bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postnatal Ovarian Transdifferentiation in the Absence of Estrogen Receptor Signaling Is Dependent on Genetic Background
Authors: Binder April K , Burns Katherine A , Rodriguez Karina F , Hamilton Katherine , Pardo-Manuel de Villena Fernando , Korach Kenneth S 
Published: November 2024

Abstract
Normal ovarian function requires the expression of estrogen receptors α (ESR1) and β (ESR2) in distinct cell types within the ovary. The double estrogen receptor knockout (αβERKO) ovary had the appearance of seminiferous tubule–like structures that expressed SOX9; this phenotype was lost when the animals were repeatedly backcrossed to the C57BL/6J genetic background. A new line of ERKO mice, Ex3αβERKO, was developed for targeted disruption on a mixed genetic background. Histological examination of the ovaries in the Ex3αβERKO showed the appearance of seminiferous tubule–like structures in mice aged 6 to 12 months. These dismorphogenic regions have cells that no longer express granulosa cell–specific FOXL2, while other cells express Sertoli cell–specific SOX9 as examined by immunohistochemistry. Whole ovarian gene expression analysis in Ex3αERKO, Ex3βRKO, and Ex3αβERKO found many genes differentially expressed compared to controls with one Esr1 and Esr2 allele. The genes specific to the Ex3αβERKO ovary were compared to other models of postnatal ovarian transdifferentiation, identifying 21 candidate genes. To examine the genetic background contributions, DNA was isolated from αβERKO mice that did not show ovarian transdifferentiation and compared to DNA from Ex3αβERKO using Mouse Diversity Array. A genomic region putatively associated with transdifferentiation was identified on Chr18 (5-15 M) and genes in this region were compared to the genes differentially expressed in models of ovarian transdifferentiation. This work demonstrates the importance of ESRs in maintaining granulosa cell differentiation within the ovary, identifies several potential gene candidates, and suggests that genetic background can be a confounding factor.
The Memories of Shipmates: Claims to Freedom in Mauritius, 1833–1835
Authors: Hooper Jane 
Published: November 2024

Abstract
In the years immediately prior to legal emancipation, dozens of enslaved people approached the Protectors of Slaves in Mauritius to demand their freedom. They argued that they had been illegally introduced to the island after the slave trade was abolished by the British. Their testimonies offer insights into the development of Afro-Creole communities in the Mascarenes and how people successfully advocated for increased autonomy. Historians of the transatlantic slave trade have argued for the significance of shipmate bonds for people who endured the Middle Passage and labored in the Americas. Such communities were also important in the Indian Ocean world for those who sought manumission. Those who were illegally enslaved shared memories of capture, transportation, and forced acculturation. Their memories and bonds highlight the complex diasporic communities that coexisted on Mauritius during the first half of the nineteenth century.
Africans, Muwallad, and the Myth of Mild Slavery: Testimonies of the Enslaved in the Persian Gulf, 1887–1949
Authors: Suzuki Hideaki 
Published: November 2024

Abstract
This article examines the testimonies prepared for manumission certificates issued by British authorities in the early twentieth-century Persian Gulf. Based on the dataset on which the author is currently working, it examines the category of “African” recorded by the colonial record keepers to distinguish between “Africans” who were born in Africa and those born in the Gulf who were also categorized as “African” by the British officers who interviewed them. Those who were born locally from enslaved parents were called muwallad and it is widely regarded that the masters treated them better than those newly enslaved. Such discourse about muwallad is called “the myth of mild slavery.” This article analyzes the dataset both quantitatively and qualitatively to clarify the experience of “African” muwallad in order to shed light on the diverse experiences of the enslaved “African” population in the early twentieth-century Persian Gulf.
Creating a Public Database of Slaving Voyages across the Indian Ocean and Asia
Authors: Allen Richard B. , Domingues da Silva Daniel B. , Hooper Jane , Hopper Matthew S. 
Published: November 2024

Abstract
This article describes a major new initiative funded by a grant from the United States National Endowment for the Humanities to identify slaving voyages by Arab, Chinese, European, Indian, Southeast Asian, Swahili, and other vessels in the Indian Ocean and Asia and add them to the existing SlaveVoyages website. The article argues that the new database is needed to expand our historical knowledge about slave trading as a global phenomenon by reconstructing the maritime commerce in slave and other forms of coerced labor in the Indian Ocean and maritime Asia in ways that will help historians and the public trace the movement and life histories of enslaved peoples within and beyond the Indian Ocean world. The article concludes with a call for collaboration from researchers who can identify and contribute new voyages to this important project.
“Unique, Divine, Unrepeatable”
Authors: Pérez Elizabeth 
Published: November 2024

Abstract
The late Bishop S. F. Makalani-MaHee (1972–2017) was a minister, activist, actor/singer, composer, and spoken word artist. His essays, songs, poetry, plays, and sermons reflect his “Blackpentecostal” and Southern Baptist upbringing as well as his embrace of liberation theology, womanism, and Black feminist thought. This article analyzes his only published collection of poems, Don’t!, as a profound repertoire and theological manifesto with the aid of his autobiographical writings, performances, and eponymous archive housed at the Stonewall National Museum and Archives. Don’t! contests patriarchal, cisgender-sexist constructions of masculinity by paying homage to Black grandmothers, mothers, femmes, and cisgender (or “nontrans”) “sister friends.” This article argues that Don’t! is a declaration of his woman-centered theorization of transmasculinity and his queer/trans Christology, which should be brought into conversation with texts in the womanist canon. The article further contends that Don’t! enriches the Black trans Christian archive and disrupts the “whitewashed” master narratives of LGBTQ experience.
Cellular retinoic acid-binding proteins regulate germ cell proliferation and sex determination in zebrafish
Authors: Fung Lianna , Dranow Daniel B. , Subramanian Arul , Libby Natalia , Schilling Thomas F. 
Published: November 2024

ABSTRACT
Cellular retinoic acid (RA)-binding proteins (Crabps) solubilize intracellular RA and transport it to its nuclear receptors or cytoplasmic degradation enzymes. Despite their extreme conservation across chordates, genetic studies of Crabp function have revealed few essential functions. We have generated loss-of-function mutations in all four zebrafish Crabps and find essential roles for Crabp2 proteins in gonad development and sex determination. Transgenic RA reporters show strong RA responses in germ cells at the bipotential stage of gonad development. Double mutants lacking the functions of both Crabp2a and Crabp2b predominantly become male, which correlates with their smaller gonad size and reduced germ cell proliferation during gonad development at late larval and early juvenile stages. In contrast, mutants lacking the functions of both Crabp1a and Crabp1b have normal sex ratios. Exogenous RA treatments at bipotential gonad stages increase germ cell number, consistent with a direct role for RA in promoting germ cell proliferation. Our results suggest essential functions for Crabps in gonad development and sex determination.
ARPP19 phosphorylation site evolution and the switch in cAMP control of oocyte maturation in vertebrates
Authors: Meneau Ferdinand , Lapébie Pascal , Daldello Enrico Maria , Le Tran , Chevalier Sandra , Assaf Sarah , Houliston Evelyn , Jessus Catherine , Miot Marika 
Published: November 2024

ABSTRACT
cAMP-PKA signaling initiates the crucial process of oocyte meiotic maturation in many animals, but inhibits it in vertebrates. To address this ‘cAMP paradox’, we exchanged the key PKA substrate ARPP19 between representative species, the vertebrate Xenopus and the cnidarian Clytia, comparing its phosphorylation and function. We found that, as in Xenopus, Clytia maturing oocytes undergo ARPP19 phosphorylation on a highly conserved Gwl site, which inhibits PP2A and promotes M-phase entry. In contrast, despite a PKA phosphorylation signature motif recognizable across most animals, Clytia ARPP19 was only poorly phosphorylated by PKA in vitro and in vivo. Furthermore, unlike Xenopus ARPP19, exogenous Clytia ARPP19 did not delay Xenopus oocyte maturation. We conclude that, in Clytia, ARPP19 does not intervene in oocyte maturation initiation because of both poor recognition by PKA and the absence of effectors that mediate vertebrate oocyte prophase arrest. We propose that ancestral ARPP19 phosphorylated by Gwl has retained a key role in M-phase across eukaryotes and has acquired new functions during animal evolution mediated by enhanced PKA phosphorylation, allowing co-option into oocyte maturation regulation in the vertebrate lineage.
Barcoding Notch signaling in the developing brain
Authors: Siniscalco Abigail M. , Perera Roshan Priyarangana , Greenslade Jessie E. , Veeravenkatasubramanian Hemagowri , Masters Aiden , Doll Hannah M. , Raj Bushra 
Published: November 2024

ABSTRACT
Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control, while the recorder obtains mutations in ancestral cells where Notch is active. We combine SABER-seq with an expanded juvenile brain atlas to identify cell types derived from Notch-active founders. Our data reveal rare examples where differential Notch activities in ancestral progenitors are detected in terminally differentiated neuronal subtypes. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.
A new cell culture resource for investigations of reptilian gene function
Authors: Samudra Sukhada P. , Park Sungdae , Esser Elizabeth A. , McDonald Tryggvi P. , Borges Arianna M. , Eggenschwiler Jonathan , Menke Douglas B. 
Published: November 2024

ABSTRACT
The establishment of CRISPR/Cas9 gene editing in Anolis sagrei has positioned this species as a powerful model for studies of reptilian gene function. To enhance this model, we developed an immortalized lizard fibroblast cell line (ASEC-1) for the exploration of reptilian gene function in cellular processes. We demonstrate the use of this cell line by scrutinizing the role of primary cilia in lizard Hedgehog (Hh) signaling. Using CRISPR/Cas9 mutagenesis, we disrupted the ift88 gene, which is required for ciliogenesis in diverse organisms. We determined that loss of itf88 from lizard cells leads to an absence of primary cilia, a partial derepression of gli1 transcription, and an inability of the cells to respond to the Smoothened agonist, SAG. Through a cross-species analysis of SAG-induced transcriptional responses in cultured limb bud cells, we further determined that ∼46% of genes induced as a response to Hh pathway activation in A. sagrei are also SAG responsive in Mus musculus limb bud cells. Our results highlight conserved and diverged aspects of Hh signaling in anoles and establish a new resource for investigations of reptilian gene function.
Detecting subtle subterranean movement via laser speckle imaging
Authors: Bagheri Hosain , Goodisman Michael A. D. , Goldman Daniel I. 
Published: November 2024

ABSTRACT
A diversity of organisms live within underground environments. However, visualizing subterranean behavior is challenging because of the opacity of most substrates. We demonstrate that laser speckle imaging, a non-invasive technique resolving nanometer-scale movements, facilitates quantifying biological activity in a granular medium. We monitored fire ants (Solenopsis invicta) at different developmental stages, burial depths (1–5 cm) and moisture fractions (0 and 0.1 by volume) in a container of 0.7 mm glass particles. Although the speckle pattern from the backscattered light precludes direct imaging of animal kinematics, analysis of integrated image differences revealed that spiking during ant movement increased with the developmental phase. Greater burial depth and saturation resulted in fewer and lower magnitude spikes. We verified that spiking correlated with movement via quasi-2D experiments. This straightforward method, involving a laser and digital camera, can be applied to laboratory and potentially field situations to gain insight into subterranean organism activities.
Intratumoral Bacteria are Uncommon in Gastrointestinal Stromal Tumor
Authors: Tardy Katherine J. , Kwak Hyunjee V. , Tieniber Andrew D. , Mangold Alina K. , Perez Juan E. , Do Kevin , Zeng Shan , Rossi Ferdinando , DeMatteo Ronald P. 
Published: November 2024

Abstract

Background
Gastrointestinal stromal tumor (GIST) is the most common human sarcoma with over 5000 new patients diagnosed in the USA each year. The tumor originates from the interstitial cells of Cajal and forms an intramural lesion most commonly in the stomach or small intestine. The gut microbiome has been linked to other gastrointestinal cancers and a recent paper purported that GISTs contain substantial intratumoral bacteria. The purpose of this study is to further evaluate the presence of bacteria in GISTs.

Patients and Methods
We collected 25 tumor samples of varying size and location from 24 patients under sterile conditions in the operating room immediately following surgical resection. 16S quantitative polymerase chain reaction (qPCR) and 16S ribosomal RNA (rRNA) gene amplicon sequencing were performed to evaluate the bacterial species present in each tumor. Retrospective chart review was performed to determine tumor characteristics, including tumor size, location, imatinib exposure, and mucosal involvement.

Results
In 23 of the 25 tumor samples, there were fewer than 100 copy numbers of 16S rRNA per uL, indicating an absence of a significant bacterial load. 16S rRNA gene amplicon sequencing of the remaining two samples, one gastric tumor and one duodenal tumor, revealed the presence of normal intestinal bacteria. These two tumors, along with three others, had disruption of the mucosal lining.

Conclusions
GISTs generally lack substantial bacteria, except in some cases when the tumor disrupts the mucosa.
Decision Centralization and Learning from Experience in Groups: Separating Context from Aggregation Effects
Authors: Park Sanghyun , Gonzalez Cleotilde , Puranam Phanish 
Published: November 2024

Organizational learning often involves groups that learn from feedback on their decisions over time (also known as “learning by doing” or “learning from experience”). Although organizational learning is frequently assumed to resemble individual learning from experience, there is limited evidence to validate this assumption. Furthermore, groups in organizations often have centralized rather than decentralized decision making, but we know little about how they differ in learning from experience. Using a combination of experimental data and computational modeling, we compare individuals to groups that are either decentralized or centralized in their decision making. We find that centralized groups behave like hyper-individuals: They update and explore more than individuals (who, in turn, update and explore more than decentralized groups). Our evidence shows that not only do groups differ from individuals because of aggregation processes but also that individuals change their behaviors simply by virtue of being in a group (a context effect). Specifically, we find that participants assigned as leaders in centralized groups become proactive learners who seek novel information to learn by deviating from experience. Implications are drawn for how this might alter the way we conceptualize and model organizational learning. This paper was accepted by Olav Sorenson, organization. Funding: This work was supported by the Defense Advanced Research Projects Agency [Grant W911NF-20-1-0006], the Strategic Management Society [Will Mitchell Dissertation Research Grant Program], NUS Presidential Young Professorship grant and the Desmarais Fund for the Organizations and Algorithms project. Supplemental Material: The online appendix and data files are available at https://doi.org/10.1287/mnsc.2022.01507 .
Spectrum of venous thromboembolism in adult patients with ulcerative colitis in Pakistan: A single center retrospective study
Authors: Karim Masood Muhammad , Shaikh Hafsa , Ismail Faisal Wasim 
Published: November 2024

BACKGROUND
Patients with inflammatory bowel disease are at a 2-8-fold higher risk of developing venous thromboembolism (VTE) as compared to the general population. Although the exact pathogenesis is unclear, the literature suggests that increased risk of thromboembolic events in such patients occurs as a result of increased coagulation factors, inflammatory cytokines, and reduction in anticoagulants leading to a prothrombotic state.
AIM
To assess the prevalence, risk factors, management, and outcome of ulcerative colitis (UC) patients who develop VTE.
METHODS
This was a retrospective chart review done in The Gastroenterology Department of The Aga Khan University Hospital. Data was collected from medical records for all patients admitted with a diagnosis of UC from January 2012 to December 2022.
RESULTS
Seventy-four patients fulfilled the inclusion criteria. The mean ± SD of age at presentation of all UC patients was 45 years ± 10 years whereas for those who developed VTE, it was 47.6 years ± 14.7 years. Hypertension and diabetes were the most common co-morbid seen among UC patients with a frequency of 17 (22.9%) and 12 (16.2%), respectively. A total of 5 (6.7%) patients developed VTE. Deep venous thrombosis was the most common thromboembolic phenomenon seen in 3 (60%) patients. All the patients with UC and concomitant VTE were discharged home (5; 100%).
CONCLUSION
The prevalence of VTE with UC in Pakistani patients corresponds with the international literature. However, multi-centric studies are required to further explore these results.
A COMPARISON OF CAUSATIVE MICROBIAL PATHOGENS IN OSTEOMYELITIS AND PERIPROSTHETIC JOINT INFECTION: A RETROSPECTIVE OBSERVATIONAL COHORT STUDY
Authors: Unsworth Annalise , McNally Martin , Young Bernadette , Scarborough Matthew 
Published: November 2024

AimsBone and joint infections cause significant morbidity, often requiring combination medical and surgical treatment. The presence of foreign material reduces the number of organisms required to cause an infection. The aim of this study was to assess whether there was a difference in the species of organism identified on culture in osteomyelitis compared to prosthetic joint infection.MethodThis was a retrospective observational cohort study of patients that had surgical intervention for prosthetic joint infection or osteomyelitis with positive microbial culture between 2019 and 2022. Data including patient demographics, site of injury, BACH score for osteomyelitis and JS-BACH score for prosthetic joint infection, organism classification and antibiotic resistance to vancomycin and gentamicin were extracted from the medical record. Logistic and multiple regressions were used to adjust for potential confounding variables.ResultsA total of 445 patients were included in the study; 267 patients with osteomyelitis or fracture-related infection and 177 patients with prosthetic joint infection. The patients with prosthetic joint infection were older (Mean age 70 for PJI; IQR 60-77 vs 56 for OM/FRI; IQR 39-64), more likely to be female (55.6% vs 26.2%) and had a higher BMI and ASA compared to those with osteomyelitis. Symptom duration tended to be longer in osteomyelitis/FRI (p<0.001).Staphylococcus aureus was the most common pathogen isolated in both osteomyelitis (155/267 (58.1%)) and prosthetic joint infection (85/177 (48.9%), followed by other Gram negative pathogens with 77/267 (28.8%) in osteomyelitis and 48/177 (27.1%) in prosthetic joint infection. On multivariate analysis, there was no difference between the rate of Staphylococcus aureus infection between the two groups. The rate of polymicrobial infection was higher in patients with osteomyelitis (92/267 (34.5%)) compared to prosthetic joint infection (38/177 (23.7%), however after adjustment for confounders there was no difference, p = 0.842. There was no difference in the presence of gentamicin resistant organisms or vancomycin resistant Gram positive organisms in osteomyelitis compared to prosthetic joint infection.ConclusionCausative pathogens are similar in these two common forms of bone and joint infection. There was no significant difference in the identification, presence of polymicrobial infection or gentamicin and vancomycin resistance in organisms isolated in osteomyelitis compared to prosthetic joint infection. This may have implications for empiric antibiotic choice and local antibiotic therapy in the management of bone and joint infection.
DAIR FOR PERIPROSTHETIC JOINT INFECTIONS: ONE WEEK TO SAVE THE JOINT?
Authors: Gupta Vatsal , Shahban Shafiq , Petrie Michael , Kimani Peter , Kozdryk Jakub , Riemer Bryan , King Richard , Westerman Richard , Foguet Pere 
Published: November 2024

AimPredicting success of a Debridement, Antibiotics and Implant Retention (DAIR) procedure for Periprosthetic Joint Infection (PJI) remains a challenge. A failed DAIR might adversely affect the outcome of any future revision surgery for PJI. Hence, the ability to identify and optimise factors predictive of DAIR success would help target the procedure to the appropriate patient cohort and avoid unnecessary surgery for patients where a DAIR is unlikely to eradicate infection.MethodA retrospective review of our prospective Bone Infection Group database was performed to identify all patients who underwent a DAIR of their hip or knee arthroplasty. Diagnosis of PJI was confirmed using the Musculoskeletal Infection Society (MSIS) 2013 and the European Bone and Joint Infection Society (EBJIS) 2021 classification systems. DAIR surgery was grouped into “successful” or “unsuccessful” outcomes as per the MSIS working group outcome-reporting tool.ResultsSixty-Four consecutive patients with an acute PJI underwent a DAIR procedure between 2009 and 2020. Treatment was successful in 44 (69%). The chance of a successful DAIR was significantly greater if performed within one week of symptom onset compared to greater than one week duration (adjusted odds ratio (OR 0.11; p=0.027; 95% CI [0.02- 0.78]). The chances of a successful DAIR was not influenced by whether the surgeon was an arthroplasty or non-arthroplasty surgeon (OR 0.28; p=0.13; 95% CI [0.05- 1.48]). Isolated Streptococcus infection had a success rate of 100%; followed by Coagulasenegative Staphylococci 71% and Methicillin-susceptible Staphylococcus Aureus 65%. Polymicrobial infection had the worst outcome with a success rate of 47%.ConclusionsIn our experience DAIR surgery performed within one week of symptom onset, significantly increased chances of successful infection eradication. Collaborative work is required to ensure arthroplasty patients access prompt appropriate surgical decision-making, remove barriers to early assessment and minimise delays to surgery.