bluuebunny/crossref_metadata_2025 huggingface dataset:
(The) Discipline and the Confessional: Toward Methodological Numenism and an Engaged, Embodied Study of Religion
Authors: Wilcox Melissa M
Published: July 2024

For all its transdisciplinarity, religious studies remains a field focused on boundaries, especially those between scholars and practitioners and between confessional and nonconfessional scholarship. The disciplinary use of the confessional in religious studies calls for a Foucauldian analysis that has not yet been central to our discussion of methods, despite important work on Foucault and religion from a number of prominent scholars. Disentangling the threads of the disciplinary and the confessional in religious studies and (re)articulating scholars’ often disjointed response to the uncanniness of the worlds beyond the human, I build on the critiques offered by scholars such as Masuzawa, Beliso-De Jesús, Driscoll and Miller, and Schaefer to argue for methodological numenism and an engaged, embodied study of religion as critical steps in the decolonization of the field.
Rapid initiation of bictegravir/emtricitabine/tenofovir alafenamide as first-line therapy in HIV infection. A prospective study
Authors: Ugarte Ainoa , De La Mora Lorena , De Lazzari Elisa , Chivite Iván , Fernández Emma , Inciarte Alexy , Laguno Montserrat , Ambrosioni Juan , Solbes Estela , Berrocal Leire , González-Cordón Ana , Martínez-Rebollar María , Foncillas Alberto , Calvo Júlia , Blanco José Luis , Martínez Esteban , Mallolas Josep , Torres Berta
Published: July 2024

Introduction

Rapid initiation of ART after HIV diagnosis is recommended for individual and public health benefits. However, certain clinical and ART-related considerations hinder immediate initiation of therapy.

Methods

An open-label, single-arm, single-centre 48-week prospective clinical trial involving ART-naïve HIV-diagnosed adults who started bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) within a week from the first hospital visit, before the availability of baseline laboratory and genotype results. The primary aim was to determine the proportion of people with at least one condition that would hinder immediate initiation of any recommended ART regimen other than BIC/FTC/TAF. Clinicaltrials.gov: NCT04416906.

Results

We included 100 participants: 79% men, 64% from Latin America, median age 32 years. According to European AIDS Clinical Society (EACS) and US Department of Health and Human Services 2023 guidelines, 11% (95%CI 6; 19) of participants had at least one condition that made any ART different from BIC/FTC/TAF less appropriate for a rapid ART strategy. Seventy-nine percent of the people started BIC/FTC/TAF within the first 48 hours of their first hospital visit. There were 16 early discontinuations (11 lost to follow-up). By week 48, 92% (95%CI 86; 98) of the participants of the ITT population with observed data achieved viral suppression. Eight grade 3–4 adverse events (AEs), five serious AEs and six ART-related AEs were identified. Adherence remained high.

Conclusions

BIC/FTC/TAF is an optimal treatment for rapid initiation of ART. However, additional strategies to improve retention in care must be implemented.
Recent Recall of Iron Reagent—Investigation of Potential Reagent Contamination and Assay Improvement Strategy
Authors: Narasimhan Madhusudhanan , Jaleta Kefyalew , Adhikari Shishir , Berihun Mizanu , SataraNatarajan Kavithalakshmi , Mahimainathan Lenin , Cao Jing , Jones Patricia Mary , Hashim Ibrahim , Muthukumar Alagar R
Published: July 2024

Background

Recently, a major manufacturer recalled several lots of iron assay reagent due to positive bias of roughly 15%–30% and the cause remains unknown. This study investigated the root cause of this positive bias and evaluated a simple practical approach to improve the assay.

Methods

Performance comparison of recalled and unimpacted iron assay kits was done utilizing calibrators, quality control (QC) materials, and 42 remnant patient samples. Spectral scan and trace elements analysis of R1 and R2 reagents was performed. Copper (Cu) and thiourea (TU) spiking experiments were utilized to elucidate the cause and prevention of positive bias seen with recalled lots.

Results

Iron measurements in QC materials and patient samples using recalled reagents generated a positive bias of 17.5% and 21%, respectively. Correspondingly, the recalled R2 reagents, but not R1, showed a rise in basal absorbance along with an unanticipated presence of Cu (22.7 µg/dL) and lead (7.5 µg/L). Cu spiking to recalled and unimpacted R2 reagent intensified the reagent color besides falsely increasing its absorbance, calibration factor, and patient iron measurements. Interestingly, addition of TU (65 mmol/L) to R2 reagent from unimpacted lot prevented the short-term and prolonged Cu-induced spurious rise in calibration factor and patient iron estimations.

Conclusions

We conclude that accidental copper contamination of R2 reagent during manufacturing could be a reason underlying the positive bias in the recalled iron reagent lots. Addition of TU in ferene-containing R2 reagent is a simple and effective means to prevent Cu-induced false elevation in iron values.
allofus: an R package to facilitate use of the All of Us Researcher Workbench
Authors: Smith Louisa H , Cavanaugh Robert
Published: July 2024

Objectives

Despite easy-to-use tools like the Cohort Builder, using All of Us Research Program data for complex research questions requires a relatively high level of technical expertise. We aimed to increase research and training capacity and reduce barriers to entry for the All of Us community through an R package, allofus. In this article, we describe functions that address common challenges we encountered while working with All of Us Research Program data, and we demonstrate this functionality with an example of creating a cohort of All of Us participants by synthesizing electronic health record and survey data with time dependencies.

Target audience

All of Us Research Program data are widely available to health researchers. The allofus R package is aimed at a wide range of researchers who wish to conduct complex analyses using best practices for reproducibility and transparency, and who have a range of experience using R. Because the All of Us data are transformed into the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM), researchers familiar with existing OMOP CDM tools or who wish to conduct network studies in conjunction with other OMOP CDM data will also find value in the package.

Scope

We developed an initial set of functions that solve problems we experienced across survey and electronic health record data in our own research and in mentoring student projects. The package will continue to grow and develop with the All of Us Research Program. The allofus R package can help build community research capacity by increasing access to the All of Us Research Program data, the efficiency of its use, and the rigor and reproducibility of the resulting research.
Automating surgical procedure extraction for society of surgeons adult cardiac surgery registry using pretrained language models
Authors: Lee Jaehyun , Sharma Ishan , Arcaro Nichole , Blackstone Eugene H , Gillinov A Marc , Svensson Lars G , Karamlou Tara , Chen David
Published: July 2024

Objective

Surgical registries play a crucial role in clinical knowledge discovery, hospital quality assurance, and quality improvement. However, maintaining a surgical registry requires significant monetary and human resources given the wide gamut of information abstracted from medical records ranging from patient co-morbidities to procedural details to post-operative outcomes. Although natural language processing (NLP) methods such as pretrained language models (PLMs) have promised automation of this process, there are yet substantial barriers to implementation. In particular, constant shifts in both underlying data and required registry content are hurdles to the application of NLP technologies.

Materials and Methods

In our work, we evaluate the application of PLMs for automating the population of the Society of Thoracic Surgeons (STSs) adult cardiac surgery registry (ACS) procedural elements, for which we term Cardiovascular Surgery Bidirectional Encoder Representations from Transformers (CS-BERT). CS-BERT was validated across multiple satellite sites and versions of the STS-ACS registry.

Results

CS-BERT performed well (F1 score of 0.8417 ± 0.1838) in common cardiac surgery procedures compared to models based on diagnosis codes (F1 score of 0.6130 ± 0.0010). The model also generalized well to satellite sites and across different versions of the STS-ACS registry.

Discussion and Conclusions

This study provides evidence that PLMs can be used to extract the more common cardiac surgery procedure variables in the STS-ACS registry, potentially reducing need for expensive human annotation and wide scale dissemination. Further research is needed for rare procedural variables which suffer from both lack of data and variable documentation quality.
An RNA evolutionary algorithm based on gradient descent for function optimization
Authors: Wu Qiuxuan , Zhao Zikai , Chen Mingming , Chi Xiaoni , Zhang Botao , Wang Jian , Zhilenkov Anton A , Chepinskiy Sergey A
Published: July 2024

The optimization of numerical functions with multiple independent variables was a significant challenge with numerous practical applications in process control systems, data fitting, and engineering designs. Although RNA genetic algorithms offer clear benefits in function optimization, including rapid convergence, they have low accuracy and can easily become trapped in local optima. To address these issues, a new heuristic algorithm was proposed, a gradient descent-based RNA genetic algorithm. Specifically, adaptive moment estimation (Adam) was employed as a mutation operator to improve the local development ability of the algorithm. Additionally, two new operators inspired by the inner-loop structure of RNA molecules were introduced: an inner-loop crossover operator and an inner-loop mutation operator. These operators enhance the global exploration ability of the algorithm in the early stages of evolution and enable it to escape from local optima. The algorithm consists of two stages: a pre-evolutionary stage that employs RNA genetic algorithms to identify individuals in the vicinity of the optimal region and a post-evolutionary stage that applies a adaptive gradient descent mutation to further enhance the solution’s quality. When compared with the current advanced algorithms for solving function optimization problems, Adam RNA Genetic Algorithm (RNA-GA) produced better optimal solutions. In comparison with RNA-GA and Genetic Algorithm (GA) across 17 benchmark functions, Adam RNA-GA ranked first with the best result of an average rank of 1.58 according to the Friedman test. In the set of 29 functions of the CEC2017 suite, compared with heuristic algorithms such as African Vulture Optimization Algorithm, Dung Beetle Optimization, Whale Optimization Algorithm, and Grey Wolf Optimizer, Adam RNA-GA ranked first with the best result of an average rank of 1.724 according to the Friedman test. Our algorithm not only achieved significant improvements over RNA-GA but also performed excellently among various current advanced algorithms for solving function optimization problems, achieving high precision in function optimization.
The U.S. Capitol Grounds and Arboretum: an iconic landscape with a holistic approach to pest management
Authors: Mueller Emily , Naas Michael , Serock Katie , Westbrook Melissa , Kaufmann James
Published: July 2024

The care and maintenance of managed urban greenspaces require integrated pest management (IPM) strategies that are best suited for their local conditions. The evolution of IPM for the public grounds of the U.S. Capitol and Congress provides a unique perspective into the distinct challenges in developing and implementing an overall plant healthcare program for the nation’s historical landscape. The Capitol Grounds and Arboretum (CGA) staff of the Architect of the Capitol are the stewards of this urban greenspace, located in the center of Washington D.C., and present an overview of their historical, current, and prospective IPM developments for urban landscape pest control. With the adoption of holistic, ecological-based pest management practices, successful IPM examples in 3 different landscape habitats on Capitol Hill—turfgrass lawns, urban forestry, and ornamental horticulture display beds—are described. Ultimately, a list of current programming and future opportunities for expanding ecological IPM practices best suited for solving the CGA’s unique landscape pest management challenges are summarized.
Impact of racial disparities in follow-up and quality of colonoscopy on colorectal cancer outcomes
Authors: Alagoz Oguzhan , May Folasade P , Doubeni Chyke A , Fendrick A Mark , Vahdat Vahab , Estes Chris , Ellis Travelle , Limburg Paul J , Brooks Durado
Published: July 2024

Background

The benefits of colorectal cancer (CRC) screening programs rely on completing follow-up colonoscopy when a noncolonoscopy test is abnormal and on quality of colonoscopy screening as measured by the endoscopists’ adenoma detection rate. Existing data demonstrate substantially lower follow-up colonoscopy rates and adenoma detection rate for Black Americans than White Americans. However, the contributions of racial differences in follow-up colonoscopy and adenoma detection rate on CRC outcomes have not been rigorously evaluated.

Methods

We used established and validated CRC-Adenoma Incidence and Mortality (CRC-AIM) model as our analysis platform, with inputs from published literature that report lower follow-up colonoscopy rates and adenoma detection rate in Black adults compared with White adults (15% and 10% lower, respectively). We simulated screening with annual fecal immunochemical test, triennial multitarget stool DNA, and colonoscopy every 10 years between ages 45 and 75 years using real-world utilization of the screening modalities vs no screening. We reported lifetime outcomes per 1000 Black adults.

Results

Elimination of Black-White disparities in follow-up colonoscopy rates would reduce CRC incidence and mortality by 5.2% and 9.3%, respectively, and improve life-years gained with screening by 3.4%. Elimination of Black-White disparities in endoscopists’ adenoma detection rate would reduce CRC incidence and mortality by 9.4% and improve life-years gained by 3.7%. Elimination of both disparities would reduce CRC incidence and mortality by 14.6% and 18.7%, respectively, and improve life-years gained by 7.1%.

Conclusions

This modeling study predicts eliminating racial differences in follow-up colonoscopy rates, and quality of screening colonoscopy would substantially reduce Black-White disparities in CRC incidence and mortality.
Big Tech Acquisitions and Product Discontinuation
Authors: Gautier Axel , Maitry Robert
Published: July 2024

The five largest firms by market capitalization, Alphabet, Amazon, Apple, Meta, and Microsoft have massively acquired companies during the last decades, mainly but not exclusively young tech startups. Interestingly, most of the acquired products are discontinued post-acquisition. In this paper, we have collected data on the acquisitions of the big techs for a period of 7 years spanning from 2015 to 2021 and we analyze the evolution of the acquired firms’ products post-acquisition. To analyze the decision to continue or not a product post-acquisition, we classify acquisition in four categories: products that are still offered under their initial brand name, products integrated in the acquirer’s ecosystem, products that are no longer available and products that are killed by the acquirer. We use these classifications to provide detailed information and statistics on the discontinuation decision of the acquiring firm and we run Probit estimation to explain their determinants.
The sound of lichens: ultrasonic acoustic emissions during desiccation question cavitation events in the hyphae
Authors: Boccato Enrico , Petruzzellis Francesco , Bordenave César Daniel , Nardini Andrea , Tretiach Mauro , Mayr Stefan , Candotto Carniel Fabio
Published: July 2024

Lichens are a mutualistic symbiosis between a fungus and one or more photosynthetic partners. They are photosynthetically active during desiccation down to relative water contents (RWCs) as low as 30% (on dry mass). Experimental evidence suggests that during desiccation, the photobionts have a higher hydration level than the surrounding fungal pseudo-tissues. Explosive cavitation events in the hyphae might cause water movements towards the photobionts. This hypothesis was tested in two foliose lichens by measurements of ultrasonic acoustic emissions (UAEs), a method commonly used in vascular plants but never in lichens, and by measurements of PSII efficiency, water potential, and RWC. Thallus structural changes were characterized by low-temperature scanning electron microscopy. The thalli were silent between 380% and 30% RWCs, when explosive cavitation events should cause movements of liquid water. Nevertheless, the thalli emitted UAEs at ~5% RWC. Accordingly, the medullary hyphae were partially shrunken at ~15% RWC, whereas they were completely shrunken at <5% RWC. These results do not support the hypothesis of hyphal cavitation and suggest that the UAEs originate from structural changes at hyphal level. The shrinking of hyphae is proposed as an adaptation to avoid cell damage at very low RWCs.
Competitive exclusion products as an antimicrobial alternative to control Salmonella Heidelberg in broilers
Authors: Kolososki Isis M M , Saraiva Mauro M S , Nascimento Camila F , Campos Isabella C , Lima Túlio S , Ferreira Viviane A , Rabelo André L C , Almeida Adriana M , Berchieri Junior Angelo
Published: July 2024

Intestinal infections caused by non-typhoidal Salmonella spp., along with antimicrobial resistance spread are a major food safety concern worldwide. Here, we evaluate the potential of competitive exclusion products developed by anaerobic or aerobic conditions to control systemic infection, cecal colonization, fecal excretion, and improve the intestinal health in broilers challenged by Salmonella Heidelberg (SH). A total of 105 day-old chickens were randomly distributed into three experimental groups: A (untreated control), B (treated with anaerobic culture), and C (treated with aerobic culture). During 21 days, morphometric parameters of the small intestine were analyzed using microscopy, fecal excretions by cloacal swabs, systemic infection, and cecal colonization by colony-forming unit counts (CFU/g). The results indicated the lowest number of positive swabs (45.33%) recovered from Group C, followed by Group B (71.8%) and Group A (85.33%). The bacterial enumeration revealed the lowest amounts in Group C at the necropsy realized in 5-, 7-, and 14-days post-infection (DPI) (P = 0.0010, P = 0.0048, and P = 0.0094, respectively). Statistical differences between intestinal morphometrics were observed in the Group C at 21 DPI. Our results suggest that the product developed under aerobic conditions can improve intestinal health, protecting birds against SH.
Rectal cancer surgery
Authors: Toda Shigeo , Kuroyanagi Hiroya , Matoba Shuichiro
Published: July 2024

Rectal cancer surgery has two major goals. One is to reduce the local recurrence, and the other is to preserve the organ function. To accomplish these goals, the most important principle of rectal cancer surgery is the total mesorectal excision (TME). Advances in surgical devices have facilitated a more accurate TME, which helps definite tumour resection and preservation of organ function. While preoperative radiotherapy followed by TME became the standard of care in western countries, lateral pelvic lymph node dissection (LPLND) has been established in Japan in order to reduce local recurrence. Recently some studies show that preoperative radiotherapy may not be sufficient for patients with lateral lymph node enlargement. Preoperative radiotherapy followed by TME and selective LPLND could be the optimal treatment option. In this chapter we describe the basic idea and the technique of rectal cancer surgery including TME and LPLND.
Cunningham's Manual of Practical Anatomy Vol 1 General Anatomy, Upper and Lower Limbs
Authors: Koshi Rachel
Published: July 2024

Cunningham’s Manual of Practical Anatomy Volume 1 General Anatomy, Upper and Lower Limbs 17th edition covers all the gross anatomy competencies required by the National Medical Council of India curricula. Designed for students of medicine, dentistry, and allied health sciences, Volume 1 provides a guide to general anatomy and the anatomy of upper and lower limbs, including common anatomical dissections. The 17th edition includes new chapters on general anatomy, osteology, and surface marking, as well as bonus multiple-choice questions in the appendix. Following a logical structure, each chapter explains key knowledge expected of students. Each dissection begins with learning objectives which reflect current medical school teaching, and clear step-by-step instructions make it easy to follow in the dissection laboratory. Throughout the book, clinical application boxes and radiology images explain how anatomy relates to clinical medical practice. Highly illustrated, the updated full-colour artwork brings the friendly explanations to life. At the end of each part, multiple-choice questions allow students to quickly review their knowledge before checking the answers in the appendix. Packed with images and learning features, this text is designed to prepare students for the dissection laboratory, university examinations, and clinical practice.
The pectoral region and axilla
Authors: Koshi Rachel
Published: July 2024

This chapter on the pectoral region and axilla begins with a description of the surface features of this region: the scapula, the clavicle, the sternum, and the sternoclavicular joint. It describes the breast, and its location, structure, extent and deep relations, age-related changes, blood supply, and lymphatic drainage, as well as applied anatomy of the breast, and provides instructions on how to dissect the breast. It describes the boundaries and contents of the axilla. It gives detailed, stepwise instructions on how to dissect the axilla and display the brachial plexus and its branches, the axillary artery and its branches, and the axillary lymph nodes. It also provides instructions on how to clean and study the pectoralis major, clavipectoral fascia, serratus anterior, and other muscles and fascia bounding the axilla. Descriptions and dissections are well illustrated. Some clinical and surgical aspects of breast disease and examination and lymph node dissection are discussed.
The shoulder
Authors: Koshi Rachel
Published: July 2024

The shoulder describes the shoulder region, including the shoulder joint, bones, surface features, muscles, vessels, and nerves of this region. The deltoid, subscapularis, suprascapular nerve, and axillary nerve are described, and instructions for dissection are provided. The quadrangular and triangular spaces are described, with their boundaries and contents. All descriptions and dissections are well illustrated. The internal and external features of the shoulder joint are described and illustrated with line drawings, radiographs, and magnetic resonance imaging. The ligaments strengthening the shoulder joint, and the coracoclavicular ligaments are described. The movements of the shoulder joint and the muscles producing them are tabulated. The clinical importance of scapular anastomosis and rotator cuff injury are discussed. The anatomical basis for injuries caused by intramuscular injections is outlined.
The nerves and nerve injuries of the upper limb
Authors: Koshi Rachel
Published: July 2024

This chapter summarizes the sensory distribution and motor distribution of the median nerve, ulnar nerve, musculocutaneous nerve, axillary nerve, radial nerve, subscapular nerve, thoracodorsal nerve, suprascapular nerve, and long thoracic nerve. Information that will help the student to predict the effects of nerve injury at each level along the course of the nerve is provided in the form of diagrams and tables. The effect of nerve injury on each of the joints is tabulated, with a description of whether the paralysis would be partial or complete. The sensory and motor distribution of the nerves is illustrated with diagrams. The neurological effects of cervical rib syndrome are discussed. The standard method for testing the integrity of myotomes C. 5, C. 6, C. 7, C. 8, and T. 1 is shown.
Surface marking of the upper limb
Authors: Koshi Rachel
Published: July 2024

This chapter demonstrates the knowledge and skills to mark the position of important structures of the upper limb on to the surface of the body. The surface marking of clinically important structures includes the cephalic vein, basilic vein, axillary artery, brachial artery, radial artery, ulnar artery, superficial palmar arch, deep palmar arch, axillary nerve, radial nerve, median nerve, ulnar nerve, and flexor retinaculum. Illustrations demonstrate the relevant bony and soft tissue landmarks, so readers can mark the structure on the surface of the body. The chapter outlines the surface marking competencies for the upper limb required in the National Medical Council of India curricula.
Osteology of the lower limb
Authors: Koshi Rachel
Published: July 2024

Osteology of the lower limb outlines essential knowledge of bones: the hip bone (the ilium, ischium, and pubis), femur, patella, tibia, fibula, and bones of the foot (tarsal bones, talus, and calcaneus). The chapter enables readers to name each bone and determine its position in the body, identify the side to which it belongs, hold it in the anatomical position, describe the important bony features, and demonstrate important muscle attachments on the bone. For each bone, the text outlines: general features, bony landmarks and muscle attachments, unique features, applied anatomy, and exercises. The chapter outlines the osteology competencies for lower limbs required by the National Medical Council of India curricula.
The popliteal fossa
Authors: Koshi Rachel
Published: July 2024

The popliteal fossa describes the popliteal fossa boundaries and contents. It lists the muscles and tendons forming the superolateral, superomedial, inferolateral, and inferomedial boundaries of the popliteal fossa, the structures forming the floor of the fossa, and the structures in the superficial fascia overlying the popliteal fossa. The tibial nerve, the common fibular nerve, and the cutaneous, muscular, and genicular branches given from these in this region are described. The popliteal artery giving the genicular arteries and the popliteal vein draining the short saphenous vein are described. Detailed, stepwise instructions are provided for dissecting this region. All descriptions and dissections are well illustrated. Some clinical anatomy of the popliteal artery is discussed.
Answers to MCQs
Authors: Koshi Rachel
Published: July 2024

The answers to multiple-choice questions in Chapter 2 MCQs on general anatomy, Chapter 14 MCQs on the upper limb, and Chapter 26 MCQs on the lower limb are all provided. Each question has a single most correct answer from four options given. The questions and answers have been designed to aid revision.
Redshift evolution and covariances for joint lensing and clustering studies with DESI Y1
Authors: Yuan Sihan , Blake Chris , Krolewski Alex , Lange Johannes , Elvin-Poole Jack , Leauthaud Alexie , DeRose Joseph , Aguilar Jessica Nicole , Ahlen Steven , Beltz-Mohrmann Gillian , Brooks David , Claybaugh Todd , de la Macorra Axel , Doel Peter , Emas Ni Putu Audita Placida , Ferraro Simone , Forero-Romero Jaime E , Garcia-Quintero Cristhian , Gaztañaga Enrique , Gontcho Satya Gontcho A , Hadzhiyska Boryana , Heydenreich Sven , Honscheid Klaus , Ishak Mustapha , Joudaki Shahab , Jullo Eric , Kisner Theodore , Kremin Anthony , Lambert Andrew , Landriau Martin , Manera Marc , Meisner Aaron , Miquel Ramon , Nie Jundan , Palanque-Delabrouille Nathalie , Poppett Claire , Porredon Anna , Rezaie Mehdi , Ross Ashley J , Rossi Graziano , Ruggeri Rossana , Sanchez Eusebio , Saulder Christoph , Seo Hee-Jong , Silber Joseph Harry , Tarlń Gregory , Vargas-Magaña Mariana , Weaver Benjamin Alan , Xhakaj Enia , Zhou Zhimin , Zou Hu
Published: July 2024

Galaxy–galaxy lensing (GGL) and clustering measurements from the Dark Energy Spectroscopic Instrument Year 1 (DESI Y1) data set promise to yield unprecedented combined-probe tests of cosmology and the galaxy–halo connection. In such analyses, it is essential to identify and characterize all relevant statistical and systematic errors. We forecast the covariances of DESI Y1 GGL + clustering measurements and the systematic bias due to redshift evolution in the lens samples. Focusing on the projected clustering and GGL correlations, we compute a Gaussian analytical covariance, using a suite of N-body and lognormal simulations to characterize the effect of the survey footprint. Using the DESI one percent survey data, we measure the evolution of galaxy bias parameters for the DESI luminous red galaxy (LRG) and bright galaxy survey (BGS) samples. We find mild evolution in the LRGs in $0.4 < z < 0.8$, subdominant to the expected statistical errors. For BGS, we find less evolution for brighter absolute magnitude cuts, at the cost of reduced sample size. We find that for a redshift bin width $\Delta z = 0.1$, evolution effects on DESI Y1 GGL is negligible across all scales, all fiducial selection cuts, all fiducial redshift bins. Galaxy clustering is more sensitive to evolution due to the bias squared scaling. Nevertheless the redshift evolution effect is insignificant for clustering above the 1-halo scale of $0.1h^{-1}$ Mpc. For studies that wish to reliably access smaller scales, additional treatment of redshift evolution is likely needed. This study serves as a reference for GGL and clustering studies using the DESI Y1 sample.
Upper limits of HO2 in the atmosphere of Mars from the ExoMars Trace Gas Orbiter
Authors: Alday Juan , Trokhimovskiy Alexander , Belyaev Denis A , Fedorova Anna A , Holmes James A , Patel Manish R , Mason Jonathon P , Lefèvre Franck , Olsen Kevin S , Montmessin Franck , Korablev Oleg , Baggio Lucio , Patrakeev Andrey
Published: July 2024

Odd-hydrogen (HO$_\mathrm{x}$) species have a crucial role in regulating the chemistry of the atmosphere of Mars and are important to understand some of the most fundamental aspects regarding its atmospheric composition such as the long-term stability of CO$_2$. Despite the key role of these species for our understanding of the Martian photochemistry, there is little observational evidence constraining their abundances. In this study, we use infrared solar occultation observations from the Atmospheric Chemistry Suite aboard the ExoMars Trace Gas Orbiter to search for spectral signatures of HO$_2$ in the atmosphere of Mars. In our analysis of the data, we retrieve vertical profiles of pressure, temperature, and water vapour mixing ratio, but are unable to confidently detect the presence of HO$_2$ features in the spectra. We report upper limits of 15 ppbv (5$\sigma$), which represents an order of magnitude improvement with respect to previous investigations. Comparing the derived upper limits with the expectations from 3-dimensional Global Climate Models, we find that approximately an order of magnitude improvement in the instrument sensitivity would be required to detect this molecule and/or constrain the models.
The translesion polymerase Pol Y1 is a constitutive component of the B. subtilis replication machinery
Authors: Marrin McKayla E , Foster Michael R , Santana Chloe M , Choi Yoonhee , Jassal Avtar S , Rancic Sarah J , Greenwald Carolyn R , Drucker Madeline N , Feldman Denholm T , Thrall Elizabeth S
Published: July 2024

Unrepaired DNA damage encountered by the cellular replication machinery can stall DNA replication, ultimately leading to cell death. In the DNA damage tolerance pathway translesion synthesis (TLS), replication stalling is alleviated by the recruitment of specialized polymerases to synthesize short stretches of DNA near a lesion. Although TLS promotes cell survival, most TLS polymerases are low-fidelity and must be tightly regulated to avoid harmful mutagenesis. The gram-negative bacterium Escherichia coli has served as the model organism for studies of the molecular mechanisms of bacterial TLS. However, it is poorly understood whether these same mechanisms apply to other bacteria. Here, we use in vivo single-molecule fluorescence microscopy to investigate the TLS polymerase Pol Y1 in the model gram-positive bacterium Bacillus subtilis. We find significant differences in the localization and dynamics of Pol Y1 in comparison to its E. coli homolog, Pol IV. Notably, Pol Y1 is constitutively enriched at or near sites of replication in the absence of DNA damage through interactions with the DnaN clamp; in contrast, Pol IV has been shown to be selectively enriched only upon replication stalling. These results suggest key differences in the roles and mechanisms of regulation of TLS polymerases across different bacterial species.
Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination
Authors: Boyd Robert D , Kennebeck Morgan M , Miranda Aurora A , Liu Zehui , Silverman Scott K
Published: July 2024

DNA and RNA nucleobase modifications are biologically relevant and valuable in fundamental biochemical and biophysical investigations of nucleic acids. However, directly introducing site-specific nucleobase modifications into long unprotected oligonucleotides is a substantial challenge. In this study, we used in vitro selection to identify DNAzymes that site-specifically N-alkylate the exocyclic nucleobase amines of particular cytidine, guanosine, and adenosine (C, G and A) nucleotides in DNA substrates, by reductive amination using a 5′-benzaldehyde oligonucleotide as the reaction partner. The new DNAzymes each require one or more of Mg2+, Mn2+, and Zn2+ as metal ion cofactors and have kobs from 0.04 to 0.3 h–1, with rate enhancement as high as ∼104 above the splinted background reaction. Several of the new DNAzymes are catalytically active when an RNA substrate is provided in place of DNA. Similarly, several new DNAzymes function when a small-molecule benzaldehyde compound replaces the 5′-benzaldehyde oligonucleotide. These findings expand the scope of DNAzyme catalysis to include nucleobase N-alkylation by reductive amination. Further development of this new class of DNAzymes is anticipated to facilitate practical covalent modification and labeling of DNA and RNA substrates.
RNA encoded peptide barcodes enable efficient in vivo screening of RNA delivery systems
Authors: Odunze Uchechukwu , Rustogi Nitin , Devine Paul , Miller Lorraine , Pereira Sara , Vashist Surender , Snijder Harm Jan , Corkill Dominic , Sabirsh Alan , Douthwaite Julie , Bond Nick , Desai Arpan
Published: July 2024

Lipid nanoparticles (LNPs) have been demonstrated to hold great promise for the clinical advancement of RNA therapeutics. Continued exploration of LNPs for application in new disease areas requires identification and optimization of leads in a high throughput way. Currently available high throughput in vivo screening platforms are well suited to screen for cellular uptake but less so for functional cargo delivery. We report on a platform which measures functional delivery of LNPs using unique peptide ‘barcodes’. We describe the design and selection of the peptide barcodes and the evaluation of these for the screening of LNPs. We show that proteomic analysis of peptide barcodes correlates with quantification and efficacy of barcoded reporter proteins both in vitro and in vivo and, that the ranking of selected LNPs using peptide barcodes in a pool correlates with ranking using alternative methods in groups of animals treated with individual LNPs. We show that this system is sensitive, selective, and capable of reducing the size of an in vivo study by screening up to 10 unique formulations in a single pool, thus accelerating the discovery of new technologies for mRNA delivery.
Cerebrospinal fluid liquid biopsy by low-pass whole genome sequencing for clinical disease monitoring in pediatric embryonal tumors
Authors: Crotty Erin E , Paulson Vera A , Ronsley Rebecca , Vitanza Nicholas A , Lee Amy , Hauptman Jason , Goldstein Hannah E , Lockwood Christina M , Leary Sarah E S , Cole Bonnie L
Published: July 2024

Background

Liquid biopsy assays that detect cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) are a promising tool for disease monitoring in pediatric patients with primary central nervous system (CNS) tumors. As a compliment to tissue-derived molecular analyses, CSF liquid biopsy has the potential to transform risk stratification, prognostication, and precision medicine approaches.

Methods

In this pilot study, we evaluated a clinical pipeline to determine feasibility and sensitivity of low-pass whole genome sequencing (LP-WGS) of CSF-derived cfDNA from patients with CNS embryonal tumors. Thirty-two longitudinal CSF samples collected from 17 patients with molecularly characterized medulloblastoma (12), embryonal tumor with multilayered rosettes (2), CNS embryonal tumor, not elsewhere classified (NEC) (2), and atypical teratoid/rhabdoid tumor (1) were analyzed.

Results

Adequate CSF-derived cfDNA for LP-WGS analysis was obtained in 94% of samples (30/32). Copy number variants compatible with neoplasia were detected in 90% (27/30) and included key alterations, such as isodicentric ch17, monosomy 6, and MYCN amplification, among others. Compared to tissue specimens, LP-WGS detected additional aberrations in CSF not previously identified in corresponding primary tumor specimens, suggesting a more comprehensive profile of tumor heterogeneity or evolution of cfDNA profiles over time. Among the 12 CSF samples obtained at initial staging, only 2 (17%) were cytologically positive, compared to 11 (92%) that were copy number positive by LP-WGS.

Conclusions

LP-WGS of CSF-derived cfDNA is feasible using a clinical platform, with greater sensitivity for tumor detection compared to conventional CSF cytologic analysis at initial staging. Large prospective studies are needed to further evaluate LP-WGS as a predictive biomarker.
Journey to the east: the oldest tetrapod fauna of east Pangea in early Permian
Authors: Chen Jianye , Liu Jun
Published: July 2024

New fossil footprints from Beijing shows that four-foot animals already roamed the east side of supercontinent Pangea ~300 million years ago, proving land connections between North China Block and Pangea.
18F-FDG PET/CT for early prediction of pathological complete response in breast cancer neoadjuvant therapy: a retrospective analysis
Authors: Wu Yilin , Li Yanling , Chen Bin , Zhang Ying , Xing Wanying , Guo Baoliang , Wang Wan
Published: July 2024

Background

Neoadjuvant treatment has been developed as a systematic approach for patients with early breast cancer and has resulted in improved breast-conserving rate and survival. However, identifying treatment-sensitive patients at the early phase of therapy remains a problem, hampering disease management and raising the possibility of disease progression during treatment.

Methods

In this retrospective analysis, we collected 2-deoxy-2-[F-18] fluoro-d-glucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT) images of primary tumor sites and axillary areas and reciprocal clinical pathological data from 121 patients who underwent neoadjuvant treatment and surgery in our center. The univariate and multivariate logistic regression analyses were performed to investigate features associated with pathological complete response (pCR). An 18F-FDG PET/CT-based prediction model was trained, and the performance was evaluated by receiver operating characteristic curves (ROC).

Results

The maximum standard uptake values (SUVmax) of 18F-FDG PET/CT were a powerful indicator of tumor status. The SUVmax values of axillary areas were closely related to metastatic lymph node counts (R = 0.62). Moreover, the early SUVmax reduction rates (between baseline and second cycle of neoadjuvant treatment) were statistically different between pCR and non-pCR patients. The early SUVmax reduction rates-based model showed great ability to predict pCR (AUC = 0.89), with all molecular subtypes (HR+HER2−, HR+HER2+, HR−HER2+, and HR−HER2−) considered.

Conclusion

Our research proved that the SUVmax reduction rate of 18F-FDG PET/CT contributed to the early prediction of pCR, providing rationales for utilizing PET/CT in NAT in the future.
Isotopic variation of non-carbonaceous meteorites caused by dust leakage across the Jovian gap in the solar nebula
Authors: Homma Kazuaki A , Okuzumi Satoshi , Arakawa Sota , Fukai Ryota
Published: July 2024

High-precision isotopic measurements of meteorites revealed that they are classified into non-carbonaceous (NC) and carbonaceous (CC) meteorites. One plausible scenario for achieving this grouping is the early formation of Jupiter, because massive planets can create gaps that suppress the mixing of dust across the gap in protoplanetary disks. However, the efficiency of this suppression by the gaps depends on dust size and the strength of turbulent diffusion, allowing some fraction of the dust particles to leak across the Jovian gap. In this study, we investigate how isotopic ratios of NC and CC meteorites are varied by the dust leaking across the Jovian gap in the solar nebula. To do this, we constructed a model to simulate the evolution of the dust size distribution and the $^{54}$Cr-isotopic anomaly $\varepsilon ^{54}$Cr in isotopically heterogeneous disks with Jupiter. Assuming that the parent bodies of NC and CC meteorites are formed in two dust-concentrated locations inside and outside Jupiter’s orbit, referred to as the NC reservoir and the CC reservoir, we derive the temporal variation of $\varepsilon ^{54}$Cr at the NC and CC reservoirs. Our results indicate that substantial contamination from CC materials occurs at the NC reservoir in the fiducial run. Nevertheless, the values of $\varepsilon ^{54}$Cr at the NC reservoir and the CC reservoir in the run are still consistent with those of NC and CC meteorites formed around $2\:$Myr after the formation of calcium–aluminum-rich inclusions (Sugiura & Fujiya 2014, Meteorit. Planet. Sci., 49, 772). Moreover, this dust leakage causes a positive correlation between the $\varepsilon ^{54}$Cr value of NC meteorites and the accretion ages of their parent bodies.
Conceptualizing ‘Liberated Africans’ and Slave Trade Abolition: Government Schemes to Indenture Enslaved People Captured from Slavery, 1800–1920
Authors: Lovejoy Henry B
Published: July 2024

A new survey of ‘Liberated Africans’ exposes how global calculations of involuntary African indentured labour after 1800 have been significantly underestimated. This analysis of the suppression of the slave trade draws upon a publicly accessible database and digital archive at LiberatedAfricans.org. A quantitative, spatial and chronological visualization of abolition in action, the website memorializes lived experiences of the victims of abolition on micro and macro levels. Results show that there were more than 700,000 individuals captured from the slave trade, ‘liberated’, and forced into periods of indenture according to anti-slave-trade law. This article consolidates the historiography to challenge dominant narratives that British-led efforts were the most voluminous, instead revealing a more complex and multifaceted global phenomenon involving the mass registration of upwards of 200,000 people by name. Digital humanities methodologies facilitate tracking migratory patterns of ‘Liberated Africans’ in diaspora, that is from African regions of departure through documented capture locations in slave trade blockades, judicial processes resulting in ‘liberation’, and settlements of indenture often involving secondary migrations. With the participation of at least eighteen different nations, key findings determine that Portugal and France contributed to upwards of 370,000 ‘Liberated Africans’, surpassing Britain which supplied about a third of global estimates.
ASYNAPSIS3 has diverse dosage-dependent effects on meiotic crossover formation in Brassica napus
Authors: Chu Lei , Zhuang Jixin , Geng Miaowei , Zhang Yashi , Zhu Jing , Zhang Chunyu , Schnittger Arp , Yi Bin , Yang Chao
Published: July 2024

Crossovers create genetic diversity and are required for equal chromosome segregation during meiosis. Crossover number and distribution are highly regulated by different mechanisms that are not yet fully understood, including crossover interference. The chromosome axis is crucial for crossover formation. Here, we explore the function of the axis protein ASYNAPSIS3. To this end, we use the allotetraploid species Brassica napus; due to its polyploid nature, this system allows a fine-grained dissection of the dosage of meiotic regulators. The simultaneous mutation of all 4 ASY3 alleles results in defective synapsis and drastic reduction of crossovers, which is largely rescued by the presence of only one functional ASY3 allele. Crucially, while the number of class I crossovers in mutants with 2 functional ASY3 alleles is comparable to that in wild type, this number is significantly increased in mutants with only one functional ASY3 allele, indicating that reducing ASY3 dosage increases crossover formation. Moreover, the class I crossovers on each bivalent in mutants with 1 functional ASY3 allele follow a random distribution, indicating compromised crossover interference. These results reveal the distinct dosage-dependent effects of ASY3 on crossover formation and provide insights into the role of the chromosome axis in patterning recombination.
Strigolactone-induced degradation of SMXL7 and SMXL8 contributes to gibberellin- and auxin-mediated fiber cell elongation in cotton
Authors: Sun Yaru , Tian Zailong , Zuo Dongyun , Cheng Hailiang , Wang Qiaolian , Zhang Youping , Lv Limin , Song Guoli
Published: July 2024

Cotton (Gossypium) fiber length, a key trait determining fiber yield and quality, is highly regulated by a class of recently identified phytohormones, strigolactones (SLs). However, the underlying molecular mechanisms of SL signaling involved in fiber cell development are largely unknown. Here, we show that the SL signaling repressors MORE AXILLARY GROWTH2-LIKE7 (GhSMXL7) and GhSMXL8 negatively regulate cotton fiber elongation. Specifically, GhSMXL7 and GhSMXL8 inhibit the polyubiquitination and degradation of the gibberellin (GA)-triggered DELLA protein (GhSLR1). Biochemical analysis revealed that GhSMXL7 and GhSMXL8 physically interact with GhSLR1, which interferes with the association of GhSLR1 with the E3 ligase GA INSENSITIVE2 (GhGID2), leading to the repression of GA signal transduction. GhSMXL7 also interacts with the transcription factor GhHOX3, preventing its binding to the promoters of essential fiber elongation regulatory genes. Moreover, both GhSMXL7 and GhSMXL8 directly bind to the promoter regions of the AUXIN RESPONSE FACTOR (ARF) genes GhARF18-10A, GhARF18-10D, and GhARF19-7D to suppress their expression. Cotton plants in which GhARF18-10A, GhARF18-10D, and GhARF19-7D transcript levels had been reduced by virus-induced gene silencing (VIGS) displayed reduced fiber length compared with control plants. Collectively, our findings reveal a mechanism illustrating how SL integrates GA and auxin signaling to coordinately regulate plant cell elongation at the single-cell level.