bluuebunny/crossref_metadata_2025 huggingface dataset:
A p-type dopable ultrawide-bandgap oxide
Authors: Lyons John L , Janotti Anderson
Published: November 2023

A major shortcoming of ultrawide-bandgap (UWBG) semiconductors is unipolar doping, in which either n-type or p-type conductivity is typically possible, but not both within the same material. For UWBG oxides, the issue is usually the p-type conductivity, which is inhibited by a strong tendency to form self-trapped holes (small polarons) in the material. Recently, rutile germanium oxide (r-GeO2), with a band gap near 4.7 eV, was identified as a material that might break this paradigm. However, the predicted acceptor ionization energies are still relatively high (∼0.4 eV), limiting p-type conductivity. To assess whether r-GeO2 is an outlier due to its crystal structure, the properties of a set of rutile oxides are calculated and compared. Hybrid density functional calculations indicate that rutile TiO2 and SnO2 strongly trap holes at acceptor impurities, consistent with previous work. Self-trapped holes are found to be unstable in r-SiO2, a metastable polymorph that has a band gap near 8.5 eV. Group-III acceptor ionization energies are also found to be lowest among the rutile oxides and approach those of GaN. Acceptor impurities have sufficiently low formation energies to not be compensated by donors such as oxygen vacancies, at least under O-rich limit conditions. Based on the results, it appears that r-SiO2 has the potential to exhibit the most efficient p-type conductivity when compared to other UWBG oxides.
Post-quantum nonlocality in the minimal triangle scenario
Authors: Pozas-Kerstjens Alejandro , Girardin Antoine , Kriváchy Tamás , Tavakoli Armin , Gisin Nicolas
Published: November 2023

We investigate network nonlocality in the triangle scenario when all three parties have no input and binary outputs. Through an explicit example, we prove that this minimal scenario supports nonlocal correlations compatible with no-signaling and independence of the three sources, but not with realisations based on independent quantum or classical sources. This nonlocality is robust to noise. Moreover, we identify the equivalent to a Popescu-Rohrlich box in the minimal triangle scenario.
DFT studies on structural stability, vibrational and linear and nonlinear optical properties of low-dimensional zinc sulfide: from the 3D bulk to the 2D monolayer and the 1D zigzag single-walled nanotubes
Authors: Masri Rimel , Larbi Tarek , Nehdi Kamel , Doll Klaus , Amlouk Mosbah
Published: November 2023

Through first-principles calculations, we investigate structural stability, vibrational and linear and nonlinear optical properties of the zinc sulfide (ZnS) in different periodic forms ranging from the 3D bulk to the 2D hexagonal monolayer and their corresponding 1D zigzag single-walled nanotubes. To first order, the electronic wave function on the ground state was constructed using linear combinations of Gaussian-type functions at the DFT/B3LYP level. Then, the Raman and IR spectrum is computed by adopting a Coupled-Perturbed-Hartree–Fock/Kohn–Sham (CPHF/KS) approach. Cohesive, relaxation, and rolling energies, elastic and piezoelectric constants, electronic and nuclear contributions to the polarizability tensor, and nonlinear first and second-order hyperpolarizability tensor components are reported. Our study shows that 3D and 2D forms are stable and show semiconducting behavior, good piezoelectric responses, and fascinating linear and nonlinear optical properties. For 1D single-walled nanotubes, dynamic stability is observed only for the smallest (6,0) nanotubes. For n > 6, imaginary mode frequencies in the simulated IR and Raman spectra indicate dynamic instability. A scanning mode procedure along the largest imaginary vibrational mode is applied in order to determine the stable structures of the largest (14,0), (18,0) and (22,0) ZnS nanotubes. After that, no more imaginary phonon frequencies are detected in their vibrational spectra. Their potential energy surface contains two minima between a saddle point corresponding to a slightly distorted nanotube structure. Our study proves that the zinc sulfide nanostructures possess diverse physical properties so useful for potential applications in nanoelectronics and for nanodevices.
Adaptive thermally tunable radiative cooling with angle insensitivity using phase-change-material-based metasurface
Authors: Boşdurmaz Ekin Bircan , Ghobadi Amir , Özbay Ekmel
Published: November 2023

Radiative cooling is the passive cooling of a material with the help of a specific spectral response to emit thermal energy into space through atmospheric transparency windows. However, most of the proposed designs have no dynamically tunable emission response. In this paper, we present a feasible inverse pyramid structure made of a phase change material (PCM) on top of a metallic mirror to realize an adaptive radiative cooler with almost angle-independent emission response. The design uses the thermally controlled PCM called Samarium nickelate (SmNiO3) to actively tune the spectral response of the design, which, in turn, allows the design to radiatively cool itself. The emission response of the design is compatible with atmospheric transmissive windows. As the design heated up to higher temperatures, the peak of the emission spectrum red-shifts and moves toward the atmospheric transparency window.
The morphology of exciting dark matter and the galactic 511 keV signal
Authors: Cappiello Christopher V. , Jafs Michael , Vincent Aaron C.
Published: November 2023

We study the morphology of the 511 keV signal that could be produced by exciting dark matter (XDM) in the Milky Way. In this model, collisions between dark matter particles excite the dark matter to a state that can then decay back to the ground state, releasing an electron-positron pair. These electrons and positrons would then annihilate, producing 511 keV photons that could explain the 511 keV signal seen by INTEGRAL at the Galactic Center. We compare the resulting flux with the most recent INTEGRAL data, performing the first full statistical analysis of the exciting dark matter model. We focus on exciting dark matter in the mass and cross section ranges 100 GeV ≲ mχ
≲ 3 TeV and 10-19 cm3 s-1 〈σv〉 10-16 cm3 s-1. We show that exciting dark matter can provide a significantly better fit than the simpler case of annihilating dark matter, with Δχ
2 > 16 for all but one of the density profiles we consider.
Primordial black holes from a curvaton scenario with strongly non-Gaussian perturbations
Authors: Gow Andrew , Miranda Tays , Nurmi Sami
Published: November 2023

We investigate the production of primordial black holes (PBHs) in a mixed inflaton-curvaton scenario with a quadratic curvaton potential, assuming the curvaton is in de Sitter equilibrium during inflation with 〈χ〉 = 0. In this setup, the curvature perturbation sourced by the curvaton is strongly non-Gaussian, containing no leading Gaussian term. We show that for m
2/H
2 ≳ 0.3, the curvaton contribution to the spectrum of primordial perturbations on CMB scales can be kept negligible but on small scales the curvaton can source PBHs. In particular, PBHs in the asteroid mass range 10-16
M
⊙ ≲ M ≲ 10-10
M
⊙ with an abundance reaching F
PBH = 1 can be produced when the inflationary Hubble scale H ≳ 1012 GeV and the curvaton decay occurs in the window from slightly before the electroweak transition to around the QCD transition.
Effects of the resonance modification by electron cyclotron current drive on the linear and nonlinear dynamics of energetic particle driven magnetohydrodynamics modes in Heliotron J
Authors: Adulsiriswad P. , Todo Y. , Yamamoto S. , Kado S. , Kobayashi S. , Ohshima S. , Okada H. , Minami T. , Nakamura Y. , Ishizawa A. , Konoshima S. , Mizuuchi T. , Nagasaki K.
Published: November 2023

This study investigates the effects of electron cyclotron current drive (ECCD) on the linear and nonlinear dynamics of energetic-particle (EP)-driven magnetohydrodynamics (MHD) instability (mode) in Heliotron J (HJ), using MEGA, a nonlinear hybrid EP-MHD simulation code. The effects of ECCD are included through the modification of the equilibrium magnetic field. Five MHD equilibria with plasma currents (

I

p

) of −2.00, −1.00, 0.00, 0.50, and 1.00 kA are considered, where negative and positive

I

p

represent counter and co-ECCD, respectively. To account for the EP finite charge-exchange loss observed in HJ, a bump-on-tail velocity distribution is assumed for EP. The study finds that the stabilization trends in terms of the linear growth rate (

γ

ω
A

−
1

) are qualitatively similar to the FAR3D linear simulation and experimental results. In addition to the enhancements of the local magnetic shear and continuum damping by ECCD as proposed in previous studies, the study suggests that changes in the linear EP and shear Alfvén wave resonance are another important factor, especially for the

n

/

m
=
1

/

2

mode. The study shows that in the currentless equilibrium, the high-velocity toroidicity-induced resonance between the

n

/

m
=
1

/

2

mode and the co-passing EP (

L
=
−
1

) has the highest EP energy transfer rate, but is located slightly below the NBI injection velocity. The co-ECCD and cntr-ECCD can shift this resonance into higher and lower velocity regions, respectively. This can lead to resonance removal for co-ECCD, while cntr-ECCD can initially increase the number of resonant EPs for a small value of shift. If the shift of the resonance by cntr-ECCD is sufficiently large, the study observes stabilization due to the reduction in the EP population in the low-velocity region. The study also finds that changes in resonance affect nonlinear dynamics such as EP transport and frequency chirping. The convective transport of the co- and counter-passing EPs can be controlled, which can only be achieved for energetic-particle-mode due to the asymmetry in the resonance velocity between co- and cntr-passing EPs. The changes in the frequency chirping from the downward chirping branch to the upward chirping branch can also be explained by the changes in the resonance velocity caused by ECCD.
Carer involvement in medication adherence: carer views and experiences of facilitating medication adherence using pharmacy-filled multi-compartment medication compliance aids and other methods of adherence support—a questionnaire survey
Authors: Thielemans Lieze , Chin Katherine , Hegarty Alice , Schiff Rebekah
Published: November 2023

Introduction

Unpaid carers are an increasing proportion of the UK population. One of the many ways in which they help those they care for is assisting with medication adherence. Many older adults have medicines dispensed in pharmacy-filled multi-compartment medication compliance aids (pMCAs). However, evidence suggests that pMCAs may increase medication-related harm, and little is known about the interaction between the user, medication adherence systems and the carer.

Aim

To explore the views of carers supporting older adults to manage their medications with and without a pMCA.

Method

A researcher-administered questionnaire survey of carers supporting older adults to manage their medicines with or without a pMCA. Participants were recruited from inpatient wards, outpatient clinics and community services in central London. Responses were analysed by two independent researchers to identify overarching themes.

Results

Eighty-eight unpaid carers were interviewed and responses were categorised according to the medication adherence method used; 47 supported a user with a pMCA and 41 supported without a pMCA. The main themes were: Time, Responsibility and Mistakes, Waste and Sustainability, and Polypharmacy, with sub-themes of design of multi-compartment medication compliance aids, organisation and reassurance.

Conclusion

Supporting medication adherence puts considerable burden on carers regardless of whether a self- or pharmacy-filled medication compliance aid is used or not. Prescribers could alleviate this burden through regular medication review by considering the prescribing frequency and duration and medication rationalisation. Redesign of both pMCAs and systems surrounding their use could also help reduce carer’s burden and environmental burden.
Food quantity and the intensity of the alarm signal combine to modulate the resource selection in a termite species
Authors: Silva Aline N F , Silva Cátila R , Santos Renan E C , Arce Carla C M , Araújo Ana Paula A , Cristaldo Paulo F
Published: November 2023

Maximizing food intake while minimizing risk is an important trade-off in the foraging behavior of most animals. In general, foragers are vulnerable and the ability to trade off benefits (food quantity) against costs (risk of being killed) may provide a considerable ecological advantage. Despite the increasing number of studies, the effects of food quantity and mortality risk signals on resource selection in eusocial insect is not well understood. Here, we investigated the combination of distinct levels of food quantity and the intensity of alarm signal on resource selection of a Neotropical termite, Nasutitermes corniger (Motschulsky) (Termitidae: Nasutitermitinae). Manipulative bioassays with binary and multiple choices were conducted over time to check the recruitment of termite groups among resources containing different levels of food quantity and alarm signals. Overall, our results showed that regardless of food quantity, termites avoid a food source if there is even a small amount of alarm signal. This work contributes to a better understanding of habitat use by termite species. Furthermore, it shows for the first time the combined effects of food quantity and alarm signals on the resource selection of an important ecological and economic termite species.
Bridging the cytogenetic gap in Trichoptera (Insecta): first karyotypic data on Neotropical species and insights into chromosomal evolution in caddisflies
Authors: Lovaglio Diez María , Bressa María J , Rodríguez Gil Sergio G , Papeschi Alba G , Sganga Julieta V
Published: November 2023

Trichoptera are a diverse group of insects with aerial adults and aquatic immature stages. Despite their importance in freshwater environments, fundamental aspects of their biology are unknown, and no chromosomal studies have been performed in Neotropical species. The aim of this study was to provide the first cytogenetic analysis of four Trichoptera species from the Neotropics. We analysed the meiotic development and chromosome behaviour in Smicridea (Rhyacophylax) pampeana Flint (Annulipalpia: Hydropsychidae), Marilia flexuosa Ulmer (Integripalpia: Odontoceridae), Triplectides misionensis Holzenthal (Integripalpia: Leptoceridae), and Grumicha grumicha (Vallot) (Integripalpia: Sericostomatidae) by conventional cytogenetic procedures. The chromosome numbers are 2n = 31/32 (female/male) in S. (R.) pampeana, 2n = 57 (female) in M. flexuosa, 2n = 47 (female) in T. misionensis, and 2n = 35 (female) in G. grumicha. All four species have a simple sex chromosome system Z/ZZ (female/male). Females are the heterogametic sex, and their meiosis is achiasmatic. Our results together with available cytogenetic data provide more information on the karyology of Trichoptera and contribute to the current scientific knowledge of the possible mechanisms involved in chromosomal evolution. Based on all the evidence, we propose the existence of possible positive relationships between biological traits, ecological strategies, and cytogenetic features in Trichoptera.
False-Reactive Fourth-Generation Human Immunodeficiency Virus Testing in Cancer Patients
Authors: Chiu Chia-Yu , Mustafayev Khalis , Bhatti Micah M , Jiang Ying , Granwehr Bruno P , Torres Harrys A
Published: November 2023

Background

The fourth-generation (4th-gen) human immunodeficiency virus (HIV)-1/2 antibody/antigen (Ab/Ag) combination immunoassay currently used for HIV screening offers greater sensitivity than previous assays, but false-reactive results occur in up to 20% of patients. Large-scale observations in cancer patients are lacking.

Methods

We conducted a retrospective study of cancer patients seen at the University of Texas MD Anderson Cancer Center (March 2016–January 2023) who had reactive 4th-gen ARCHITECT HIV-1/2 Ab/Ag combination immunoassay results. We analyzed characteristics of patients with true-reactive and false-reactive results, defined based on Centers for Disease Control and Prevention criteria.

Results

A total of 43 637 patients underwent 4th-gen HIV screening, and 293 had reactive 4th-gen HIV test results. Twenty-one patients were excluded because they did not have cancer. Among the remaining 272 patients, 78 (29%) had false-reactive results. None of these patients experienced delays in their cancer treatment, but 26% experienced mental distress. Multivariate logistic regression analysis identified 5 predictors of having false-reactive results: age >60 years (adjusted odds ratio [aOR], 6.983; P < .0001), female sex (aOR, 6.060; P < .0001), race/ethnicity (Black: aOR, 0.274; Hispanic: aOR, 0.236; P = .002), syphilis coinfection (aOR, 0.046; P = .038), and plant alkaloids therapy (aOR, 2.870; P = .013).

Conclusions

False-reactive 4th-gen HIV test results occur in almost one-third of cancer patients. Physicians should be aware of the high rates of false-reactive HIV screening results in this patient population. These findings may have implications for counseling regarding testing, especially among those at low risk for HIV infection.
International Law and the Agony of Animals in Industrial Meat Production
Authors: Nollkaemper André
Published: November 2023

International law leaves states and meat-producing corporations full freedom to annually subject billions of animals to extreme suffering during intensive meat production. In the last two decades, the World Organisation for Animal Health (WOAH) has taken the lead in developing international standards for animal welfare. WOAH alone will not be able to restrict the liberty of international law, given the fact that demanding legal standards may hinder the push to provide nutrients to a growing world population and given global diversity in socio-economic situations, consumer preferences for meat products and cultural values. However, the push to regulate meat production has received new impulses from international institutions that seek to address adverse impacts of industrial animal farming on human interests – in particular, global health, climate change and biodiversity. As yet, this has done little to restrain the freedom under international law to subject farm animals to suffering, but it has expanded the grounds for future global agreements to regulate industrial farming as well as the range of principles and institutions that together constitute the framework within which decisions on industrial meat production that may benefit animal welfare have to be taken.
Two zebrafish cacna1s loss-of-function variants provide models of mild and severe CACNA1S-related myopathy
Authors: Endo Yukari , Groom Linda , Wang Sabrina M , Pannia Emanuela , Griffiths Nigel W , Van Gennip Jenica L M , Ciruna Brian , Laporte Jocelyn , Dirksen Robert T , Dowling James J
Published: November 2023

CACNA1S-related myopathy, due to pathogenic variants in the CACNA1S gene, is a recently described congenital muscle disease. Disease associated variants result in loss of gene expression and/or reduction of Cav1.1 protein stability. There is an incomplete understanding of the underlying disease pathomechanisms and no effective therapies are currently available. A barrier to the study of this myopathy is the lack of a suitable animal model that phenocopies key aspects of the disease. To address this barrier, we generated knockouts of the two zebrafish CACNA1S paralogs, cacna1sa and cacna1sb. Double knockout fish exhibit severe weakness and early death, and are characterized by the absence of Cav1.1 α1 subunit expression, abnormal triad structure, and impaired excitation-contraction coupling, thus mirroring the severe form of human CACNA1S-related myopathy. A double mutant (cacna1sa homozygous, cacna1sb heterozygote) exhibits normal development, but displays reduced body size, abnormal facial structure, and cores on muscle pathologic examination, thus phenocopying the mild form of human CACNA1S-related myopathy. In summary, we generated and characterized the first cacna1s zebrafish loss-of-function mutants, and show them to be faithful models of severe and mild forms of human CACNA1S-related myopathy suitable for future mechanistic studies and therapy development.
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

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 >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

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

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 < 0.05), significant increase in average daily gain (ADG) at 21, 28 d (P < 0.05), significantly increased levels of total protein (TP), albumin (ALB), insulin (INS), thyroxine (T3), growth hormone (GH) at 14, 28 d (P < 0.05), significantly decreased levels of glucose (GLU), total cholesterol (TC), glucagon (GC), and triglyceride (TG) at 28 d in Group C (P < 0.05). There were significantly increased levels of TP, ALB at 14, 21 d (P < 0.05), significantly increased level of TP at 35 d (P < 0.05), significantly increased level of GH at 28 d (P < 0.05), significantly decreased levels of GLU, GC at 28 d (P < 0.05), significant reduction in F/G at 14, 21 d in Groups B and D (P < 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

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

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

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

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

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

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 >3 ARVs. Alternatively, in scenarios of viremia with moderate to high-level NRTI resistance, >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

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

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

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

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 Rude Hand of Innovation
Authors: Hackett David G
Published: November 2023

Tracing the social and religious transformation of Albany, New York, from its colonial origins through the industrialization of the early nineteenth century, Hackett’s study not only illuminates the social history of Albany, but abundantly demonstrates the central role played by religion in the creation of American social life.
The Legacy of Fazlur Rahman
Authors: Denny Frederick Mathewson
Published: November 2023

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

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

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

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.
Submitting To Freedom
Authors: Ramsey Bennett
Published: November 2023

Bennett Ramsey presents a new analysis of the religious views of the nineteenth-century American philosopher William James. Ramsey argues that James was primarily motivated by religious concerns in all of his writings and that this fact has been obscured by the artificial scholarly division of his work into philosophy’,psychology’, and religion’.
“Dear Sammy” Samuel Wesley Jr. School Correspondence
Authors: Charles Wallace
Published: November 2023

The next grouping of letters was sent to the Wesleys’ eldest child, Samuel Jr., between March 1704 and February 1707, his first years away from home. Young Samuel had been born in London in 1690 before the family moved to Lincolnshire, first to South Ormsby and finally to Epworth. Education at his mother’s knee did not begin propitiously: the family story had it that he did not speak until the age of four or five, though then, quite suddenly, in a complete sentence.1 Nevertheless, he became the first object of the home-schooling enterprise, which Susanna Wesley later detailed in a famous letter to her son John, included in part III of this volume.
The Iconographies of Sati
Authors: Courtright Paul B
Published: November 2023

The word sati conjures up a mental picture of a Hindu wife meeting her violent death amidst the flames of her deceased husband’s funeral pyre. This violent image usually expresses the notion that the woman is under-going her death out of a sense of duty, even love, and in the belief that her self-sacrifice will bring great reward in a future incarnation. Perhaps, too, she will for many generations be honored as a goddess by the community she leaves behind.
Sati as Profit Versus Sati as a Spectacle: The Public Debate on Roop Kanwar’s Death
Authors: Nandy Ashis
Published: November 2023

The peculiar mix of fascination, fear, dramatics, moral self-righteousness, and anger with which India’s Westernized middle classes reacted to the sati committed by Roop Kanwar at Deorala in Rajasthan in 1987 should have been a psychologist’s delight. Evidently, the very idea of suicide on the funeral pyre of one’s husband-or the possibility that someone might exploit this ancient and rare rite to hide the murder of a young widow—had its own strange fascination for the modem mind. For a small minority of thinking Indians, however, the middle-class reaction to the sati only deepened the tragedy of the death of a teenage widow.
Surviving Victoria
Authors: Dickson Jay
Published: November 2023

If the British modern period must be given a starting date, we might do well to propose January 22, 1901, the day Queen Victoria died. The modernist imagination consistently seized upon the notion of a moment of historical rupture when human character and the old ways and mores of the nineteenth century irreversibly changed. Most of the dates proposed (such as Virginia Woolf’s suggestion of December 1910, the month of the opening of the Post-Impressionist Show, and D. H. Lawrence’s selection of 19153) acquired significance retrospectively. Yet even at the time of Victoria’s death, almost all of her subjects were aware of its epochal importance, and they remembered it long after. “In spite of all the excitements which have crowded upon us since:’ Edmund Gosse wrote in 1923, “noone can forget the emotion of emerging into the cold night of January 22, 1901, and seeing the newspaper boys, for once discreetly silent, hurrying hither and thither with a huge announcement that the Queen was dead.