lt; 0.05), significant reduction in F/G at 14, 21 d in Groups B and D (P &lt; 0.05). Based on the above results, the livers from chicks in Groups A and C at 28 d were selected for transcriptome sequencing. The sequencing results showed that significantly differentially expressed genes (SDEGs) were enriched in growth and development, oxidative phosphorylation, the PPAR signaling pathway and the lipid metabolism pathway. All these results revealed that the addition of 200 mg/kg PHP in the diet promoted the growth and development, lipid metabolism and energy metabolism of chicks, inhibit inflammation and tumor development, and improve the function of the liver.
Epigenetic regulation and epigenetic memory resetting during plant rejuvenation
Authors: Liu Jie , Ke Meng , Sun Yuhan , Niu Shihui , Zhang Wenli , Li Yun 
Published: November 2023

Abstract
Reversal of plant developmental status from the mature to the juvenile phase, thus leading to the restoration of the developmental potential, is referred to as plant rejuvenation. It involves multilayer regulation, including resetting gene expression patterns, chromatin remodeling, and histone modifications, eventually resulting in the restoration of juvenile characteristics. Although plants can be successfully rejuvenated using some forestry practices to restore juvenile morphology, physiology, and reproductive capabilities, studies on the epigenetic mechanisms underlying this process are in the nascent stage. This review provides an overview of the plant rejuvenation process and discusses the key epigenetic mechanisms involved in DNA methylation, histone modification, and chromatin remodeling in the process of rejuvenation, as well as the roles of small RNAs in this process. Additionally, we present new inquiries regarding the epigenetic regulation of plant rejuvenation, aiming to advance our understanding of rejuvenation in sexually and asexually propagated plants. Overall, we highlight the importance of epigenetic mechanisms in the regulation of plant rejuvenation, providing valuable insights into the complexity of this process.
INTEDE 2.0: the metabolic roadmap of drugs
Authors: Zhang Yang , Liu Xingang , Li Fengcheng , Yin Jiayi , Yang Hao , Li Xuedong , Liu Xinyu , Chai Xu , Niu Tianle , Zeng Su , Jia Qingzhong , Zhu Feng 
Published: November 2023

Abstract
The metabolic roadmap of drugs (MRD) is a comprehensive atlas for understanding the stepwise and sequential metabolism of certain drug in living organisms. It plays a vital role in lead optimization, personalized medication, and ADMET research. The MRD consists of three main components: (i) the sequential catalyses of drug and its metabolites by different drug-metabolizing enzymes (DMEs), (ii) a comprehensive collection of metabolic reactions along the entire MRD and (iii) a systematic description on efficacy & toxicity for all metabolites of a studied drug. However, there is no database available for describing the comprehensive metabolic roadmaps of drugs. Therefore, in this study, a major update of INTEDE was conducted, which provided the stepwise & sequential metabolic roadmaps for a total of 4701 drugs, and a total of 22 165 metabolic reactions containing 1088 DMEs and 18 882 drug metabolites. Additionally, the INTEDE 2.0 labeled the pharmacological properties (pharmacological activity or toxicity) of metabolites and provided their structural information. Furthermore, 3717 drug metabolism relationships were supplemented (from 7338 to 11 055). All in all, INTEDE 2.0 is highly expected to attract broad interests from related research community and serve as an essential supplement to existing pharmaceutical/biological/chemical databases. INTEDE 2.0 can now be accessible freely without any login requirement at: http://idrblab.org/intede/
Molecular basis for SOX2-dependent regulation of super-enhancer activity
Authors: Yoo Wanki , Song Yi Wei , Kim Jihyun , Ahn Jihye , Kim Jaehoon , Shin Yongdae , Ryu Je-Kyung , Kim Kyeong Kyu 
Published: November 2023

Abstract
Pioneer transcription factors (TFs) like SOX2 are vital for stemness and cancer through enhancing gene expression within transcriptional condensates formed with coactivators, RNAs and mediators on super-enhancers (SEs). Despite their importance, how these factors work together for transcriptional condensation and activation remains unclear. SOX2, a pioneer TF found in SEs of pluripotent and cancer stem cells, initiates SE-mediated transcription by binding to nucleosomes, though the mechanism isn’t fully understood. To address SOX2’s role in SEs, we identified mSE078 as a model SOX2-enriched SE and p300 as a coactivator through bioinformatic analysis. In vitro and cell assays showed SOX2 forms condensates with p300 and SOX2-binding motifs in mSE078. We further proved that SOX2 condensation is highly correlated with mSE078’s enhancer activity in cells. Moreover, we successfully demonstrated that p300 not only elevated transcriptional activity but also triggered chromatin acetylation via its direct interaction with SOX2 within these transcriptional condensates. Finally, our validation of SOX2-enriched SEs showcased their contribution to target gene expression in both stem cells and cancer cells. In its entirety, this study imparts valuable mechanistic insights into the collaborative interplay of SOX2 and its coactivator p300, shedding light on the regulation of transcriptional condensation and activation within SOX2-enriched SEs.
Guanine-containing ssDNA and RNA induce dimeric and tetrameric structural forms of SAMHD1
Authors: Orris Benjamin , Sung Min Woo , Bhat Shridhar , Xu Yingrong , Huynh Kevin W , Han Seungil , Johnson Darren C , Bosbach Benedikt , Shields David J , Stivers James T 
Published: November 2023

Abstract
The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish in cryo-EM and biochemical studies that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ∼20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.
Comparative Performance of Anyplex II HPV28 and Cobas 4800 Human Papillomavirus (HPV) Assays for High-Risk HPV Detection in Self-collected Anal Samples
Authors: Delvallez Gauthier , Cheng Sokleaph , Marot Stéphane , Malonga Gervillien Arnold , Cocherie Théophile , Wignall Steve , Calvez Vincent , Phal Sophat , Vichet Kem , Marcelin Anne-Geneviève , Jary Aude 
Published: November 2023

Abstract
We compared 2 human papillomavirus (HPV) assays to detect the 14 high-risk HPV (hrHPV) genotypes in self-collected anal samples. We found a good agreement and similar performance to detect HPV-16, HPV-18, and the 12 other hrHPV genotypes. The global performance to detect the 14 hrHPV genotypes was not significantly different between the 2 assays.
A National HIV Provider Survey of Antiretroviral Therapy Preferences for Management of Treatment-Naive and Experienced Individuals With Drug Resistance
Authors: Krishnan Sonya , Lippincott Christopher K , Bjerrum Stephanie , Martinez Rivera Marina B , Shah Maunank 
Published: November 2023

Abstract

Background
HIV clinical practice guidelines outline broad treatment principles but offer less explicit recommendations by permutations of encountered viral resistance. We hypothesize that there is variability in antiretroviral (ARV) regimen decision making among providers when considering HIV drug resistance (HIVDR).

Methods
US HIV providers provided ARV regimen recommendations for case vignettes in a series of electronic surveys encompassing variations of HIVDR. Responses were characterized by drugs and classes selected and anticipated activity based on genotypic susceptibility. Heterogeneity was defined as the proportion of unique ARV regimens from total responses.

Results
An overall 119 providers from the United States participated. Among case vignettes with isolated M184V and viremia, 85.9% selected a regimen with 2 nucleoside reverse transcriptase inhibitors (NRTIs) + integrase strand transfer inhibitor (INSTI); 9.9% selected regimens with &gt;3 ARVs. Alternatively, in scenarios of viremia with moderate to high-level NRTI resistance, &gt;50% of providers selected an NRTI-sparing regimen, while a minority recommended 2 NRTIs + INSTI (21/123, 17%). In moderate to high-level INSTI resistance, there was response heterogeneity, with no common unifying approach to management (127 unique regimens/181 responses, 70% heterogeneity). Providers used cabotegravir/rilpivirine for treatment simplification in suppressed cases, despite a history of treatment failure (37/205, 36%).

Conclusions
Our national survey of US HIV providers revealed a consensus to management of HIV resistance with potential alternative options in cases with low heterogeneity. Providers selected cabotegravir/rilpivirine as a viable treatment simplification strategy in suppressed cases with a history of treatment failure. The responses to the case vignettes could be used an education tool for ARV decision making in HIVDR.
Introduction to Logic and to the Methodology of the Deductive Sciences
Authors: Tarski Alfred 
Published: November 2023

Abstract
Now in its fourth edition, this classic work clearly and concisely introduces the subject of logic and its applications. The first part of the book explains the basic concepts and principles which make up the elements of logic. The author demonstrates that these ideas are found in all branches of mathematics, and that logical laws are constantly applied in mathematical reasoning. The second part of the book shows the applications of logic in mathematical theory building with concrete examples that draw upon the concepts and principles presented in the first section. Numerous exercises and an introduction to the theory of real numbers are also presented. Students, teachers and general readers interested in logic and mathematics will find this book to be an invaluable introduction to the subject.
Poetic Form and British Romanticism
Authors: Curran Stuart 
Published: November 2023

Abstract
Curran here confronts the popular stereotype that the Romantics either accepted or rejected previously established literary genres. He proposes rather that they adapted traditional poetic forms to suit their own democratic, secular, and sceptical ethos. This artistic merger of traditional genre with the tenets of Romanticism was a fruitful one, not only resulting in the revival of the ode and the sonnet, but also leading to the imaginative rethinking of major forms like the pastoral, the epic, and the romance which gave the movement its name.
Literary Subjectivity and Other Possibilities in Some Classic Texts
Authors: Gagnier Regenia 
Published: November 2023

Abstract
Between 1848 and 1860 many of the major Victorian novelists experi mented with autobiographical fiction. In Thackeray’s Pendennis (1848–1850), Dickens’s David Copperfield (1849-1850) and later, revisionary, Great Expectations(1860-1861), Bronte’s Villette(l853), Trollope’s The Three Clerks (1858), Meredith’s Ordeal of Richard Feverel (1859), and Eliot’s The Mill on the Floss (1860), the protagonists’ identities unfold in antagonistic relations with family, religion, and social role (often called “duty” by the Victorians): this is to say no more than that the individual’s relation to society, or more specifically the relation of individual development to social institutions, was the great problem of Victorian realism, as it was of Victorian social science.
Mathematical Thought from Ancient to Modern Times
Authors: Kline Morris 
Published: November 2023

Abstract
This comprehensive history traces the development of mathematical ideas and the careers of the mathematicians responsible for them. Originally published in 1972, it is now available as a three volume paperback edition. Volume 1 looks at the discipline's origins in Babylon and Egypt, the creation of geometry and trigonometry by the Greeks, and the role of mathematics in the medieval and early modern periods. Volume 2 focuses on calculus, the rise of analysis in the nineteenth century, and the number theories of Dedekind and Dirichlet. The concluding volume covers the revival of projective geometry, the emergence of abstract algebra, the beginnings of topology, and the influence of Gödel on recent mathematical study.
The Legacy of Fazlur Rahman
Authors: Denny Frederick Mathewson 
Published: November 2023

Abstract
Among the major Muslim thinkers of the second half of the twentieth century, Fazlur Rahman was one of the most learned in both classical Islamic and Western philosophical-theological discourse and had the widest scope in viewing and applying fundamental elements of the Islamic belief and action system. This essay is intended as a descriptive appreciation of his legacy through a selective sampling of his scholarly work, focusing on three main aspects: the philosophical-theological, the moral-ethical, and the religious-communal. Al though the first aspect is the most purely “intellectual,” in terms of following an argument to its logical conclusion (and Rahman was certainly one to do that), Rahman was in fact a Muslim intellectual who applied keen critical and analytical awareness to every serious topic, whether theoretical or practical, individual or communal, textual or contextual.
Introduction: A Moral Pause
Authors: Gross Larry , Katz John Stuart , Ruby Jay 
Published: November 2023

Abstract
In 1839 two French inventors, Daguerre and Niepce, achieved a goal long sought after: the technologically mediated production of images drawn directly from nature. The impact of this achievement was both immediate and widespread; within a year Daguerre’s pamphlet describing his invention had been published in thirty editions and nearly as many languages (Rudisill, 1971:48), and the technology of daguerreotypy was diffused with astounding rapidity. By 1842 the U.S. Congress accepted daguerreotypes as “undeniably accurate evidence in settling the Maine-Canada boundary” ( Rudisill, 1971:240). One of the first proponents of daguerreotypy in the United States was the inventor and artist Samuel Morse, who introduced the new marvel in a speech to the National Academy of Design in 1840, describing the images as having been, “painted by Nature’s self … they cannot be called copies of nature, but portions of nature herself.”
Frontier Gender: Livestock Castration and Square Dancing
Authors: Allmendinger Blake 
Published: November 2023

Abstract
In August 1911, a woman was tried in a Colorado opera house for allegedly having stolen another ranch owner’s stock. Ora Haley had recently purchased a parcel of land that straddled the Colorado and Wyoming state borders. His ranch adjoined Ann Bassett’s homestead, which lay to the south of his land. Haley stated that, in March 1911, two of his cowboys and a stock detective had discovered the carcass of one of his heifers in Bassett’s supply room. Later they had found the animal’s hide on her property and had noticed that someone had cut a piece of skin-with the brand-from the right flank of the animal. The missing brand prevented Haley from contending in court that the heifer had belonged to him or from proving that Bassett had rustled his stock. But Haley triumphed over this absence of evidence, claiming that his cowboys had not only branded his heifer, but spayed it by performing a unique surgical task that differed from the technique that Bassett and his other neighbors used to castrate their animals. His removal of the heifer’s internal reproductive organs had left an external scar that one could read as a brand mark and interpret as a distinct sign of ownership.
Women,s Silence as a Ritual of Truth: A Study of Literary Expressions in Austen, Bronte, and Woolf
Authors: Laurence Patricia 
Published: November 2023

Abstract
Beginning with Tillie Olsen and continuing in the work of American and French feminist critics, silence in women has been viewed as the place of oppression, the mark of women’s exclusion from the public spheres of life and from respresentation as speakers in a text. But it is time to recognize that there is a female tradition of writing beginning in the nineteenth century that invites us to reread certain paradigms of silence and expression. Knowing that women in certain times and places are unable to speak openly, the novelists Jane Austen, Charlotte Bronte, and Virginia Woolf narrate the inwardness of female listeners and observers in conventional frameworks in life and texts, inviting us to interpret their silences not as passivity, submission and oppression, but as an enlightened presence. The silences represent women’s different ways of feeling and knowing-perhaps silences hiding fears, angers, taboo thoughts-as well as representing the available means of expression in particular historical and cultural circumstances. This female tradition, which is connected with the development of the novel and its ability to record inner life, replaces the speaking subject in the English novel with the observing, listening, thinking, dreaming female subject.