bluuebunny/crossref_metadata_2025 huggingface dataset:
Regularity with Respect to the Parameter of Lyapunov Exponents for Diffeomorphisms with Dominated Splitting
Authors: Saghin Radu , Valenzuela-Henríquez Pancho , H. Vásquez Carlos
Published: August 2024

We consider families of diffeomorphisms with dominated splittings and preserving a Borel probability measure, and we study the regularity of the Lyapunov exponents associated to the invariant bundles with respect to the parameter. We obtain that the regularity is at least the sum of the regularities of the two invariant bundles (for regularities in

[
0
,
1
]

[0,1]

), and under suitable conditions we obtain formulas for the derivatives. Similar results are obtained for families of flows, and for the case when the invariant measure depends on the map.

We also obtain several applications. Near the time one map of a geodesic flow of a surface of negative curvature the metric entropy of the volume is Lipschitz with respect to the parameter. At the time one map of a geodesic flow on a manifold of constant negative curvature the topological entropy is differentiable with respect to the parameter, and we give a formula for the derivative. Under some regularity conditions, the critical points of the Lyapunov exponent function are nonflat (the second derivative is nonzero for some families). Also, again under some regularity conditions, the criticality of the Lyapunov exponent function implies some rigidity of the map, in the sense that the volume decomposes as a product along the two complementary foliations. In particular for area preserving Anosov diffeomorphisms, the only critical points are the maps smoothly conjugated to the linear map, corresponding to the global extrema.
P4-ATPase endosomal recycling relies on multiple retromer-dependent localization signals
Authors: Jiménez Mariana , Kyoung Claire K. , Nabukhotna Kateryna , Watkins Davia , Jain Bhawik K. , Best Jordan T. , Graham Todd R.
Published: August 2024

Type IV P-type ATPases (P4-ATPases) are lipid flippases that generate an asymmetric membrane organization essential for cell viability. The five budding yeast P4-ATPases traffic between the Golgi complex, plasma membrane, and endosomes but how they are recycled from the endolysosomal system to the Golgi complex is poorly understood. In this study, we find that P4-ATPase endosomal recycling is primarily driven by the retromer complex and the F-box protein Rcy1. Defects in P4-ATPase recycling result in their mislocalization to the vacuole and a substantial loss of membrane asymmetry. The P4-ATPases contain multiple predicted retromer sorting signals, and the characterization of these signals in Dnf1 and Dnf2 led to the identification of a novel retromer-dependent signal, IPM[ST] that acts redundantly with predicted motifs. Together, these results emphasize the importance of endosomal recycling for the functional localization of P4-ATPases and membrane organization.
A List of Early Modern Spanish Literary Texts with Black Characters
Authors: Berruezo-Sánchez Diana
Published: August 2024

This Appendix lists pieces of early modern Spanish literature that contain black characters. There have been several useful previous inventories, but the list here augments the former works by collecting the details of sixteenth- and seventeenth-century literary texts with black characters who have a voice, whether they have major or minor roles. The primary purpose of this chart is to provide not just numbers and bibliographic details but also a clear picture of the literary impact of early modern black Africans. The list itemises ninety pieces of literature, including poems, novels, short stories, and theatrical texts, which, along with the three hundred villancicos de negros explored in chapter 3 (including fourteen newly edited ones in Appendix C), make for a total of nearly four hundred literary texts depicting blackness—a remarkably large number that highlights the need for scholars to reconsider the reasons behind the trend.
Fourteen New Villancicos de Negros
Authors: Berruezo-Sánchez Diana
Published: August 2024

This Appendix offers the edition of fourteen villancicos de negros that have not yet been catalogued in a modern collection nor mentioned in major volumes about early modern Spanish villancicos. These editions and translations are sourced from a number of original seventeenth-century manuscripts at the Biblioteca Nacional de España and the Hispanic Society of America and contain villancicos de negros that were performed in Spain as early as 1616. These fourteen newly collected poems exhibit some of the most salient, well-known features of villancicos de negros, while providing further material for a more comprehensive picture of this important seventeenth-century genre. Each villancico is accompanied by an introduction showing features of black communities in early modern Spain discussed in the book.
Comparison of antigenicity between frozen section vs non−frozen section tissue blocks: An immunohistochemical study of antibodies commonly used in gynecologic pathology
Authors: Obaid Quratulain , Nadji Mehrdad , Schlumbrecht Matthew , Pinto Andre
Published: August 2024

Objectives

Frozen section (FS) is a technique widely used intraoperatively to render a preliminary histopathologic diagnosis, allowing for immediate decisions at the time of surgery. We aimed to investigate potential variations in tissue antigenicity induced by rapid freezing in a variety of gynecologic tumor samples.

Methods

A total of 177 FS and 177 non–frozen section (NFS) tissue slides were tested using a panel of immunostains commonly used in gynecologic pathology, including hormone receptors (estrogen receptor, progesterone receptor), HER2, mismatch repair proteins (MSH6, PMS2), programmed cell death 1 ligand 1 (PD-L1), p53, napsin A, and ɑ-methylacyl coenzyme-A racemase. Immunohistochemistry results were categorized as positive or negative, and positive cases were subsequently scored based on the distribution and intensity of the staining. Certain immunostains, such as HER2, PD-L1, and p53, were scored according to the established guidelines.

Results

The overall concordance between FS and NFS blocks was 87%; among the 13% of discrepant cases, most (10.7%) were classified as minor, with only quantitative differences without foreseeable clinical significance. In 2.3% of cases, there were major qualitative changes with potential impact on disease management.

Conclusions

We concluded that FS tissue blocks may, in most cases, safely be used for immunohistochemical studies because most discrepant cases showed only minor differences in staining, with no anticipated clinical significance. Nevertheless, for certain markers, including HER2, p53, and PMS2, a NFS block is preferred when that option is available.
Association of a novel restrictive housing diversion program with rates of mental health and self-injury in prison
Authors: Remch Molly , Swink Gregory , Mautz Charles , Austin Anna E , Naumann Rebecca B
Published: August 2024

Restrictive housing for control purposes (RHCP, a form of solitary confinement) is used in prisons in response to disruptive behaviors, including violence. North Carolina prisons introduced the rehabilitative diversion unit (RDU) in 2016 as an alternative to and stepdown from RHCP. We compared rates of psychiatric treatment and self-injury among men enrolled in the RDU and men eligible for the RDU but placed in RHCP. We used Poisson regression to calculate rate ratios (RRs) and 95% confidence intervals (CIs) for these outcomes, using inverse probability of treatment weights to adjust for confounders. The cohort included 1225 men in the RDU group and 3059 in the RHCP group. In RHCP, the adjusted psychiatric treatment rate was 2.6 times (95% CI, 1.8-3.8) and the adjusted self-injury incident rate was 1.2 times (95% CI, 0.6-2.8) that in RDU. Nearly all self-injury incidents in RDU occurred during “nonparticipating time” (ie, in a restrictive housing setting and not actively participating in RDU). After excluding nonparticipating time from the RDU group’s person time, the adjusted RR for self-injury incidents was 23.5 (95% CI, 8.6-64.2). These results further knowledge of potential benefits of diversion from restrictive housing. Continued development, implementation, and evaluation is needed.
BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model
Authors: Luo Hanyu , Tang Li , Zeng Min , Yin Rui , Ding Pingjian , Luo Lingyun , Li Min
Published: August 2024

Motivation

Transcription factors are pivotal in the regulation of gene expression, and accurate identification of transcription factor binding sites (TFBSs) at high resolution is crucial for understanding the mechanisms underlying gene regulation. The task of identifying TFBSs from DNA sequences is a significant challenge in the field of computational biology today. To address this challenge, a variety of computational approaches have been developed. However, these methods face limitations in their ability to achieve high-resolution identification and often lack interpretability.

Results

We propose BertSNR, an interpretable deep learning framework for identifying TFBSs at single-nucleotide resolution. BertSNR integrates sequence-level and token-level information by multi-task learning based on pre-trained DNA language models. Benchmarking comparisons show that our BertSNR outperforms the existing state-of-the-art methods in TFBS predictions. Importantly, we enhanced the interpretability of the model through attentional weight visualization and motif analysis, and discovered the subtle relationship between attention weight and motif. Moreover, BertSNR effectively identifies TFBSs in promoter regions, facilitating the study of intricate gene regulation.

Availability and implementation

The BertSNR source code can be found at https://github.com/lhy0322/BertSNR.
Transcriptome comparisons of trophoblasts from regenerative cell models with peri-implantation human embryos
Authors: Logsdon Deirdre M , Ming Hao , Ezashi Toshihiko , West Rachel C , Schoolcraft William B , Roberts R Michael , Jiang Zongliang , Yuan Ye
Published: August 2024

Mechanisms controlling trophoblast (TB) proliferation and differentiation during embryo implantation are poorly understood. Human trophoblast stem cells (TSC) and BMP4/A83–01/PD173074-treated pluripotent stem cell-derived trophoblast cells (BAP) are two widely employed, contemporary models to study TB development and function, but how faithfully they mimic early TB cells has not been fully examined. We evaluated the transcriptomes of TB cells from BAP and TSC and directly compared them with those from peri-implantation human embryos during extended embryo culture (EEC) between embryonic days 8 to 12. The BAP and TSC grouped closely with TB cells from EEC within each TB sublineage following dimensional analysis and unsupervised hierarchical clustering. However, subtle differences in transcriptional programs existed within each TB sublineage. We also validated the presence of six genes in peri-implantation human embryos by immunolocalization. Our analysis reveals that both BAP and TSC models have features of peri-implantation TB s, while maintaining minor transcriptomic differences, and thus serve as valuable tools for studying implantation in lieu of human embryos.
Understanding hair disorders through artificial intelligence: DALLE's role in image creation
Authors: Deliyannis Eduardo P
Published: August 2024

In the study of DALL-E 2’s capability to replicate hair disorders, the model displayed varying accuracy in generating images from textual prompts. While it produced realistic hair images, its portrayal of specific conditions, such as alopecia areata, often lacked precision. The findings emphasize the need for collaboration between artificial intelligence developers and medical experts to enhance model reliability in dermatology.
Effectiveness of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccination Against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 Lineage Hospitalization and a Comparison of Clinical Severity—IVY Network, 26 Hospitals, 18 October 2023–9 March 2024
Authors: Ma Kevin C , Surie Diya , Lauring Adam S , Martin Emily T , Leis Aleda M , Papalambros Leigh , Gaglani Manjusha , Columbus Christie , Gottlieb Robert L , Ghamande Shekhar , Peltan Ithan D , Brown Samuel M , Ginde Adit A , Mohr Nicholas M , Gibbs Kevin W , Hager David N , Saeed Safa , Prekker Matthew E , Gong Michelle Ng , Mohamed Amira , Johnson Nicholas J , Srinivasan Vasisht , Steingrub Jay S , Khan Akram , Hough Catherine L , Duggal Abhijit , Wilson Jennifer G , Qadir Nida , Chang Steven Y , Mallow Christopher , Kwon Jennie H , Parikh Bijal , Exline Matthew C , Vaughn Ivana A , Ramesh Mayur , Safdar Basmah , Mosier Jarrod , Harris Estelle S , Shapiro Nathan I , Felzer Jamie , Zhu Yuwei , Grijalva Carlos G , Halasa Natasha , Chappell James D , Womack Kelsey N , Rhoads Jillian P , Baughman Adrienne , Swan Sydney A , Johnson Cassandra A , Rice Todd W , Casey Jonathan D , Blair Paul W , Han Jin H , Ellington Sascha , Lewis Nathaniel M , Thornburg Natalie , Paden Clinton R , Atherton Lydia J , Self Wesley H , Dawood Fatimah S , DeCuir Jennifer
Published: August 2024

Background

Assessing variant-specific coronavirus disease 2019 (COVID-19) vaccine effectiveness (VE) and severity can inform public health risk assessments and decisions about vaccine composition. BA.2.86 and its descendants, including JN.1 (referred to collectively as “JN lineages”), emerged in late 2023 and exhibited substantial divergence from co-circulating XBB lineages.

Methods

We analyzed patients hospitalized with COVID-19–like illness at 26 hospitals in 20 US states admitted 18 October 2023–9 March 2024. Using a test-negative, case-control design, we estimated effectiveness of an updated 2023–2024 (monovalent XBB.1.5) COVID-19 vaccine dose against sequence-confirmed XBB and JN lineage hospitalization using logistic regression. Odds of severe outcomes, including intensive care unit (ICU) admission and invasive mechanical ventilation (IMV) or death, were compared for JN versus XBB lineage hospitalizations using logistic regression.

Results

A total of 585 case-patients with XBB lineages, 397 case-patients with JN lineages, and 4580 control patients were included. VE in the first 7–89 days after receipt of an updated dose was 54.2% (95% confidence interval [CI], 36.1–67.1%) against XBB lineage hospitalization and 32.7% (95% CI, 1.9–53.8%) against JN lineage hospitalization. Odds of ICU admission (adjusted odds ratio [aOR], .80; 95% CI, .46–1.38) and IMV or death (aOR, .69; 95% CI, .34–1.40) were not significantly different among JN compared with XBB lineage hospitalizations.

Conclusions

Updated 2023–2024 COVID-19 vaccination provided protection against both XBB and JN lineage hospitalization, but protection against the latter may be attenuated by immune escape. Clinical severity of JN lineage hospitalizations was not higher relative to XBB.
Cost-effectiveness analysis and return on investment of SunSmart Western Australia to prevent skin cancer
Authors: Collins Louisa G , Minto Carolyn , Ledger Melissa , Blane Sally , Hendrie Delia
Published: August 2024

Each year, malignant melanoma accounts for 57 000 deaths globally. If current rates continue, there will be an estimated 510 000 new cases annually and 96 000 deaths by 2040. Melanoma and keratinocyte cancers (KCs) incur a large societal burden. Using a mathematical population model, we performed an economic evaluation of the SunSmart program in the state of Western Australia (WA), a primary prevention program to reduce the incidence of skin cancer, versus no program. A societal perspective was taken combining costs to the health system, patients and lost productivity. The model combined data from pragmatic trial evidence of sun protection, epidemiological studies and national cost reports. The main outcomes modelled were societal and government costs, skin cancer counts, melanoma deaths, life years and quality-adjusted life years. Over the next 20 years, the model predicted that implementing the WA SunSmart program would prevent 13 728 KCs, 636 melanomas and 46 melanoma deaths per 100 000 population. Furthermore, 251 life years would be saved, 358 quality-adjusted life years gained and AU$2.95 million in cost savings to society per 100 000 population would be achieved. Key drivers of the model were the rate reduction of benign lesions from sunscreen use, the costs of purchasing sunscreen and the effectiveness of reducing KCs in sunscreen users. The likelihood of WA SunSmart being cost-effective was 90.1%. For the WA Government, the estimated return on investment was $8.70 gained for every $1 invested. Primary prevention of skin cancer is a cost-effective strategy for preventing skin cancers.
Causal diagrams for disease latency bias
Authors: Etminan Mahyar , Rezaeianzadeh Ramin , Mansournia Mohammad A
Published: August 2024

Background

Disease latency is defined as the time from disease initiation to disease diagnosis. Disease latency bias (DLB) can arise in epidemiological studies that examine latent outcomes, since the exact timing of the disease inception is unknown and might occur before exposure initiation, potentially leading to bias. Although DLB can affect epidemiological studies that examine different types of chronic disease (e.g. Alzheimer’s disease, cancer etc), the manner by which DLB can introduce bias into these studies has not been previously elucidated. Information on the specific types of bias, and their structure, that can arise secondary to DLB is critical for researchers, to enable better understanding and control for DLB.

Development

Here we describe four scenarios by which DLB can introduce bias (through different structures) into epidemiological studies that address latent outcomes, using directed acyclic graphs (DAGs). We also discuss potential strategies to better understand, examine and control for DLB in these studies.

Application

Using causal diagrams, we show that disease latency bias can affect results of epidemiological studies through: (i) unmeasured confounding; (ii) reverse causality; (iii) selection bias; (iv) bias through a mediator.

Conclusion

Disease latency bias is an important bias that can affect a number of epidemiological studies that address latent outcomes. Causal diagrams can assist researchers better identify and control for this bias.
Transnational Repression: International Cooperation in Silencing Dissent
Authors: Cordell Rebecca , Medhi Kashmiri
Published: August 2024

Why do some states assist other countries to reach across national borders and repress their diaspora, while others do not? Transnational repression involves host countries (including democracies) working closely with origin states (typically autocracies) to transfer their citizens living abroad into their custody and silence dissent. We expect international cooperation on transnational repression to rely on a host country’s domestic rule of law (opportunity to repress) and economic ties with the origin country (leverage to cooperate). To measure international cooperation on transnational repression, we present new data containing 608 direct physical cases of transnational repression from 2014 to 2020 involving 160 unique country dyads (79 host countries and 31 origin countries). We test our hypotheses using a dataset of 33,615 directed dyad-years that accounts for refugee flows between pairs of countries and find empirical support for our theoretical argument. Autocracies are better able to elicit cooperation on human rights violations from states that have shared economic interests and a weak rule of law. Our findings provide one of the first quantitative accounts of foreign complicity in extraterritorial repression and have policy implications for civil society activists that seek to prevent governments from committing future human rights abuses against foreign nationals living abroad.
“The Promises of Scripture Were All for the Black People”: Sojourner Truth on the Blood of Abel and the Lamb
Authors: Schipper Jeremy
Published: August 2024

In a speech delivered on July 4, 1854, Sojourner Truth declared “the blood of one man, Abel, did not call from the ground in vain [Genesis 4:10]. The promises of Scripture were all for the black people.” Some recent biographers of Truth interpret this as a reference to the curse of Cain (Genesis 4:11–13), which, they contend, Truth calls down upon white people. Other scholars have shown how some nineteenth-century Black interpreters used the Cain and Abel story to explain white violence and hatred. Building on both lines of research, I argue that Truth typologically links Abel’s blood to the blood of the lamb in Revelation 7:14. In doing so, Truth is not only invoking the curse of Cain and providing an explanation for white hatred but also offering a scriptural promise for Black people.
Investigating the treatment shortening potential of a combination of bedaquiline, delamanid and moxifloxacin with and without sutezolid, in a murine tuberculosis model with confirmed drug exposures
Authors: Walter Kerstin , te Brake Lindsey H M , Lemm Ann-Kathrin , Hoelscher Michael , Svensson Elin M , Hölscher Christoph , Heinrich Norbert
Published: August 2024

Background

New and shorter regimens against multi-drug resistant tuberculosis (TB) remain urgently needed. To inform treatment duration in clinical trials, this study aimed to identify human pharmacokinetic equivalent doses, antimycobacterial and sterilizing activity of a novel regimen, containing bedaquiline, delamanid, moxifloxacin and sutezolid (BDMU), in the standard mouse model (BALB/c) of Mycobacterium tuberculosis (Mtb) infection.

Methods

Treatment of mice with B25D0.6M200U200, B25D0.6M200, B25D0.6M200(U2003) or H10R10Z150E100 (isoniazid, rifampicin, pyrazinamide, ethambutol, HRZE), started 3 weeks after Mtb infection. Bactericidal activity was assessed after 1, 2, 3 and 4 months of treatment and relapse rates were assessed 3 months after completing treatment durations of 2, 3 and 4 months.

Results

B25D0.6M200U200 generated human equivalent exposures in uninfected BALB/c mice. After 1 month of treatment, a higher bactericidal activity was observed for the B25D0.6M200U200 and the B25D0.6M200 regimen compared to the standard H10R10Z150E100 regimen. Furthermore, 3 months of therapy with both BDM-based regimens resulted in negative lung cultures, whereas all H10R10Z150E100 treated mice were still culture positive. After 3 months of therapy 7% and 13% of mice relapsed receiving B25D0.6M200U200 and B25D0.6M200, respectively, compared to 40% for H10R10Z150E100 treatment showing an increased sterilizing activity of both BDM-based regimens.

Conclusions

BDM-based regimens, with and without sutezolid, have a higher efficacy than the HRZE regimen in the BALB/c model of TB, with some improvement by adding sutezolid. By translating these results to TB patients, this novel BDMU regimen should be able to reduce treatment duration by 25% compared to HRZE therapy.
Do predictions destroy predictability? A study focusing on stock markets
Authors: Ippoliti Emiliano
Published: August 2024

Predicting stock markets is a problem that has generated many answers. According to one group of responses, the divergence thesis, it is impossible to accomplish this since the prediction has a ‘bending effect’ that would cause the market to behave in a way that would permanently depart from what was predicted, i.e. the prediction would falsify itself. There are at least three types of impossibility: logical, theoretical and empirical. A second class of responses argues that despite the ‘bending effect’ of predictions, it is still feasible to predicting stock markets. These responses, the convergence thesis, contend that we can achieve it by demonstrating that there are fixed points or that the prediction and market behavior will eventually converge. I expand this line of reasoning by showing that the performativity makes it possible certain predictions by an alignment between the ‘ontic’ and the ‘epistemic’ state of the markets. In addition, I show that performativity enables us to explain how a prediction is produced, why it works initially and then why it fails (i.e. why its predictive power is destroyed).
Drug and biomarker tissue levels in a randomized presurgical trial on exemestane alternative schedules
Authors: Serrano Davide , Johansson Harriet , Bertelsen Bjørn-Erik , Gandini Sara , Mellgren Gunnar , Thomas Parijatham , Crew Katherine D , Kumar Nagi B , Macis Debora , Aristarco Valentina , Guerrieri-Gonzaga Aliana , Lazzeroni Matteo , D’Amico Mauro , Buttiron-Webber Tania , Briata Irene Maria , Spinaci Stefano , Galimberti Viviana , Vornik Lana A , Vilar Eduardo , Brown Powel H , Heckman-Stoddard Brandy M , Szabo Eva , Bonanni Bernardo , DeCensi Andrea
Published: August 2024

The drug’s activity at the target tissue could help to define the minimal effective dose to promote cancer preventive therapy. Here we present exemestane and sex hormone concentrations within breast tissue from a presurgical study of alternative exemestane schedules. Postmenopausal women candidates for breast surgery for estrogen receptor-positive breast cancer were randomly assigned to exemestane 25 mg once daily (QD), 25 mg 3 times/week (TIW), or 25 mg per week (QW) for 4-6 weeks before surgery. Drug and sex hormones were analyzed from homogenized frozen tissue using a QTRAP 6500+ LC-MS/MS System. Tissue drug concentrations were detectable only in the QD arm with higher concentrations in nonmalignant tissue. Estradiol was nearly suppressed in all groups in the nonmalignant tissue (QD vs TIW P = .364 and QD vs QW P = .693). In contrast, a dose-response trend was observed in cancer tissue. Based on estradiol suppression in nonmalignant tissue, lower exemestane schedules should be explored for breast cancer preventive therapy.

Trial Registration: Clinical Trials.gov NCT02598557 and EudraCT 2015-005063-1
Allegory and the Canonization of the Song of Songs
Authors: Lim Timothy H
Published: August 2024

The canonical process that led to the inclusion of the Song of Songs in the lists of books of the Hebrew Bible or Old Testament is investigated with focus on the saying attributed to Rabbi Aqiva in Mishnah Yadayim 3:5, and also investigated is whether he referred to the Holy of Holies of the Jerusalem Temple. It is demonstrated that he asserted that all the writings are holy and the Song of Songs is holiest. But the framing of the mishnah associates all scriptures, including the Song of Songs, with the Temple, the Ark of the Covenant, and the Holy of Holies. Allegorical interpretation of the Song likely preceded the book’s canonization.
Development of a Modular Cryo-Transfer Station for the Side-Entry Transmission Electron Microscope
Authors: Reifsnyder Alexander , Hachtel Jordan A , Lupini Andrew R , McComb David W
Published: August 2024

Cryo-transfer stations are essential tools in the field of cryo-electron microscopy, enabling the safe transfer of frozen vitreous samples between different stages of the workflow. However, existing cryo-transfer stations are typically configured for only the two most popular sample holder geometries and are not commercially available for all electron microscopes. Additionally, they are expensive and difficult to customize, which limits their accessibility and adaptability for research laboratories. Here, we present a new modular cryo-transfer station that addresses these limitations. The station is composed entirely of 3D-printed and off the shelf parts, allowing it to be reconfigured to a fit variety of microscopes and experimental protocols. We describe the design and construction of the station and report on the results of testing the cryo-transfer station, including its ability to maintain cryogenic temperatures and transfer frozen vitreous samples as demonstrated by vibrational spectroscopy. Our findings demonstrate that the cryo-transfer station performs comparably to existing commercial models, while offering greater accessibility and customizability. The design for the station is open source to encourage other groups to replicate and build on this development. We hope that this project will increase access to cryo-transfer stations for researchers in a variety of disciplines with nonstandard equipment.
The conditional colour–magnitude distribution – II. A comparison of galaxy colour and luminosity distribution in galaxy groups
Authors: Xu Haojie , Zheng Zheng , Yang Xiaohu , Li Qingyang , Guo Hong
Published: August 2024

The Conditional Colour-Magnitude Distribution (CCMD) is a comprehensive formalism of the colour–magnitude–halo mass relation of galaxies. With joint modelling of a large sample of SDSS galaxies in fine bins of galaxy colour and luminosity, Xu et al. inferred parameters of a CCMD model that well reproduces colour- and luminosity-dependent abundance and clustering of present-day galaxies. In this work, we provide a test and investigation of the CCMD model by studying the colour and luminosity distribution of galaxies in galaxy groups. An apples-to-apples comparison of group galaxies is achieved by applying the same galaxy group finder to identify groups from the CCMD galaxy mocks and from the SDSS data, avoiding any systematic effect of group finding and mass assignment on the comparison. We find an overall nice agreement in the conditional luminosity function (CLF), the conditional colour function (CCF), and the CCMD of galaxies in galaxy groups inferred from CCMD mock and SDSS data. We also discuss the subtle differences revealed by the comparison. In addition, using two external catalogues constructed to only include central galaxies with halo mass measured through weak lensing, we find that their colour-magnitude distribution shows two distinct and orthogonal components, in line with the prediction of the CCMD model. Our results suggest that the CCMD model provides a good description of halo mass-dependent galaxy colour and luminosity distribution. The halo and CCMD mock catalogues are made publicly available to facilitate other investigations.
The dark days are overcast: iron-bearing clouds on HD 209458 b and WASP-43 b can explain low-dayside albedos
Authors: Chubb K L , Samra D , Helling Ch , Carone L , Stam D M
Published: August 2024

We simulate the geometric albedo spectra of hot Jupiter exoplanets HD 209458 b and WASP-43 b, based on global climate model post-processed with kinetic cloud models. We predict WASP-43 b to be cloudy throughout its dayside, while HD 209458 b has a clear upper atmosphere around the hot subsolar point, largely due to the inclusion of strong optical absorbers TiO and VO in the general circulation model for the latter causes a temperature inversion. In both cases our models find low-geometric albedos – 0.026 for WASP-43 b and 0.028 for HD 209458 b when averaged over the CHaracterizing ExOPlanet Satellite bandpass of $\sim$0.35–1.1 μm – indicating dark daysides, similar to the low albedos measured by observations. We demonstrate the strong impact of clouds that contain Fe-bearing species on the modelled geometric albedos; without Fe-bearing species forming in the clouds, the albedos of both planets would be much higher (0.518 for WASP-43 b, 1.37 for HD 209458 b). We conclude that a cloudy upper or mid-to-lower atmosphere that contains strongly absorbing Fe-bearing aerosol species, is an alternative to a cloud-free atmosphere in explaining the low-dayside albedos of hot Jupiter atmospheres such as HD 209458 b and WASP-43 b.
Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs
Authors: Morales Ariadna E , Burbrink Frank T , Segall Marion , Meza Maria , Munegowda Chetan , Webala Paul W , Patterson Bruce D , Thong Vu Dinh , Ruedi Manuel , Hiller Michael , Simmons Nancy B
Published: August 2024

Convergence offers an opportunity to explore to what extent evolution can be predictable when genomic composition and environmental triggers are similar. Here, we present an emergent model system to study convergent evolution in nature in a mammalian group, the bat genus Myotis. Three foraging strategies—gleaning, trawling, and aerial hawking, each characterized by different sets of phenotypic features—have evolved independently multiple times in different biogeographic regions in isolation for millions of years. To investigate the genomic basis of convergence and explore the functional genomic changes linked to ecomorphological convergence, we sequenced and annotated 17 new genomes and screened 16,426 genes for positive selection and associations between relative evolutionary rates and foraging strategies across 30 bat species representing all Myotis ecomorphs across geographic regions as well as among sister groups. We identify genomic changes that describe both phylogenetic and ecomorphological trends. We infer that colonization of new environments may have first required changes in genes linked to hearing sensory perception, followed by changes linked to fecundity and development, metabolism of carbohydrates, and heme degradation. These changes may be linked to prey acquisition and digestion and match phylogenetic trends. Our findings also suggest that the repeated evolution of ecomorphs does not always involve changes in the same genes but rather in genes with the same molecular functions such as developmental and cellular processes.
Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq
Authors: Morgan Ian L , McKie Shannon J , Kim Rachel , Seol Yeonee , Xu Jing , Harami Gabor M , Maxwell Anthony , Neuman Keir C
Published: August 2024

Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability and a number of clinically important anticancer and antibacterial drugs, e.g. quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20–50-fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e. negative versus positive supercoiling. SHAN-seq's exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.
H3T11 phosphorylation by CKII is required for heterochromatin formation in Neurospora
Authors: Tian Yuan , Zhang Chengcheng , Tian Xiang , Zhang Lu , Yin Tong , Dang Yunkun , Liu Yi , Lou Huiqiang , He Qun
Published: August 2024

Heterochromatin is a key feature of eukaryotic genomes and is crucial for maintaining genomic stability. In fission yeast, heterochromatin nucleation is mainly mediated by DNA-binding proteins or the RNA interference (RNAi) pathway. In the filamentous fungus Neurospora crassa, however, the mechanism that causes the initiation of heterochromatin at the relics of repeat-induced point mutation is unknown and independent of the classical RNAi pathway. Here, we show that casein kinase II (CKII) and its kinase activity are required for heterochromatin formation at the well-defined 5-kb heterochromatin of the 5H-cat-3 region and transcriptional repression of its adjacent cat-3 gene. Similarly, mutation of the histone H3 phosphorylation site T11 also impairs heterochromatin formation at the same locus. The catalytic subunit CKA colocalizes with H3T11 phosphorylation (H3pT11) within the 5H-cat-3 domain and the deletion of cka results in a significant decrease in H3T11 phosphorylation. Furthermore, the loss of kinase activity of CKII results in a significant reduction of H3pT11, H3K9me3 (histone H3 lysine 9 trimethylation) and DNA methylation levels, suggesting that CKII regulates heterochromatin formation by promoting H3T11 phosphorylation. Together, our results establish that histone H3 phosphorylation by CKII is a critical event required for heterochromatin formation.
The characteristics of CTCF binding sequences contribute to enhancer blocking activity
Authors: Tsang Felice H , Stolper Rosa J , Hanifi Muhammad , Cornell Lucy J , Francis Helena S , Davies Benjamin , Higgs Douglas R , Kassouf Mira T
Published: August 2024

While the elements encoding enhancers and promoters have been relatively well studied, the full spectrum of insulator elements which bind the CCCTC binding factor (CTCF), is relatively poorly characterized. This is partly due to the genomic context of CTCF sites greatly influencing their roles and activity. Here we have developed an experimental system to determine the ability of minimal, consistently sized, individual CTCF elements to interpose between enhancers and promoters and thereby reduce gene expression during differentiation. Importantly, each element is tested in the identical location thereby minimising the effect of genomic context. We found no correlation between the ability of CTCF elements to block enhancer–promoter activity with the degree of evolutionary conservation; their resemblance to the consensus core sequences; or the number of CTCF core motifs harboured in the element. Nevertheless, we have shown that the strongest enhancer–promoter blockers include a previously described bound element lying upstream of the CTCF core motif. In addition, we found other uncharacterised DNaseI footprints located close to the core motif that may affect function. We have developed an assay of CTCF sequences which will enable researchers to sub-classify individual CTCF elements in a uniform and unbiased way.
Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase γ
Authors: Riccio Amanda A , Bouvette Jonathan , Pedersen Lars C , Somai Shruti , Dutcher Robert C , Borgnia Mario J , Copeland William C
Published: August 2024

The mitochondrial single-stranded DNA (ssDNA) binding protein, mtSSB or SSBP1, binds to ssDNA to prevent secondary structures of DNA that could impede downstream replication or repair processes. Clinical mutations in the SSBP1 gene have been linked to a range of mitochondrial disorders affecting nearly all organs and systems. Yet, the molecular determinants governing the interaction between mtSSB and ssDNA have remained elusive. Similarly, the structural interaction between mtSSB and other replisome components, such as the mitochondrial DNA polymerase, Polγ, has been minimally explored. Here, we determined a 1.9-Å X-ray crystallography structure of the human mtSSB bound to ssDNA. This structure uncovered two distinct DNA binding sites, a low-affinity site and a high-affinity site, confirmed through site-directed mutagenesis. The high-affinity binding site encompasses a clinically relevant residue, R38, and a highly conserved DNA base stacking residue, W84. Employing cryo-electron microscopy, we confirmed the tetrameric assembly in solution and capture its interaction with Polγ. Finally, we derived a model depicting modes of ssDNA wrapping around mtSSB and a region within Polγ that mtSSB binds.
Effects of Very Low Nicotine Content Cigarettes and Nicotine Vaping Device Characteristics on Choices to Smoke, Vape, or Abstain in Early Young Adults
Authors: Cassidy Rachel N , Tidey Jennifer W , Bello Mariel S , Denlinger-Apte Rachel , Goodwin Christine , Godin Julissa , Cioe Patricia A , Swift Robert , Demorest Connor , Koopmeiners Joseph S , Donny Eric , Hatsukami Dorothy , Colby Suzanne M
Published: August 2024

Introduction

A national nicotine reduction policy could reduce the public health toll of smoking. However, reducing nicotine in cigarettes may lead to changes in the use of other tobacco products such as nicotine vaping devices, particularly among young people. Product use outcomes may depend on the characteristics of available nicotine vaping devices. We aimed to determine the impact of cigarette nicotine content, vaping device nicotine concentration, and vaping device flavors on choices to smoke, vape, or abstain.

Aims and Methods

Early young adults (ages 18–20 inclusive, N = 80) who reported smoking daily and vaping nicotine at least twice in their lifetime participated in a laboratory study. Participants received either very low nicotine content (VLNC; 0.4 mg nicotine/g of tobacco) or normal nicotine content (NNC; 15.8 mg/g) cigarettes. First, participants chose between their assigned cigarette or abstaining. Subsequently, participants chose between 2 cigarette puffs, 2 vape puffs, or abstaining. Vaping device nicotine concentration (3 mg vs. 18 mg/mL) and flavor (tobacco vs. non-tobacco) were manipulated within subjects.

Results

When only cigarettes were available, there were no differences between the VLNC and NNC groups on cigarette choices. When the nicotine vaping device was concurrently available, the VLNC group made fewer choices to smoke than the NNC group. Non-tobacco flavors and lower vaping device nicotine concentration were associated with fewer choices to smoke.

Conclusions

Nicotine vaping device availability reduced choices to smoke VLNC cigarettes, and vaping devices with lower nicotine and non-tobacco flavors led to the fewest choices to smoke. Regulators should consider that the availability and characteristics of alternative tobacco products can moderate the product standard’s impact.

Implications

The U.S. Food and Drug Administration may enact a reduced nicotine product standard that would affect all commercially available cigarettes. One important population affected by this policy would be early young adults who smoke. We aimed to determine the impact of cigarette nicotine content, vaping device nicotine concentration, and vaping device flavors on choices to smoke, vape, or abstain. Lower nicotine in cigarettes, along with non-tobacco flavors and lower nicotine concentration in the vaping device, were associated with the fewest choices to smoke. Regulators should consider that the availability and characteristics of alternative tobacco products can moderate the product standard’s impact.
An unstable Union? The Conservative Party, the British Political Tradition, and devolution in Scotland and Wales 2010–23
Authors: Anderson Paul , Brown Swan Coree
Published: August 2024

While devolution in Scotland and Wales is often established as the settled will, it has been built on unsettled ground, lacking a robust system of intergovernmental relations, and sitting increasingly at odds with the central principle of parliamentary sovereignty. Examining successive UK Conservative-led governments, we evaluate devolution in Scotland and Wales through the lens of the Asymmetric Power Model and the British Political Tradition, documenting changes in the position of successive Conservative governments, from the more plurinationally sensitive respect agenda of David Cameron to the more assertive and intrusive Unionism advanced under those in post after 2016, notably Theresa May and Boris Johnson.
Electoral Violence in England and Wales, 1832–1914
Authors: Blaxill Luke , Cohen Gidon , Hutchison Gary , Kuhn Patrick M , Vivyan Nick
Published: August 2024

This article analyses over 19,000 articles from newspapers and parliamentary commission reports to reveal endemic electoral violence in England and Wales between 1832 and 1914. It offers a new understanding of the phenomenon in three main ways. First, the extent of election violence, which regularly featured major riots requiring police and military intervention, disturbances of the peace, and deaths, questions conventional understandings of Britain's comparatively peaceful political development through a century of gradual suffrage expansion, rising literacy and economic development. Second, the trajectory of the electoral violence, which peaked in the period after the Second Reform Act of 1867 rather than after the Great Reform Act of 1832, challenges the linearity of these accounts. Third, despite the recent historiographical emphasis on explaining electoral violence as a ritual expression of discontent, much violence resulted from elites strategizing to win elections. Electoral violence occurred disproportionately when and where it was most useful to candidates and parties, and often involved the previously overlooked figure of the ‘hired rough’: men employed to disrupt elections by force. We thus advance a political, rather than cultural, explanation for electoral violence.
Wheat Cybrid Plants, OryzaWheat, Regenerated from Wheat–Rice Hybrid Zygotes via in Vitro Fertilization System Possess Wheat–Rice Hybrid Mitochondria
Authors: Maryenti Tety , Koshimizu Shizuka , Onda Nonoka , Ishii Takayoshi , Yano Kentaro , Okamoto Takashi
Published: August 2024

Hybridization generates biodiversity, and wide hybridization plays a pivotal role in enhancing and broadening the useful attributes of crops. The hybridization barrier between wheat and rice, the two most important cereals, was recently overcome by in vitro production of allopolyploid wheat–rice hybrid zygotes, which can develop and grow into mature plants. In the study, genomic sequences and compositions of the possible hybrid plants were investigated through short- and long-read sequencing analyses and fluorescence in situ hybridization (FISH)-based visualization. The possible hybrid possessed whole wheat nuclear and cytoplasmic DNAs and rice mitochondrial (mt) DNA, along with variable retention rates of rice mtDNA ranging from 11% to 47%. The rice mtDNA retained in the wheat cybrid, termed Oryzawheat, can be transmitted across generations. In addition to mitochondrial hybridization, translocation of rice chromosome 1 into wheat chromosome 6A was detected in a F1 hybrid individual. OryzaWheat can provide a new horizon for utilizing inter-subfamily genetic resources among wheat and rice belonging to different subfamilies, Pooideae and Ehrhartoideae, respectively.
Behavioral nudges in social media ads show limited ability to encourage COVID-19 vaccination across countries
Authors: Çat Olgahan , Chang Jiseon , Hlatky Roman , Li Huimin , Nielson Daniel L
Published: August 2024

Behavioral nudges in Facebook ads reached nearly 15 million people across six diverse countries and, consequently, many thousands took the step of navigating to governments’ vaccine signup sites. However, none of the treatment ads caused significantly more vaccine signup intent than placebo uniformly across all countries. Critically, reporting the descriptive norm that 87% of people worldwide had either been vaccinated or planned vaccination—social proof—did not meaningfully increase vaccine signup intent in any country and significantly backfired in Taiwan. This result contradicts prominent prior findings. A charge to “protect lives in your family” significantly outperformed placebo in Taiwan and Turkey but saw null effects elsewhere. A message noting that vaccination significantly reduces hospitalization risk decreased signup intent in Brazil and had no significant effects in any other country. Such heterogeneity was the hallmark of the study: some messages saw significant treatment effects in some countries but failed in others. No nudge outperformed the placebo in Russia, a location of high vaccine skepticism. In all, widely touted behavioral nudges often failed to promote vaccine signup intent and appear to be moderated by cultural context.