bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract
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.
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

Abstract

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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

ABSTRACT
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

ABSTRACT
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.