bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S2 from Time-Dependent Prognostic Value of Serological and Measurable Residual Disease Assessments after Idecabtagene Vicleucel
Authors: Paiva Bruno , Manrique Irene , Rytlewski Julie , Campbell Timothy , Kazanecki Christian C. , Martin Nathan , Anderson Larry D. , Berdeja Jesús G. , Lonial Sagar , Raje Noopur S. , Lin Yi , Moreau Philippe , San-Miguel Jesús F. , Munshi Nikhil C. , Kaiser Shari M.
Published: January 2024

Landmark PFS
Supplementary Figures S1-S11 from ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma
Authors: Neri Paola , Barwick Benjamin G. , Jung David , Patton Jonathan C. , Maity Ranjan , Tagoug Ines , Stein Caleb K. , Tilmont Remi , Leblay Noemie , Ahn Sungwoo , Lee Holly , Welsh Seth J. , Riggs Daniel L. , Stong Nicholas , Flynt Erin , Thakurta Anjan , Keats Jonathan J. , Lonial Sagar , Bergsagel P. Leif , Boise Lawrence H. , Bahlis Nizar J.
Published: January 2024

Supplementary Figures S1-S11, which provide supporting data for the main figures.
Supplementary Data 5 from ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma
Authors: Neri Paola , Barwick Benjamin G. , Jung David , Patton Jonathan C. , Maity Ranjan , Tagoug Ines , Stein Caleb K. , Tilmont Remi , Leblay Noemie , Ahn Sungwoo , Lee Holly , Welsh Seth J. , Riggs Daniel L. , Stong Nicholas , Flynt Erin , Thakurta Anjan , Keats Jonathan J. , Lonial Sagar , Bergsagel P. Leif , Boise Lawrence H. , Bahlis Nizar J.
Published: January 2024

ETV4 ChIP-seq binding sites in RPMI8226 cells.
Supplementary Data 1 from ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma
Authors: Neri Paola , Barwick Benjamin G. , Jung David , Patton Jonathan C. , Maity Ranjan , Tagoug Ines , Stein Caleb K. , Tilmont Remi , Leblay Noemie , Ahn Sungwoo , Lee Holly , Welsh Seth J. , Riggs Daniel L. , Stong Nicholas , Flynt Erin , Thakurta Anjan , Keats Jonathan J. , Lonial Sagar , Bergsagel P. Leif , Boise Lawrence H. , Bahlis Nizar J.
Published: January 2024

Lenalidomide differentially expressed genes and GSEA for MM1S and OPM2 cells treated with 10 µM lenalidomide for 12 and 24 hours, respectively.
Table S4 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: January 2024

Experimental reagents and resources with identifiers used in this study.
Table S2 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: January 2024

Mouse cluster 2 genes whose H3K27me3 in TSS's was decreased.
Figure S2 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: January 2024

HBZ protein alters epigenetic regulation of TAp73 by EZH2.
Figure S1 from HTLV-1 bZIP Factor-Induced Reprogramming of Lactate Metabolism and Epigenetic Status Promote Leukemic Cell Expansion
Authors: Toyoda Kosuke , Yasunaga Jun-ichirou , Shichijo Takafumi , Arima Yuichiro , Tsujita Kenichi , Tanaka Azusa , Salah Tarig , Zhang Wenyi , Hussein Osama , Sonoda Miyu , Watanabe Miho , Kurita Daisuke , Nakashima Kazutaka , Yamada Kyohei , Miyoshi Hiroaki , Ohshima Koichi , Matsuoka Masao
Published: January 2024

Transcriptional regulation by HBZ protein and RNA and the status of TP73 expression.
Table S7 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: January 2024

Table S7 Gene list reflecting the inflammatory remodeling of stromal niches in AML
Table S1 from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: January 2024

Table S1 patient characteristics
Data from A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML
Authors: Chen Lanpeng , Pronk Eline , van Dijk Claire , Bian Yujie , Feyen Jacqueline , van Tienhoven Tim , Yildirim Meltem , Pisterzi Paola , de Jong Madelon M.E. , Bastidas Alejandro , Hoogenboezem Remco M. , Wevers Chiel , Bindels Eric M. , Löwenberg Bob , Cupedo Tom , Sanders Mathijs A. , Raaijmakers Marc H.G.P.
Published: January 2024

Abstract
Cancer initiation is orchestrated by an interplay between tumor-initiating cells and their stromal/immune environment. Here, by adapted single-cell RNA sequencing, we decipher the predicted signaling between tissue-resident hematopoietic stem/progenitor cells (HSPC) and their neoplastic counterparts with their native niches in the human bone marrow. LEPR+ stromal cells are identified as central regulators of hematopoiesis through predicted interactions with all cells in the marrow. Inflammatory niche remodeling and the resulting deprivation of critical HSPC regulatory factors are predicted to repress high-output hematopoietic stem cell subsets in NPM1-mutated acute myeloid leukemia (AML), with relative resistance of clonal cells. Stromal gene signatures reflective of niche remodeling are associated with reduced relapse rates and favorable outcomes after chemotherapy across all genetic risk categories. Elucidation of the intercellular signaling defining human AML, thus, predicts that inflammatory remodeling of stem cell niches drives tissue repression and clonal selection but may pose a vulnerability for relapse-initiating cells in the context of chemotherapeutic treatment.
Significance:
Tumor-promoting inflammation is considered an enabling characteristic of tumorigenesis, but mechanisms remain incompletely understood. By deciphering the predicted signaling between tissue-resident stem cells and their neoplastic counterparts with their environment, we identify inflammatory remodeling of stromal niches as a determinant of normal tissue repression and clinical outcomes in human AML.

See related commentary by Lisi-Vega and Méndez-Ferrer, p. 349.

This article is featured in Selected Articles from This Issue, p. 337
Supplementary Table 2 from Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer
Authors: Soto Maira , Filbert Erin L. , Yang Hai , Starzinski Stephanie , Starzinski Alec , Gin Marissa , Chen Brandon , Le Phi , Li Tony , Bol Brandon , Cheung Alexander , Zhang Li , Hsu Frank J. , Ko Andrew , Fong Lawrence , Keenan Bridget P.
Published: January 2024

Antibody details for mass cytometry.
Supplementary Figure 4 from Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer
Authors: Soto Maira , Filbert Erin L. , Yang Hai , Starzinski Stephanie , Starzinski Alec , Gin Marissa , Chen Brandon , Le Phi , Li Tony , Bol Brandon , Cheung Alexander , Zhang Li , Hsu Frank J. , Ko Andrew , Fong Lawrence , Keenan Bridget P.
Published: January 2024

Supplementary Figure 4
Supplementary Figure 3 from Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer
Authors: Soto Maira , Filbert Erin L. , Yang Hai , Starzinski Stephanie , Starzinski Alec , Gin Marissa , Chen Brandon , Le Phi , Li Tony , Bol Brandon , Cheung Alexander , Zhang Li , Hsu Frank J. , Ko Andrew , Fong Lawrence , Keenan Bridget P.
Published: January 2024

Supplementary Figure 3
Supplementary Figure 1 from Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer
Authors: Soto Maira , Filbert Erin L. , Yang Hai , Starzinski Stephanie , Starzinski Alec , Gin Marissa , Chen Brandon , Le Phi , Li Tony , Bol Brandon , Cheung Alexander , Zhang Li , Hsu Frank J. , Ko Andrew , Fong Lawrence , Keenan Bridget P.
Published: January 2024

Supplementary Figure 1
FIGURE 5 from Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer
Authors: Soto Maira , Filbert Erin L. , Yang Hai , Starzinski Stephanie , Starzinski Alec , Gin Marissa , Chen Brandon , Le Phi , Li Tony , Bol Brandon , Cheung Alexander , Zhang Li , Hsu Frank J. , Ko Andrew , Fong Lawrence , Keenan Bridget P.
Published: January 2024

Sotigalimab results in immunomodulation and apoptosis of tumor cells. A, Tumor cells in the TME were characterized using MIBI analysis of keratin, HLA-I, HLA-II, PD-L1, and CD40 (representative image: patient 04). B, Quantification of tumor cell density by MIBI (pre n = 5, post n = 4). C–E, Expression of the phenotypic markers was also quantified in the MIBI analysis for HLA I and II (C), PD-L1 (D), and CD40 (E; pre n = 5, post n = 4). F–H, Differential expression by timepoint using scRNAseq of CD274 (F), HLA I and II genes (G), and apoptosis genes (H) on tumor cells. For scRNAseq data, comparisons denoted as significant have adjusted P < 0.05, and those without an asterisk are not significant.
FIGURE 1 from Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer
Authors: Soto Maira , Filbert Erin L. , Yang Hai , Starzinski Stephanie , Starzinski Alec , Gin Marissa , Chen Brandon , Le Phi , Li Tony , Bol Brandon , Cheung Alexander , Zhang Li , Hsu Frank J. , Ko Andrew , Fong Lawrence , Keenan Bridget P.
Published: January 2024

Treatment with sotigalimab increases immune infiltration into the TME, including T cells and myeloid cells. A, Patients were treated with sotigalimab at the initiation of the study (a), at the beginning of week 3 (b) and at week 8 (c). Chemotherapy and radiation were initiated after the second dose of sotigalimab (b). Tissue biopsies and blood samples were collected at timepoints pre-treatment, at week 3, and at surgery. Blood samples were used to assess changes to the peripheral immune system using CyTOF (1) and scRNAseq (3). Fixed tissue samples were sectioned, stained, and analyzed using MIBI (2). The tumor tissue was also dissociated into a single-cell suspension and analyzed by scRNAseq (3). B, Images from MIBI analysis from samples taken pre- and post-sotigalimab treatment for patient 04, showing markers for DNA, keratin (tumor cells) and CD45 for immune cells. The square at the center of the image indicates the 5x zoom image depicting DNA, keratin, CD3 and CD68 (representative image: Patient 04). C and D, The density of each immune cell type per tumor area (C) and the frequency out of total immune cells (D) is shown for each paired sample pre-sotigalimab (pre) and post-sotigalimab (post; n = 4). E, Uniform Manifold Approximation and Projection (UMAP) plot demonstrates all immune cell types within samples analyzed by scRNAseq (top). The abundance of cells within the UMAP is shown by density heat map for pre and post samples (bottom; pre n = 3, post n = 4). F and G, Distances between each tumor cell and the nearest immune cell are depicted (F) and quantified (G; n = 4). All statistical changes were measured by t test. *, P ≤ 0.05.
Systematic Review and Meta‐Analysis of Endovascular Therapy Effectiveness for Unruptured Saccular Intracranial Aneurysms
Authors: Pineda‐Castillo Sergio A. , Jones Evan R. , Laurence Keely A. , Thoendel Lauren R. , Cabaniss Tanner L. , Zhao Yan D. , Bohnstedt Bradley N. , Lee Chung‐Hao
Published: January 2024

Background

Currently, endovascular treatment of intracranial aneurysms is limited by low complete occlusion rates. The advent of novel endovascular technology has expanded the applicability of endovascular therapies; however, the superiority of novel embolic devices over the traditional Guglielmi detachable coils is still debated. We performed a systematic review of literature that reported the Raymond–Roy occlusion classification (RROC) rates of modern endovascular devices to determine their immediate and follow‐up occlusion effectivenesses for the treatment of unruptured saccular intracranial aneurysms.

Methods

A search was conducted using electronic databases (PUBMED, Cochrane, ClinicalTrials.gov, and Web of Science). We retrieved studies published between 2000 and 2022, reporting immediate and follow‐up RROC rates of subjects treated with different endovascular intracranial aneurysm therapies. We extracted demographic information of the treated patients and their reported angiographic RROC rates.

Results

A total of 80 studies from 15 countries were included for data extraction. The RROC rates determined from angiogram were obtained for 21 331 patients (72.5% women, pooled mean age: 58.2 [95% CI]: 56.8–59.6), harboring 22 791 aneurysms. The most frequent aneurysm locations were the internal carotid artery (46.4%, 95% CI: 41.9%–50.9%), the anterior communicating artery (26.4%, 95% CI: 22.5%–30.8%), the middle cerebral artery (24.5%, 95% CI: 19.2%–30.8%), and the basilar tip (14.4%, 95% CI: 11.3%–18.3%). The
complete
occlusion probability (RROC‐I) was analyzed for Guglielmi detachable coils, the Woven EndoBridge, and flow diverters. The RROC‐I rate was the highest in balloon‐assisted coiling (73.9%, 95% CI: 65.0%–81.2%) and the lowest in the Woven EndoBridge (27.8%, 95% CI: 13.2%–49.2%). The follow‐up RROC‐I probability was homogenous in all analyzed devices.

Conclusion

We observed that the coil‐based endovascular therapy provides acceptable rates of complete occlusion, and these rates are improved in balloon‐assisted coils. Out of the analyzed devices, the Woven EndoBridge exhibited the shortest time to achieve >90% probability of follow‐up complete occlusion (∼18 months). Overall, the Guglielmi detachable coils remain the
gold standard
for endovascular treatment of unruptured saccular aneurysms.
Patterns of Care in the Diagnosis and Management of Intracranial Atherosclerosis‐Related Large‐Vessel Occlusion: The Rescue‐LVO Survey
Authors: Siddiqui Fazeel M. , Fletcher Jeffrey J. , Elias Augusto E. , Dandapat Sudeepta , Kale Sushant P. , Heiferman Daniel , Riedy Loren , Farooqui Mudassir , Rodriguez‐Calienes Aaron , Vivanco‐Suarez Juan , Pandey Aditya S. , Ortega‐Gutierrez Santiago
Published: January 2024

Background

We aimed to determine the current practice patterns among neurointerventional practitioners frequently involved in treating intracranial atherosclerosis‐related large‐vessel occlusion (ICAS‐LVO) during mechanical thrombectomy.

Methods

We conducted an international online survey of neurointerventionalist members of the Society of Vascular and Interventional Neurology and Society of Neurointerventional Surgery. The 28‐question poll evaluated the preferences on diagnosis, treatment, and endovascular approach to ICAS‐LVO.

Results

A total of 184 individual survey responses were obtained from practicing neurointerventional physicians. Overall, 38.3% reported an incidence of 6% to 10% of ICAS‐LVO during mechanical thrombectomy. Most neurointerventionalists (91%) diagnose ICAS‐LVO after a continued or recurrent occlusion or by the presence of fixed focal stenosis after multiple mechanical thrombectomy attempts. Most respondents (86%) preferred acute treatment of ICAS‐LVO with rescue stenting (RS)±angioplasty. However, in patients who achieved recanalization with a severe fixed focal stenosis, most (58%) recommended primary medical management. The preferred medication during acute RS was intravenous antiplatelet therapy (65%), and after acute RS, it was dual oral antiplatelet therapy (65%). Fear of hemorrhagic complications (74%) was the most compelling reason not to perform RS±angioplasty. Of respondents, 24% were hesitant to randomize patients to acute RS versus medical therapy in a future randomized trial because of the lack of sensitive and specific biomarkers to diagnose ICAS‐LVO before mechanical thrombectomy treatment.

Conclusions

The findings of this survey highlight the variations in practice in the medical and endovascular management of ICAS‐LVO. In addition, it informs the situation of equipoise in the treatment decision in ICAS‐LVO, which can then be incorporated into the design of future randomized clinical trials.
Informed Down-Sampled Lexicase Selection: Identifying Productive Training Cases for Efficient Problem Solving
Authors: Boldi Ryan , Briesch Martin , Sobania Dominik , Lalejini Alexander , Helmuth Thomas , Rothlauf Franz , Ofria Charles , Spector Lee
Published: January 2024

Genetic Programming (GP) often uses large training sets and requires all individuals to be evaluated on all training cases during selection. Random down-sampled lexicase selection evaluates individuals on only a random subset of the training cases, allowing for more individuals to be explored with the same number of program executions. However, sampling randomly can exclude important cases from the down-sample for a number of generations, while cases that measure the same behavior (synonymous cases) may be overused. In this work, we introduce Informed Down-Sampled Lexicase Selection. This method leverages population statistics to build down-samples that contain more distinct and therefore informative training cases. Through an empirical investigation across two different GP systems (PushGP and Grammar-Guided GP), we find that informed down-sampling significantly outperforms random down-sampling on a set of contemporary program synthesis benchmark problems. Through an analysis of the created down-samples, we find that important training cases are included in the down-sample consistently across independent evolutionary runs and systems. We hypothesize that this improvement can be attributed to the ability of Informed Down-Sampled Lexicase Selection to maintain more specialist individuals over the course of evolution, while still benefiting from reduced per-evaluation costs.
Bian Que’s Twelve Channels?
Authors: Li Jianmin , Yang Dolly
Published: January 2024

The name Bian Que, like that of the Yellow Emperor (Huangdi), has reverberated through the development of Chinese medicine since the time of the Warring States. The discovery of a human figurine showing channels and strategic points, together with a number of medical texts, during the excavation of the Laoguanshan Han tomb in Chengdu, Sichuan, in 2012–13 has reignited controversies about whether it is correct to speak of a specific Bian Que school, or whether, as this paper argues, these texts were written by the Han physicians who used Bian Que as a mouthpiece to record their own medical expositions. The paper begins by examining the main characteristics of the Laoguanshan human figurine and discusses what this excavated artifact reveals about the early history of Chinese medicine. It questions the existence of the so-called Bian Que school and, obliquely, the suggested relationships between the school and the figurine and between the school and medical texts found in the same tomb. The paper shows how diverse the disjointed knowledge of medicine was and that the idea of a “school” does not accurately reflect what was happening in the transmission of medical knowledge during the Warring States, Qin, and Han periods (475 BCE–220 CE).
Looms of Life
Authors: Lo Vivienne
Published: January 2024

The classics of Chinese medicine are redolent with allusions to weaving as they describe a new imperial anatomy and physiology of the medical body. The superior physician in the Yellow Emperor’s corpus manipulated ji 機, the trigger mechanisms at strategic points on the surface of the body, which provided remote relief from the symptoms of illness. Through stimulating these points, medical practice with needle and moxibustion could control the many spirits that inhabited the body, weaving them into a numinous fabric. This paper explores the spatiotemporal geographies of meaning expressed in the manuscripts and artifacts excavated at the Laoguanshan tomb sites. In particular, an analysis of the medical texts, models of mechanical pattern shaft looms, and a tiny lacquered medical figurine recovered there suggest that local translational knowledge transfer between medicine, weaving, and water technologies occurred in the upper reaches of the Yangzi Valley. The resulting innovations were at the heart of a new imperial Chinese medicine.
Preliminary Translation of the Tianhui Laoguanshan Manuscript on Piercing as Therapy
Authors: Lo Vivienne
Published: January 2024

This translation forms a triptych with the following two articles in this double special issue: Gu Man, Zhou Qi, and Liu Changhua, “Techniques for Piercing the Mai Recorded in the Laoguanshan Han Tomb Bamboo Slips” and Zhou Qi, “Research on the Lacquered Channel Figurine Excavated from a Han Tomb in Tianhui.” Here you can read an entire Tianhui Laoguanshan text in translation on the subject of therapeutic piercing. The contribution by Gu, Zhou, and Liu positions the therapy in relation to ideas and techniques in other manuscript texts contemporary to the one translated here and the printed classics of Chinese medicine. These articles are accompanied by opinion pieces written by current practitioners of Chinese medicine as expert witnesses to the evolution of the techniques and their relevance, or not, to modern practice. Together, we present an interdisciplinary analysis that we hope will engage the reader actively in the process of multifocal interpretation. The text here is introduced by a translator’s introduction that reflects broadly on the unique challenges of rendering this fascinating work into English.
Observed 10–20-Day Deep-Current Variability at 5°N, 90.5°E in the Eastern Indian Ocean
Authors: Wang Jinghong , Shu Yeqiang , Wang Dongxiao , Chen Ju , Yang Yang , Wang Weiqiang , Guo Binbin , Huang Ke , He Yunkai
Published: January 2024

In the eastern off-equatorial Indian Ocean, deep current intraseasonal variability within a typical period of 10–20 days was revealed by a mooring at 5°N, 90.5°E, accounting for over 50% of the total bottom subtidal velocity variability. The 10–20-day oscillations were more energetic in the cross-isobathic direction (STD = 3.02 cm s−1) than those in the along-isobathic direction (STD = 1.50 cm s−1). The oscillations were interpreted as topographic Rossby waves (TRWs) because they satisfied the TRWs dispersion relation that considered the smaller Coriolis parameter and stronger β effect at low latitude. Further analysis indicated significant vertical coupling between the deep cross-slope oscillations and cross-isobathic 10–20-day perturbations at the depth of 300–950 m. The 10–20-day TRWs were generated by cross-isobathic motions under the potential vorticity conservation adjustment. The Mercator Ocean output reproduced the generation of kinetic energy (KE) of deep current variability. The associated diagnostic analysis of multiscale energetics showed that the KE of TRWs was mainly supplied by vertical pressure work. In the seamount region (2°–10°N, 89°–92°E), vertical and horizontal pressure works were identified to be the dominant energy source (contributing to 94% of the total KE source) and sink (contributing to 98% of the total KE sink) of the deep current variability, transporting energy downward and redistributing energy horizontally, respectively.
An Assessment of Dropsonde Sampling Strategies for Atmospheric River Reconnaissance
Authors: Zheng Minghua , Torn Ryan , Delle Monache Luca , Doyle James , Ralph Fred Martin , Tallapragada Vijay , Davis Christopher , Steinhoff Daniel , Wu Xingren , Wilson Anna , Papadopoulos Caroline , Mulrooney Patrick
Published: January 2024

During a 6-day intensive observing period in January 2021, Atmospheric River Reconnaissance (AR Recon) aircraft sampled a series of atmospheric rivers (ARs) over the northeastern Pacific that caused heavy precipitation over coastal California and the Sierra Nevada. Using these observations, data denial experiments were conducted with a regional modeling and data assimilation system to explore the impacts of research flight frequency and spatial resolution of dropsondes on model analyses and forecasts. Results indicate that dropsondes significantly improve the representation of ARs in the model analyses and positively impact the forecast skill of ARs and quantitative precipitation forecasts (QPF), particularly for lead times > 1 day. Both reduced mission frequency and reduced dropsonde horizontal resolution degrade forecast skill. On the other hand, experiments that assimilated only G-IV data and experiments that assimilated both G-IV and C-130 data show better forecast skill than experiments that only assimilated C-130 data, suggesting that the additional information provided by G-IV data is necessary for improving forecast skill. Although this is a case study, the 6-day period studied encompassed multiple AR events that are representative of typical AR behavior. Therefore, the results indicate that future operational AR Recon missions incorporate daily mission or back-to-back flights, maintain current dropsonde spacing, support high-resolution data transfer capacity on the C-130s, and utilize G-IV aircraft in addition to C-130s.
Is There a Relationship Between Birth Quartile and Vertical Jump Performance Among Young Male Elite Volleyball Athletes?
Authors: Castro Henrique de Oliveira , Lima Ricardo Franco , Figueiredo Lucas Savassi , de Oliveira Vivian , Alexandre Peyré-Tartaruga Leonardo , Kruel Luiz Fernando Martins , Laporta Lorenzo Iop , Teixeira Costa Gustavo De Conti , Berriel Guilherme Pereira
Published: January 2024

Vertical jump is an important skill that influences volleyball performance. In this study, we analyzed the relationship between vertical jump performance and birth quartile of Brazilian male youth volleyball players. We calculated chi-square goodness-of-fit tests to compare the athletes’ birthdate distributions in quarters of their birth years (Q1, Q2, Q3, and Q4) according to player age categories (U17, U18, U19, and U21). We calculated one-way ANOVAs to compare spike jump and block jump heights of players born in different quarters of the same year. Overall, we found a relative age effect (i.e., more players with birth dates early in the birth year) in U17 ( p < .001), U18 ( p < .001), U19 ( p < .001), and U21 ( p = .04). Regarding vertical jump performance, U18 athletes born in Q2 reached higher spike jump heights ( p = .006) and block jump heights ( p = .002) than athletes born in Q4, and U19 athletes born in Q1 reached higher block jump heights than athletes born in Q3 ( p = .049). There were no significant differences in vertical jump performance across birth quartiles among U17 and U21 athletes. Thus, a relative age effect was present in all age categories but not always reflected in vertical jump performance. Volleyball coaches and policymakers are still advised to employ strategies to ensure fairer opportunities for players born later in the year of their eligibility dates, as we found RAE to be sometimes, but not always, related to higher spike or block jump heights even among these older adolescents and young adult athletes.
Documentation of the Patient Characteristics Morbid Obesity and Bariatric Surgery in the Hospital Information System and the Influence on the Number of Medication-Related Problems
Authors: Kingma Jurjen S. , Brenkman Iris A. M. , van den Broek Marcel P. H. , van den Bemt Patricia M. L.A. , Janssen Karin , Knibbe Catherijne A. J. , Burgers Desirée M. T.
Published: January 2024

Background:

As a result of pharmacokinetic changes, individuals with morbid obesity and/or with bariatric surgery may require dose adjustments, additional monitoring or medication should be avoided. Clinical decision support (CDS) may provide automated alerts enabling correct prescribing but requires documentation of these patient characteristics in the Hospital Information System (HIS) to prevent medication-related problems (MRPs).

Objective:

The primary objective is to determine the proportion of patients with documentation of the patient characteristics morbid obesity and bariatric surgery in the HIS. The secondary objective is to compare the proportion of patients with an MRP in the group with versus without documentation. Also, the type and severity of MRPs and the medication involved are determined.

Methods:

A prospective cohort study was performed. Patients admitted to the hospital were identified as morbidly obese and/or with bariatric surgery. In the identified patients, the proportion of patients with documentation of the patient characteristics in the HIS was evaluated as primary outcome. Subsequently, patient records were reviewed for MRPs, which were categorized and associated medication was registered. For the primary objective, descriptive statistics was used. For the secondary outcome, the Fisher’s exact test was used.

Results:

In 43 (21.4%, 95% confidence interval [CI]: 15.7%-27.1%) of 201 included patient (113 morbid obesity, 70 bariatric surgery and 18 both), the patient characteristics were documented. An MRP occurred in 2.3% versus 13.9% ( P = 0.032) of patients with and without documentation, respectively. The most common MRP was underdosing in morbid obesity, while in patients with bariatric surgery it was prescription of contra-indicated medication.

Conclusion and relevance:

The proportion of patients with documentation of the patient characteristics bariatric surgery and/or morbid obesity in the HIS is low, which appears to be associated with more MRPs. To improve medication safety, it is important to document these patient characteristics.
Diversity and Dynamics in Care Networks of Older Americans
Authors: Lin Zhiyong
Published: January 2024

Despite growing interest in exploring caregiving alternatives beyond traditional models, limited research has focused on the diverse care networks that provide assistance to older adults. The aim of this study is to illuminate the complexity of older adults’ care networks by developing a typology that considers care from various sources. Using latent class analysis on longitudinal data from the National Health and Aging Trends Study, the authors identify five distinct care network types: spousal care, care exclusively from children, care from both children and other sources, self-care with assistive technology, and care exclusively from nonfamily sources. Further analysis, including multinomial logistic regression and latent transition analysis, reveals that when a spouse is available, older adults, particularly older men, are more likely to rely on spousal care. However, in cases in which spouses and/or children are unavailable, older adults are inclined to turn to diverse care networks involving nontraditional caregivers or resort to self-care using assistive technologies. Additionally, declining health conditions are associated with a higher likelihood of receiving care from more varied care networks. This underscores the evolving nature of care arrangements in response to changing family structures and health needs.
Matched control analysis suggests that R-CHOP followed by (R)-ICE may improve outcome in non-GCB DLBCL compared with R-CHOP
Authors: Bantilan Kurt S. , Smith Alexandra N. , Maurer Matthew J. , Teruya-Feldstein Julie , Matasar Matthew J. , Moskowitz Alison J. , Straus David J. , Noy Ariela , Palomba M. Lia , Horwitz Steven M. , Hamlin Paul A. , Portlock Carol S. , Cerhan James R. , Habermann Thomas M. , Salles Gilles A. , Nowakowski Grzegorz S. , Moskowitz Craig H. , Zelenetz Andrew D.
Published: January 2024

Rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) is considered the standard-of-care for patients with advanced-stage diffuse large B-cell lymphoma (DLBCL), despite findings that patients with nongerminal center B-cell like (non-GCB) have significantly worse outcome with this regimen. We evaluated the prognostic significance of baseline risk factors, including cell of origin (COO) classified by the Hans algorithm, within an alternative chemoimmunotherapy program. At Memorial Sloan Kettering Cancer Center (MSK), 151 patients with DLBCL received sequential R-CHOP induction and (R)-ICE (rituximab, ifosfamide, carboplatin, and etoposide) consolidation. Outcome analysis based on COO was validated with a propensity score–matched cohort treated with R-CHOP from the Mayo Clinic component of the Molecular Epidemiology Resource (MER). Among the patients with GCB (n = 69) and non-GCB (n = 69) at MSK, event-free survival (EFS) of non-GCB was superior to that of GCB (hazard ratio [HR], 0.53; 95% confidence interval [CI], 0.29-0.98). Overall survival (OS) demonstrated an association in the same direction but was not statistically significant (HR, 0.68; 95% CI, 0.33-1.42). Propensity score–matched patients from MSK (n = 108) demonstrated a small attenuation in the HRs for EFS (HR, 0.57; 95% CI, 0.27-1.18) and OS (HR, 0.76; 95% CI, 0.33-1.79) and were no longer statistically significant. In contrast, the matched MER cohort (n = 108) demonstrated an EFS association (HR, 1.17; 95% CI, 0.70-1.95) and OS association (HR, 1.13; 95% CI, 0.64-2.00) in the opposite direction, but were also not statistically significant. R-CHOP induction and (R)-ICE consolidation may overcome the negative prognostic impact of the non-GCB phenotype, per the Hans algorithm, and can be preferentially selected for this population. This trial was registered at www.ClinicalTrials.gov as #NCT00039195 and #NCT00712582.
Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae
Authors: Liu Daliang , Zhang Zhihan , Hao Yanlin , Li Mengge , Yu Houlin , Zhang Xingruo , Mi Haoyang , Cheng Lin , Zhao Yiyong
Published: January 2024

Background

Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history.

Result

We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae.

Conclusions

We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.
Intersectional race and gender disparities in kidney transplant access in the United States: a scoping review
Authors: Gompers Annika , Rossi Ana , Harding Jessica L
Published: January 2024

Background

Gender and racial disparities in kidney transplant access are well established, however how gender and race interact to shape access to kidney transplant is less clear. Therefore, we examined existing literature to assess what is known about the potential interaction of gender and race and the impact on access to kidney transplantation in the US.

Methods

Following PRISMA guidelines, we conducted a scoping review and included quantitative and qualitative studies published in English between 1990 and May 31, 2023 among adult end-stage kidney disease patients in the US. All studies reported on access to specific transplant steps or perceived barriers to transplant access in gender and race subgroups, and the intersection between the two. We narratively synthesized findings across studies.

Results

Fourteen studies met inclusion criteria and included outcomes of referral (n = 4, 29%), evaluation (n = 2, 14%), waitlisting (n = 4, 29%), transplantation (n = 5, 36%), provider perceptions of patient transplant candidacy (n = 3, 21%), and patient preferences and requests for a living donor (n = 5, 36%). Overall, we found that White men have the greatest access at all steps of the transplant process, from referral to eventual living or deceased donor transplantation. In contrast, women from racial or ethnic minorities tend to have the lowest access to kidney transplant, in particular living donor transplant, though this was not consistent across all studies.

Conclusions

Examining how racism and sexism interact to shape kidney transplant access should be investigated in future research, in order to ultimately shape policies and interventions to improve equity.
Screening, identifying, and treating chronic kidney disease: why, who, when, how, and what?
Authors: Farrell Douglas R. , Vassalotti Joseph A.
Published: January 2024

1 in 7 American adults have chronic kidney disease (CKD); a disease that increases risk for CKD progression, cardiovascular events, and mortality. Currently, the US Preventative Services Task Force does not have a screening recommendation, though evidence suggests that screening can prevent progression and is cost-effective.

Populations at risk for CKD, such as those with hypertension, diabetes, and age greater than 50 years should be targeted for screening. CKD is diagnosed and risk stratified with estimated glomerular filtration rate utilizing serum creatinine and measuring urine albumin-to-creatinine ratio. Once identified, CKD is staged according to C-G-A classification, and managed with lifestyle modification, interdisciplinary care and the recently expanding repertoire of pharmacotherapy which includes angiotensin converting enzyme inhibitors or angiotensin-II receptor blockers, sodium-glucose-cotransporter-2 inhibitors, and mineralocorticorticoid receptor antagonists.

In this paper, we present the why, who, when, how, and what of CKD screening.
Colonoscopy screening for colorectal cancer in Egypt: a nationwide cross-sectional study
Authors: Allam Abdallah R. , Elsayed Mostafa A. , Daghash Ibrahim Tawfiq , Abdelaziz Ali M. , Mostafa Omnia M. , Sabra Hamdy Khaled , Eldaboush Ahmed Monib , Ahmed Noor Maged Badrawy , Elweza Rawan Tarek , Adwy Enas Sherif , Hammad Abdelrahman Elbendary , Kabbash Ibrahim Ali , Allam Ahmed Hafez , Bahbah Ammar Ayman , Ewis Marwa Ibrahim , Mohamed Shawqi Mohamed , Behery Mostafa B. , Mohamed El-Said Yara , Radwan Ahmed Eid , KhallafAllah Mahmoud T. , Aboshady Omar Ali , Gouda Mohamed A.
Published: January 2024

Background

Current guidelines advocate for colorectal cancer (CRC) screening in adults who are at risk by using direct visualization methods such as colonoscopy. However, in Egypt, there is a paucity of data regarding the current practice of colonoscopy screening. Moreover, more information is needed about the knowledge and attitudes of potential participants regarding the procedure and possible barriers that can limit their participation.

Methods

We conducted a nationwide cross-sectional study using an interview-based survey of patients aged 45 years or above who presented to outpatient clinics of nine university hospitals throughout Egypt. Participants were surveyed to assess their compliance with CRC colonoscopy screening guidelines, their knowledge of and attitude towards colonoscopy screening, and their perspective on potential barriers to colonoscopy screening.

Results

A total of 1,453 participants responded to our survey in the nine study centers. Only a minority of participants (2.3%) were referred for CRC screening. Referral rates were higher among those who knew someone with a history of CRC (5.3% vs 1.5%, p < 0.001) or had a discussion with their physician about CRC (25.8% vs 0.7%, p < 0.001). Few responders (3.2%) had good knowledge regarding CRC screening. After introducing the concept of CRC screening to all participants, most patients (66.7%) showed a positive attitude towards having the procedure. Financial burden and fear of results were the two most frequently cited barriers to undergoing CRC screening (81.1%; and 60.1%, respecteively).

Conclusions

Despite the positive attitude, there is insufficient knowledge about CRC screening among eligible participants in Egypt. This has probably contributed to low compliance with current CRC screening guidelines and needs to be addressed at the national level.
The evaluation of bariatric surgery effect on cardiac structure and function using transthoracic echocardiography: a cohort study
Authors: Abtahi Firoozeh , Atashbarg Malek , Rahmanian Mahdi , Moeinvaziri Nader , Bazrafshan Mehdi , Bazrafshan Hanieh , Moammer Farzaneh , Bazroodi Helia , Zolghadrasli Abdolali , Bazrafshan drissi Hamed
Published: January 2024

Background

Obesity is a pathology and a leading cause of death worldwide. Obesity can harm multiple organs, including the heart. In this study, we aim to investigate the effect of bariatric surgery and following weight loss on cardiac structure and functions using echocardiography parameters in patients with morbid obesity.

Methods

In this cohort study, 30 patients older than 18 with BMI > 40 or BMI > 35 and comorbidity between March 2020 to March 2021 were studied. The patients underwent transthoracic echocardiography before and after six months of the bariatric surgery.

Results

In total, 30 patients (28 women, 93.3%) with a mean age of 38.70 ± 9.19 were studied. Nine (30%) were diabetic, and 9 (30%) had hypertension. After six months of bariatric surgery, all physical measurements, including weight, Body mass index, and Body surface area, decreased significantly (p < 0.001). After bariatric surgery, all parameters regarding left ventricular morphology, including left ventricular mass, interventricular septal thickness, left ventricular posterior wall thickness, left ventricular end-systolic diameter, and left ventricular end-diastolic diameter, improved significantly (p < 0.001). Also, LVEF rose post-bariatric surgery (p < 0.001). TAPSE parameter indicating right ventricular function also improved (p < 0.001). Right ventricular diameter, left atrium volume, and mitral inflow E/e’ decreased significantly (p < 0.001).

Conclusion

Systolic and diastolic parameters refine significantly after bariatric surgery in patients with obesity. Bariatric surgery lead to significant cardiac structure and function improvement.
Characterization, modeling, and anticancer activity of L.arginase production from marine Bacillus licheniformis OF2
Authors: Selim Manal S. , Mounier Marwa M. , Abdelhamid Sayeda A. , Hamed Ahmed Abdelghani , Abo Elsoud Mostafa M. , Mohamed Sahar S.
Published: January 2024

Background

L-arginase, is a powerful anticancer that hydrolyzes L-arginine to L-ornithine and urea. This enzyme is widely distributed and expressed in organisms like plants, fungi, however very scarce from bacteria. Our study is based on isolating, purifying, and screening the marine bacteria that can produce arginase.

Results

The highest arginase producing bacteria will be identified by using microbiological and molecular biology methods as Bacillus licheniformis OF2. Characterization of arginase is the objective of this study. The activity of enzyme was screened, and estimated beside partial sequencing of arginase gene was analyzed. In silico homology modeling was applied to generate the protein's 3D structure, and COACH and COFACTOR were applied to determine the protein's binding sites and biological annotations based on the I-TASSER structure prediction. The purified enzyme was undergone an in vitro anticancer test.

Conclusions

L-arginase demonstrated more strong anti-cancer cells with an IC50 of 21.4 ug/ml in a dose-dependent manner. L-arginase underwent another investigation for its impact on the caspase 7 and BCL2 family of proteins (BCL2, Bax, and Bax/Bcl2). Through cell arrest in the G1/S phase, L-arginase signals the apoptotic cascade, which is supported by a flow cytometry analysis of cell cycle phases.
Alterations and correlations in dental plaque microbial communities and metabolome characteristics in patients with caries, periodontitis, and comorbid diseases
Authors: Wang Ying , Yang Fei , Wang Yuan , Deng Shuli , Zhu Rui
Published: January 2024

Backgrounds

The pathogenic microorganisms and clinical manifestations of caries and periodontitis are different, caries and periodontitis are usually discussed separately, and the relationship between them is ignored. Clinically, patients prone to dental caries generally have a healthier periodontal status, whereas patients with periodontitis generally have a lower incidence of dental caries. The relationship between dental caries and periodontitis remains unclear.

Objectives

This study aimed to explain the clinical phenomenon of antagonism between dental caries and periodontitis by exploring the ecological chain and bacterial interactions in dental caries, periodontitis, and other comorbid diseases.

Methods

The dental plaque microbiomes of 30 patients with oral diseases (10 each with caries, periodontitis, and comorbid diseases) were sequenced and analysed using 16 S rRNA gene sequencing. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) database was used for a differential functional analysis of dental plaque microbial communities in caries, periodontitis, and comorbid diseases.

Results

The coinfection group had the greatest bacterial richness in dental plaque. The principal coordinate analysis showed that caries and periodontitis were separate from each other, and comorbid diseases were located at the overlap of caries and periodontitis, with most of them being periodontitis. Simultaneously, we compared the microbiomes with significant differences among the three groups and the correlations between the microbiome samples. In addition, KEGG pathway analysis revealed significant differences in functional changes among the three groups.

Conclusions

This study revealed the composition of the dental plaque microbial communities in caries, periodontitis, and comorbidities and the differences among the three. Additionally, we identified a possible antagonism between periodontitis and caries. We identified a new treatment strategy for the prediction and diagnosis of caries and periodontitis.