tbuckley/cabot-search huggingface dataset:
The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics
Authors: Sònia Garcia, Ales Kovarik, Sophie Maiwald, Ludwig Mann, Nicola Schmidt, Joan Pere Pascual-Díaz, Daniel Vitales, Beatrice Weber, Tony Heitkam
Journal: Molecular Biology and Evolution (2024)

Abstract Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA–transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA–transposable element associations.
“Now We Got Bad Blood”: Beyond Phenotype Labels in an “Era” of Meta-omics in Critical Illness
Authors: Georgios D. Kitsios, William Bain
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

""Now We Got Bad Blood:" Beyond Phenotype Labels in an "Era" of Meta-Omics in Critical Illness." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Precise CRISPR-Cas9 gene repair in autologous memory T cells to treat familial hemophagocytic lymphohistiocytosis
Authors: Xun Li, Tristan Wirtz, Timm Weber, Mikhail Lebedin, Elijah D. Lowenstein, Thomas Sommermann, Andreas Zach, Tomoharu Yasuda, Kathrin de la Rosa, Van Trung Chu, Johannes H. Schulte, Ingo Müller, Christine Kocks, Klaus Rajewsky
Journal: Science Immunology (2024)

Familial hemophagocytic lymphohistiocytosis (FHL) is an inherited, often fatal immune deficiency characterized by severe systemic hyperinflammation. Although allogeneic bone marrow transplantation can be curative, more effective therapies are urgently needed. FHL is caused by inactivating mutations in proteins that regulate cellular immunity. Here, we used an adeno-associated virus–based CRISPR-Cas9 system with an inhibitor of nonhomologous end joining to repair such mutations in potentially long-lived T cells ex vivo. Repaired CD8 memory T cells efficiently cured lethal hyperinflammation in a mouse model of Epstein-Barr virus–triggered FHL2, a subtype caused by perforin-1 ( Prf1 ) deficiency. Furthermore, repair of PRF1 and Munc13-4 ( UNC13D )—whose deficiency causes the FHL subtype FHL3—in mutant memory T cells from two critically ill patients with FHL restored T cell cytotoxicity. These results provide a starting point for the treatment of genetic T cell immune dysregulation syndromes with repaired autologous T cells.
Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8 <sup>+</sup> T-myeloid cell networks in melanoma
Authors: David Barras, Eleonora Ghisoni, Johanna Chiffelle, Angela Orcurto, Julien Dagher, Noémie Fahr, Fabrizio Benedetti, Isaac Crespo, Alizée J. Grimm, Matteo Morotti, Stefan Zimmermann, Rafael Duran, Martina Imbimbo, Maria Ochoa de Olza, Blanca Navarro, Krisztian Homicsko, Sara Bobisse, Danny Labes, Zoe Tsourti, Charitini Andriakopoulou, Fernanda Herrera, Rémy Pétremand, Reinhard Dummer, Gregoire Berthod, Anne I. Kraemer, Florian Huber, Jonathan Thevenet, Michal Bassani-Sternberg, Niklaus Schaefer, John O. Prior, Maurice Matter, Veronica Aedo, Clarisse Dromain, Jesus Corria-Osorio, Stéphanie Tissot, Lana E. Kandalaft, Raphael Gottardo, Mikaël Pittet, Christine Sempoux, Olivier Michielin, Urania Dafni, Lionel Trueb, Alexandre Harari, Denarda Dangaj Laniti, George Coukos
Journal: Science Immunology (2024)

Adoptive cell therapy (ACT) using ex vivo–expanded tumor-infiltrating lymphocytes (TILs) can eliminate or shrink metastatic melanoma, but its long-term efficacy remains limited to a fraction of patients. Using longitudinal samples from 13 patients with metastatic melanoma treated with TIL-ACT in a phase 1 clinical study, we interrogated cellular states within the tumor microenvironment (TME) and their interactions. We performed bulk and single-cell RNA sequencing, whole-exome sequencing, and spatial proteomic analyses in pre- and post-ACT tumor tissues, finding that ACT responders exhibited higher basal tumor cell–intrinsic immunogenicity and mutational burden. Compared with nonresponders, CD8 + TILs exhibited increased cytotoxicity, exhaustion, and costimulation, whereas myeloid cells had increased type I interferon signaling in responders. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders had rich baseline intratumoral and stromal tumor–reactive T cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study identifies potential T-myeloid cell network–based biomarkers that could improve patient selection and guide the design of ACT clinical trials.
Rare Occurrence of Scapulothoracic and Ischiogluteal Bursitis Signifying Poorly Controlled Rheumatoid Arthritis
Authors: Tsz-Kit Chow
Journal: Clinical Nuclear Medicine (2024)

Abstract A 74-year-old man with poorly controlled seropositive rheumatoid arthritis was referred for 18 F-FDG PET/CT for follow-up of lung cancer, which demonstrated intense FDG activity in atlantoaxial, sternoclavicular, glenohumeral, and hip joints consistent with active rheumatoid arthritis. There was also unexpected intense uptake at scapulothoracic, ischiogluteal, and trochanteric bursae signifying active bursitis.
Misleading FDG Uptake in Oncology Assessment
Authors: Aurélie Moreau, Thomas Mognetti, David Kryza
Journal: Clinical Nuclear Medicine (2024)

Abstract Here, we report the case of a 35-year-old woman who performed PET/CT 18 F-FDG as an initial workup for HER2+ right breast invasive ductal carcinoma. Examination revealed multifocal breast involvement with homolateral lymph node involvement. Contralateral axillary adenopathy and diffuse splenic and osteomedullary hypermetabolism were also observed, suggesting associated lymphoma in the absence of a recent COVID-19 vaccination. Cytopuncture was discussed and finally postponed after the patient was found to have recently received a pneumococcal vaccination.
A nasal cell atlas reveals heterogeneity of tuft cells and their role in directing olfactory stem cell proliferation
Authors: Saltanat Ualiyeva, Evan Lemire, Caitlin Wong, Alexander Perniss, Amelia A. Boyd, Evelyn C. Avilés, Dante G. Minichetti, Alice Maxfield, Rachel Roditi, Ichiro Matsumoto, Xin Wang, Wenjiang Deng, Nora A. Barrett, Kathleen M. Buchheit, Tanya M. Laidlaw, Joshua A. Boyce, Lora G. Bankova, Adam L. Haber
Journal: Science Immunology (2024)

The olfactory neuroepithelium serves as a sensory organ for odors and forms part of the nasal mucosal barrier. Olfactory sensory neurons are surrounded and supported by epithelial cells. Among them, microvillous cells (MVCs) are strategically positioned at the apical surface, but their specific functions are enigmatic, and their relationship to the other specialized epithelial cells is unclear. Here, we establish that the family of MVCs comprises tuft cells and ionocytes in both mice and humans. Integrating analysis of the respiratory and olfactory epithelia, we define the distinct receptor expression of TRPM5 + tuft-MVCs compared with Gɑ-gustducin high respiratory tuft cells and characterize a previously undescribed population of glandular DCLK1 + tuft cells. To establish how allergen sensing by tuft-MVCs might direct olfactory mucosal responses, we used an integrated single-cell transcriptional and protein analysis. Inhalation of Alternaria induced mucosal epithelial effector molecules including Chil4 and a distinct pathway leading to proliferation of the quiescent olfactory horizontal basal stem cell (HBC) pool, both triggered in the absence of olfactory apoptosis. Alternaria- and ATP-elicited HBC proliferation was dependent on TRPM5 + tuft-MVCs, identifying these specialized epithelial cells as regulators of olfactory stem cell responses. Together, our data provide high-resolution characterization of nasal tuft cell heterogeneity and identify a function of TRPM5 + tuft-MVCs in directing the olfactory mucosal response to allergens.
18F-FDG PET/CT and 99mTc-MDP Bone Scintigraphy Findings of Multifocal Desmoid Fibromatosis
Authors: Nuh Filizoglu, Salih Ozguven, Tunc Ones, Fuat Dede, Tanju Yusuf Erdil
Journal: Clinical Nuclear Medicine (2024)

Abstract Desmoid fibromatosis, also called desmoid tumors, is a group of locally aggressive fibromatous proliferative disorders. They represent less than 3% of all soft tissue sarcoma and are multifocal in approximately 10% of cases. However, there are only a few cases in the literature describing 18 F-FDG PET/CT and 99m Tc-MDP bone scan features of extra-abdominal desmoid fibromas, and all were solitary bone lesions. Herein, we presented a unique case of multifocal desmoid fibromatosis of bone illustrating the prospective value of 18 F-FDG PET/CT and 99m Tc-MDP bone scan in the evaluation of desmoid tumors.
Stent with vacuum therapy for treatment of colonic anastomotic leakage
Authors: Kirill Basiliya, Erik J. van Helden, Myrthe de Jong, Indy Planting, Fabian Holman, Akin Inderson
Journal: Endoscopy (2024)

A 64-year-old patient with a history of severe biliary pancreatitis complicated by partial small-bowel resection and extensive adhesiolysis, and a sigmoid resection with colostomy formation due to diverticulitis, presented with an anastomotic leak and intra-abdominal collections after colostomy reversal ([Fig. 1]). This case presented a challenge as there was no possibility of surgical correction, and thus, any endoscopic option would have to contend with ongoing fecal flow.
18F-FDG PET/CT Findings of Tibia Metastasis From Endometrial Adenocarcinoma
Authors: Jian Chen, Liqiong Ma, Tingting Zhao, Jiqin Yang, Yanmei Li
Journal: Clinical Nuclear Medicine (2024)

Abstract Bone metastases from endometrial carcinoma are rare, especially when the bone is the sole metastatic site. A 55-year-old woman with a history of endometrial carcinoma was referred for FGD PET/CT scan due to pain in the left knee. The images showed that multiple lesions with intense activity were detected in the left tibia. Histopathological examination and immunohistochemistry of the left tibial lesion confirmed metastases from the endometrial adenocarcinoma.
Cerebellar Ataxia With Neuropathy and Vestibular Areflexia Syndrome Due to Replication Factor C Subunit 1 Gene Repeat Expansion
Authors: Mitsuteru Tsuchiya, Tomoyasu Bunai, Kazuki Watanabe, Hirotomo Saitsu, Satoshi Goshima
Journal: Clinical Nuclear Medicine (2024)

Abstract A 56-year-old man was born to consanguineous parents. He experienced slow-progressing sensory disturbances in the upper extremities. T1-weighted images showed cerebellar atrophy. 123 I-IMP SPECT revealed reduced cerebral blood flow in the cerebellum. 123 I-FP-CIT SPECT showed low uptake of dopamine transporter in the bilateral tail of the striatum. 123 I-MIBG scintigraphy shows a decreased heart-to-mediastinum ratio. Flanking polymerase chain reaction suggested biallelic repeat expansion in intron 2 of RFC1 , and subsequent repeat-primed polymerase chain reaction revealed ACAGG repeat expansion. Thus, he was diagnosed as cerebellar ataxia with neuropathy and vestibular areflexia syndrome.
Concurrent Benign Iodine-Avid Thymic and Liver Cysts Mimicking Metastatic Disease on 131I Whole-Body Scintigraphy
Authors: Kamalia Kamarulzaman, Mohd Fazrin Mohd Rohani, Norazlina Mat Nawi, Siti Zarina Amir Hassan
Journal: Clinical Nuclear Medicine (2024)

Abstract A 57-year-old woman received radioiodine therapy post total thyroidectomy for pT3aNxMx follicular thyroid carcinoma. Posttherapy 131 I whole-body scan showed 131 I concentration in the chest, mediastinum, and left upper thigh with stimulated thyroglobulin (Tg) of 89 μg/L. Subsequent radioiodine therapies showed persistent 131 I accumulation in the anterior mediastinal soft tissue lesions and a hypodense segment VII liver lesion visualized on SPECT/CT, suggestive of iodine-avid metastatic disease despite the undetectable serum Tg (&lt;1.0 μg/L) with no Tg antibody interference. Biopsy of the liver lesion revealed liver cyst, and consequent removal of the mediastinal lesions showed benign thymic cysts.
FDG PET/CT Imaging of Liver and Spleen Histiocytic Sarcoma
Authors: Meifu Gan, Xiaoxiao He, Xiaohe Zheng
Journal: Clinical Nuclear Medicine (2024)

Abstract Histiocytic sarcoma is a tumor of the lymphohematopoietic system characterized by macrophage morphology and immunophenotype. Here, we report FDG PET/CT images of a 50-year-old man with coexisting histiocytic sarcoma of the liver and spleen. Images showed multiple enhanced uptake lesions of FDG in both the liver and spleen. Ultimately, histiocytic sarcoma was confirmed by the biopsy histopathology.
Quadruplet Therapy in De Novo High-Volume Mixed Neuroendocrine Prostate Cancer Using 177Lu-PSMA
Authors: Emran Askari, Kamran Aryana, Amir Hosein Jafarian, Alireza Bari, Somaye Barashki
Journal: Clinical Nuclear Medicine (2024)

Abstract We present a case of de novo high-volume metastatic prostate cancer with high PSMA expression, partially PSMA-negative, using quadruplet therapy (PROMISE ver. 2 miTNM; miT4N2M1aM1b(dmi) PRIMARY score: 5, PSMA-expression score: 0–3). Because of our patient’s partial PSMA negativity and after a multidisciplinary tumor board discussion, we decided to use a modified protocol involving doublet hormonal therapy along with 177 Lu-PSMA and radiation therapy to address the PSMA-negative disease. The patient responded well to this treatment, but recurrence was ultimately inevitable. This case represents a typical example of mixed neuroendocrine prostate carcinoma and highlights its resistant phenotype in response to quadruplet therapy.
Histologic Heterogeneity of Chondrosarcoma Reflected on Bone SPECT/CT
Authors: Woo Hee Choi, Min Wook Joo, Hong-Sik Park
Journal: Clinical Nuclear Medicine (2024)

Abstract Chondrosarcomas are a heterogeneous group of cartilage-forming tumors. The tumor is graded on areas demonstrating the highest grade. A 71-year-old man underwent bone SPECT/CT to investigate a tumorous lesion on his right femur. Correlating with the pathological findings, the high-grade area showed higher uptake in bone SPECT/CT. This case suggests that bone SPECT/CT could aid in selecting an optimal biopsy site for diagnosis, and determining the proper treatment of patients with suspected chondroid tumors.
MALT Lymphoma in Histologic Transformation
Authors: Ranbie Tang, Xi Chen, Mengna Liu, Qiaoqiao Shu, Liang Cai
Journal: Clinical Nuclear Medicine (2024)

Abstract An 81-year-old woman experienced compression symptoms due to diffuse enlargement of the thyroid gland. The cytopathological results of thyroid fine-needle suggested malignancy. Therefore, she underwent bilateral thyroidectomy. Postoperative pathology indicated mucosa-associated lymphoid tissue (MALT) lymphoma. Three months later, she found a progressively enlarged mass in her neck. The biopsy showed MALT lymphoma with highly aggressive B-cell lymphoma transformation. 18 F-FDG PET/CT showed increased metabolism in multiple lymph nodes. However, some of these lymph nodes were negative in 68 Ga-pentxafor PET/CT. Our case demonstrated that 68 Ga-pentixafor may have limited value in evaluating MALT lymphoma transformation.
Remote vision-based digital patient monitoring of pulse and respiratory rates in acute medical wards
Authors: Adam Lewis, Bindia Venugopal, Varsha Gandhi, Oliver Gibson, Laura Swanton, Malcolm Green, Jordan Bowen, Michael I Polkey
Journal: Thorax (2024)

Remote Vision-Based digital Patient Monitoring (VBPM) of pulse (PR) and respiratory rate (RR) was set up in six single rooms in an acute medical and an orthopaedic ward. We compared 102 PR and 154 RR VBPM measurements (from 27 patients) with paired routine nurse measurements. VBPM measurements of RR were validated by reviewing video footage. Nurse measurements of RR were often 16–18 breaths/minute, and did not match VBPM RR (overestimating at low RR and underestimating at high RR). Nurse measurements of pulse were on average 3.9 beats per minute greater than matched VBPM measurements. VBPM was unobtrusive and well accepted.
From Short Circuit to Completed Circuit: Conductive Hydrogel Facilitating Oral Wound Healing
Authors: Qiangqiang Zhou, Hanqing Dai, Yukun Yan, Zhiming Qin, Mengqi Zhou, Wanlu Zhang, Guoqi Zhang, Ruiqian Guo, Xiaoling Wei
Journal: Advanced Healthcare Materials (2024)

Abstract The primary challenges posed by oral mucosal diseases are their high incidence and the difficulty in managing symptoms. Inspired by the ability of bioelectricity to activate cells, accelerate metabolism, and enhance immunity, a conductive polyacrylamide/sodium alginate crosslinked hydrogel composite containing reduced graphene oxide (PAA‐SA@rGO) is developed. This composite possesses antibacterial, anti‐inflammatory, and antioxidant properties, serving as a bridge to turn the “short circuit” of the injured site into a “completed circuit,” thereby prompting fibroblasts in proximity to the wound site to secrete growth factors and expedite tissue regeneration. Simultaneously, the PAA‐SA@rGO hydrogel effectively seals wounds to form a barrier, exhibits antibacterial and anti‐inflammatory properties, and prevents foreign bacterial invasion. As the electric field of the wound is rebuilt and repaired by the PAA‐SA@rGO hydrogel, a 5 × 5 mm 2 wound in the full‐thickness buccal mucosa of rats can be expeditiously mended within mere 7 days. The theoretical calculations indicate that the PAA‐SA@rGO hydrogel can aggregate and express SOX2, PITX1, and PITX2 at the wound site, which has a promoting effect on rapid wound healing. Importantly, this PAA‐SA@rGO hydrogel has a fast curative effect and only needs to be applied for the first three days, which significantly improves patient satisfaction during treatment.
Importance of pain management in cancer patients and survivors
Authors: K. Bhatt, A.C. Palomares, P. Forget, D. Ryan, Maria Rosario Alonso, Antonia Barke, Ketan Bhatt, Anna Bjarnegård Sellius, Gertrude Buttigieg, Paul Cameron, Angela Cano Palomares, Duarte Correia, Beatriz Craveiro Lopes, Gustavo Fabregat, Maria Teresa Flor de Lima, Patrice Forget, Marisol García Penalta, Gunilla Goran, Liisa Jutila, Marja Kinnunen, Aleksandra Kotlinska-Lemieszek, Mateja Krzan, Françoise Launois, André Ljutow, Ivone Machado, Cesar Margarit, Maiju Marttinen, Bart Morlion, Joanne O’Brien, María Luz
Journal: Annals of Oncology (2024)
Reanalysis of PFO5DoA Levels in Blood from Wilmington, North Carolina, Residents, 2017–2018
Authors: Nadine Kotlarz, James McCord, Nate Wiecha, Rebecca A. Weed, Michael Cuffney, Jeffrey R. Enders, Mark Strynar, Detlef R.U. Knappe, Brian J. Reich, Jane A. Hoppin
Journal: Environmental Health Perspectives (2024)
Measurement of Hydro-EVE and 6:2 FTS in Blood from Wilmington, North Carolina, Residents, 2017–2018
Authors: Nadine Kotlarz, James McCord, Nate Wiecha, Rebecca A. Weed, Michael Cuffney, Jeffrey R. Enders, Mark Strynar, Detlef R.U. Knappe, Brian J. Reich, Jane A. Hoppin
Journal: Environmental Health Perspectives (2024)
Determinants of PFOA Serum Half-Life after End of Exposure: A Longitudinal Study on Highly Exposed Subjects in the Veneto Region
Authors: Erich Batzella, Isabella Rosato, Gisella Pitter, Filippo Da Re, Francesca Russo, Cristina Canova, Tony Fletcher
Journal: Environmental Health Perspectives (2024)

Perfluoroalkyl substances (PFAS) are widely used, ubiquitous, and highly persistent man-made chemicals. Groundwater of a vast area of the Veneto Region (northeastern Italy) was found to be contaminated by PFAS from a manufacturing plant active since the late 1960s. As a result, residents were overexposed to PFAS through drinking water until 2013, mainly to perfluorooctanoic acid (PFOA).
Personal Care Product Use during Puberty and Incident Breast Cancer among Black, Hispanic/Latina, and White Women in a Prospective US-Wide Cohort
Authors: Mandy Goldberg, Che-Jung Chang, Kemi Ogunsina, Katie M. O’Brien, Kyla W. Taylor, Alexandra J. White, Dale P. Sandler
Journal: Environmental Health Perspectives (2024)

Some personal care products (PCPs) contain endocrine-disrupting chemicals that may affect breast cancer (BC) risk. Patterns of use vary by race and ethnicity. Use often starts in adolescence, when rapidly developing breast tissue may be more susceptible to environmental carcinogens. Few studies have examined associations of BC with PCP use during this susceptible window.
Impact of climate change on immune responses and barrier defense
Authors: Chrysanthi Skevaki, Kari C. Nadeau, Marc E. Rothenberg, Barrak Alahmad, Blandina T. Mmbaga, Gileard G. Masenga, Vanitha Sampath, David C. Christiani, Tari Haahtela, Harald Renz
Journal: Journal of Allergy and Clinical Immunology (2024)

Climate change is not just jeopardizing the health of our planet, but it is increasingly impacting our immune health.There is an expanding body of evidence that climaterelated exposures, such as air pollution, heat, wildfires, extreme weather events, and biodiversity loss significantly disrupt the functioning of the human immune system.These exposures manifest in a broad range of stimuli including antigens, allergens, heat stress, pollutants, microbiota changes, and other toxic substances.Such exposures pose a direct and indirect threat to our body's primary line of defense, the epithelial barrier, affecting its physical integrity and functional efficacy.Furthermore, these climate-related environmental stressors can hyper-stimulate the innate immune system and influence adaptive immunity, notably in terms of developing and preserving immune tolerance.The loss or failure of immune tolerance can instigate a wide spectrum of non-communicable diseases such as autoimmune conditions, allergy, respiratory illnesses, metabolic diseases, obesity, and others.As the evidence continues to unravel, there is a need for additional research in climate change and immunology that covers diverse environments in different global settings, employing modern biological and epidemiological tools.
Tumor-secreted FGF21 acts as an immune suppressor by rewiring cholesterol metabolism of CD8+T cells
Authors: Cegui Hu, Wen Qiao, Xiang Li, Zhi-kun Ning, Jiang Liu, Sumiya Dalangood, Hanjun Li, Xiang Yu, Zhen Zong, Zhenke Wen, Jun Gui
Journal: Cell Metabolism (2024)
Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis
Authors: Thomas M. Savage, Katherine T. Fortson, Kenia de los Santos-Alexis, Angelica Oliveras-Alsina, Mathieu Rouanne, Sarah S. Rae, Jennifer R. Gamarra, Hani Shayya, Adam Kornberg, Renzo Cavero, Fangda Li, Arnold Han, Rebecca A. Haeusler, Julien Adam, Robert F. Schwabe, Nicholas Arpaia
Journal: Immunity (2024)