bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation analysis of laboratory indicators, genetic abnormalities and staging in patients with newly diagnosed multiple myeloma
Authors: Li Zhenrui , Zhao Huihan , Li Zhongqing , He Yu
Published: November 2024

To explore the correlation between immune status, genetic profile, laboratory parameters, and staging in patients with newly diagnosed multiple myeloma (NDMM) and to investigate the clinical characteristics of these patients along with their associated risk factors. The clinical data of 135 patients with multiple myeloma (MM) admitted to the First Affiliated Hospital of Guangxi Medical University between March 2020 and December 2023 were retrospectively collected. These data were systematically organized to evaluate the staging status of patients, including the Durie-Salmon, International Staging System, Revised International Staging System, and mSMART 3.0 staging systems. Additionally, the study included analysis of peripheral blood T-lymphocyte subpopulations and Fluorescence In Situ Hybridization results. Laboratory indices were collected at the initial diagnosis of patients with MM prior to any treatment. These data were subsequently analyzed to ascertain their significance in staging patients with multiple myeloma. Among 135 patients with MM, N-terminal pro-brain natriuretic peptide (NT-proBNP) and lambda light chain (λ light chain) levels were higher in patients with abnormal kidney function (P < .05). NT-proBNP and λ light chain levels can predict abnormal renal function in patients with NDMM. The λ light chain levels were significantly higher in Zhuang patients than in Han patients (P < .05). Patients with high staging differed in total T cell percentages, CD8+ cell percentages, T cells, CD3+/CD4-/CD8- double-negative cell percentages, CD8+T cells, age, NT-proBNP, and M protein levels (P < .05). In addition, M protein levels and age were positively correlated with CD4+T cells and negatively correlated with CD8+T cells (P < .05). CD8+ T cells, age, NT-proBNP, M protein level, and cytogenetic abnormalities represent distinct aspects of immune status, tumor load, and cytogenetic status at the initial diagnosis of patients. These indices are closely associated with the clinical stage of patients and can be combined to assess the clinical stage of multiple myeloma patients after admission to the hospital. Additionally, NT-proBNP and λ light chain levels play a role in predicting abnormal renal function in patients with NDMM.
Exploring the correlation between knee osteoarthritis and musculoskeletal ultrasound manifestations based on changes in traditional Chinese medical syndrome types
Authors: Qiang Qun , Zhou Mingwang , Lv YongXin , Wang Weibin , Liu Jia , Wu Jinqiu , Chen Xiaofei , Yu Huan
Published: November 2024

This study explores the correlation between knee osteoarthritis and musculoskeletal ultrasound manifestations based on changes in traditional Chinese medicine (TCM) syndrome types. The study enrolled 104 patients with knee osteoarthritis admitted to the Gansu Provincial Hospital of TCM between January 2019 and January 2021. According to the principle of syndrome differentiation and treatment in TCM, the patients were divided into wind-cold-damp obstruction (n = 17), damp-heat accumulation (n = 22), qi-stagnation and blood stasis (n = 31), and liver and kidney deficiency (n = 34) types. The degrees of cartilage injury, synovial hyperplasia, synovial blood flow, and joint effusion in patients with different TCM syndrome types were compared using ultrasound. There were no significant differences in the degree of cartilage injury or synovial hyperplasia among the 4 TCM syndrome types (P > .05). The proportion of grade III blood flow signals in the liver and kidney deficiency group was lower than that in the damp-heat accumulation and wind-cold-damp obstruction groups, and the proportion of no blood flow and grade I blood flow signals were higher than those in the damp-heat accumulation and wind-cold-damp obstruction groups (P < .05). The proportion of non-joint effusion in the liver and kidney deficiency and wind-cold-damp obstruction groups was higher than that in the damp-heat accumulation and qi-stagnation and blood stasis groups (P < .05), and the proportion of grade I effusion in the damp-heat accumulation group was higher than that in the liver and kidney deficiency group (P < .05). Musculoskeletal ultrasound manifestations of knee osteoarthritis are related to TCM syndrome differentiation and classification and can provide a reference for TCM syndrome differentiation and treatment of knee osteoarthritis.
The correlation between the number of endothelial progenitor cells in the peripheral blood and abdominal aortic aneurysm
Authors: Zhang Jinlong , Zheng Lei
Published: November 2024

This study was to investigate the correlation between the number of endothelial progenitor cells (EPCs) in peripheral blood and abdominal aortic aneurysm (AAA), and provide a potential biomarker for the diagnosis and treatment monitoring of AAA. Patients with AAA evaluated in the First Affiliated Hospital of Soochow University from June 2018 to October 2018 (n = 7) were included in this study. All patients were confirmed as AAA by vascular CTA with an increase of more than 50% of the abdominal aortic diameter. Patients (n = 7) with normal abdominal aorta diameter were included as control group with matching age, sex, blood pressure, and blood sugar concentration between experimental and control groups. Mononuclear cells were collected by density gradient centrifugation, stained by CD34-FITC and CD309-PE antibodies, and analyzed by flow cytometry. The number of EPCs in the peripheral blood of patients with AAA (0.874 ± 0.129‰) was significantly lower than that in the control group (1.420 ± 0.289‰) (P < .01). The number of EPCs may be used as a potential biomarker for the diagnosis and monitoring of AAA following treatment.
Association between severity of pancreatic exocrine insufficiency and computed tomography-based morphological severity in patients with chronic pancreatitis
Authors: Lee Jae Min , Lee Sang Hyub , Choi Young Hoon , Han Sung Yong , Jo Jung Hyun , Choe Jung Wan , Kim Eui Joo , Jang Dong Kee , Jung Min Kyu
Published: November 2024

The association between pancreatic exocrine insufficiency (PEI) and morphologic findings in chronic pancreatitis has not yet been fully studied. Thus, the aim of this study was to investigate the correlation between PEI severity and computed tomography (CT)-based morphological severity in patients with chronic pancreatitis. This nationwide survey included 180 Korean participants with chronic pancreatitis aged 18 years or older between January 2018 and December 2021. PEI severity was measured by the PEI questionnaire (PEI-Q). Morphological severity was measured using a CT-based scoring system, which included pancreatic duct caliber, pancreatic duct stricture or intraductal obstructing calculus, pancreatic atrophy, and pancreatic calcification. In addition, 35 patients who received pancreatic enzyme replacement therapy (PERT) were evaluated by PEI-Q to determine whether PEI improved after PERT. PEI severity was normal (n = 89), mild (n = 69), moderate (n = 14), or severe (n = 8). Severities of pancreatic duct caliber and pancreatic duct stricture or intraductal obstructing calculus had small but significant associations with PEI severity (Cramer V = 0.121 and 0.141, respectively). Severities of pancreatic atrophy and pancreatic calcification were not significantly associated with PEI severity. PEI severity showed a significant improvement after PERT (P < .001). In conclusion, PEI severity had significant associations with CT-based morphological severities, including severities of pancreatic duct caliber and pancreatic duct stricture or intraductal obstructing calculus. In addition, PEI-Q could be a useful indicator for evaluating the therapeutic effect of PERT in clinical practice.
The correlation between rapid eye movement sleep and nocturnal hypertension in patients with obstructive sleep apnea: A retrospective study
Authors: Zhang Wenjing , Tu Chunlin , Yu Yanfang
Published: November 2024

Obstructive sleep apnea (OSA) is a respiratory disease closely associated with hypertension and heart disease. This study aimed to evaluate the diagnostic value of rapid eye movement (REM) sleep during nocturnal hypertension in OSA patients. We selected 194 patients who underwent polysomnography (PSG) at the Respiratory and Critical Care Medicine Department of Jiading District Central Hospital in Shanghai between January 2021 and August 2023. All patients were assigned to the hypertension and normal blood pressure groups, and the differences between the 2 groups were compared. This study included 194 patients (137 with nocturnal hypertension and 57 with normal nocturnal blood pressure). The proportion of male sex, body mass index, apnea–hypopnea index (AHI), REM sleep duration, percentage of REM sleep duration to total sleep duration, REM-AHI, nonrapid eye movement-AHI, oxygen desaturation index (ODI), REM-ODI, nonrapid eye movement-ODI, and average nighttime heart rate during sleep were higher in the hypertension group than in the normal blood pressure group, and the lowest oxygen saturation was lower than that in the normal blood pressure group (P < .05). Logistic regression analysis showed that REM-AHI was an independent risk factor for nocturnal hypertension (adjusted odds ratio, 1.048; 95% confidence interval, 1.011–1.086; P = .01). Receiver operating characteristic curve analysis showed that the REM-AHI had an area under the curve of 0.721 (95% confidence interval, 0.641–0.801; P < .001) for diagnosing nocturnal hypertension in patients with OSA, with a maximum Youden index of 0.379. The optimal critical value of the REM-AHI was 23.6 times/h, with a sensitivity of 64.2% and specificity of 73.7%. REM sleep is closely related to nocturnal hypertension, and patients with OSA are more prone to cardiovascular events.
Comprehensive analysis of rheumatic diseases, comorbidities, and mortality in geriatric population: Real-world data of 515 patients in a single rheumatology clinic
Authors: Tekeoglu Senem
Published: November 2024

Rheumatic diseases present unique challenges in the elderly, with changes in the immune system contributing to varied clinical presentations. More individuals are now living with chronic diseases due to greater life expectancy, but there is a lack of real-world data about rheumatic diseases and comorbidities in older people. This study aimed to investigate disease types, comorbidities, treatments, and mortality in geriatric patients in comparison to non-geriatric patients at a rheumatology clinic. This retrospective observational cohort study reviewed the medical records of 2610 patients from January 2021 to January 2024 at 2 branches of a private hospital’s rheumatology clinics. Demographic information and data on rheumatic diseases, noninflammatory conditions, treatments, comorbidities, and mortality were collected, and geriatric patients were compared to non-geriatric patients. Geriatric patients (n = 515) had a significantly higher prevalence of rheumatoid arthritis (50.6% vs 28.8%, P < .001), polymyalgia rheumatica (11.1% vs 0.2%, P < .001), and crystal arthritis (19.6% vs 8.8%, P < .001), with more frequent geriatric-onset cases. Osteoarthritis was also more prevalent in geriatric patients (51.2% vs 11.3%, P < .001), while fibromyalgia was more common in the non-geriatric group (15.9% vs 4.1%, P < .001). Geriatric patients experienced higher rates of comorbidities, including hypertension (72.4% vs 17.8%, P < .001), diabetes (33.6% vs 12.1%, P < .001), and osteoporosis (64.9% vs 35.4%, P < .001). These patients used more corticosteroids (74.5% vs 44%, P < .001), and conventional synthetic disease-modifying antirheumatic drugs (62.4% vs 49.4%, P < .001) but fewer biological disease-modifying antirheumatic drugs (9.2% vs 23.1%, P < .001). Mortality rates were significantly higher in geriatric patients (6% vs 0.3%), with cancer (P = .001), ischemic heart disease (P = .04), heart failure (P = .01), chronic kidney disease (P = .02), and interstitial lung disease (P = .01) being associated with increased mortality. Geriatric rheumatology should receive greater focus in future research to help address the anticipated increases in demand and to develop tailored management strategies for elderly patients with rheumatic diseases and comorbidities.
Spermatic cord myxoma: A rare case report
Authors: Wang XuHui , Gao Xinghua , Zhang LongYang
Published: November 2024

Rationale:

Spermatic cord myxomas are rare benign tumors, typically characterized by the production of mucopolysaccharides. These tumors are infrequently found in the urinary system, making this case noteworthy.

Patient concerns:

A 55-year-old male presented with a painless swelling on the right side of his scrotum, which had persisted for over 3 months. There were no associated symptoms, and the patient had no significant medical history.

Diagnoses:

Initial diagnostic workup included physical examination, ultrasonography, and CT scans, which revealed a 2 cm cystic nodule near the right spermatic vein. Postoperative histopathology confirmed the diagnosis of myxoma.

Interventions:

The patient underwent laparoscopic high ligation of the left spermatic vein and excision of the right spermatic sheath cyst. The surgery was successful, with the cyst being completely removed.

Outcomes:

Postoperative recovery was uneventful, and histopathological examination confirmed the benign nature of the tumor. Follow-up was advised to monitor for any recurrence.

Lessons:

Although rare, spermatic cord myxomas should be considered in the differential diagnosis of scrotal masses. Surgical excision is both diagnostic and therapeutic, providing a favorable prognosis with minimal risk of recurrence.
Continuous nursing care improving outcomes of patients after percutaneous coronary intervention
Authors: Zhang Yuan-yuan , Cui Li-Xia , Zhang Ling , Wang You
Published: November 2024

Percutaneous coronary intervention (PCI) is an effective method for the treatment of coronary heart disease. Cardiac rehabilitation and continuous nursing management after discharge are the key to ensure the quality of treatment and the quality of life of patients. This study aimed to explore the significance of WeChat platform in continuous care after PCI. We collected the clinical data of 90 PCI patients in 2 centers from January 2020 to July 2023, and divided the patients into 2 groups: the continuous nursing care group based on the WeChat platform and the control group. Continuous nursing care was implemented immediately after discharge. After 1-year follow-up, we compared the outcomes of the 2 groups, including postoperative complications, lifestyle changes and psychological status. There were no heart-related postoperative complications in either group. The incidence of vagal reflex was significantly decreased in the continuous nursing group (P = .042). The improvement of life style, such as smoking cessation (P = .001) and alcohol withdrawal (P = .003), was significantly better than that of the control group. The continuous nursing group was better than the control group in improving psychological status based on the Hamilton’s depression scale. Continuous nursing care based on WeChat platform could reduce the incidence of complications of patients after PCI, alleviate patients’ depression, and improve patients’ quality of life.
Association between substance use disorders and sustained viral suppression: a longitudinal analysis among people with HIV in South Carolina
Authors: He Buwei , Chen Shujie , Yang Xueying , Olatosi Bankole , Weissman Sharon , Li Xiaoming , Zhang Jiajia
Published: November 2024

Objectives:

Substance use disorders (SUDs) are a significant public health concern across the United States and may pose a risk to achieving sustained viral suppression (SVS) in people with HIV (PWH). This study aims to examine the association between SUDs and SVS among PWH.

Design:

Using electronic health records from the South Carolina Department of Health, we conducted a retrospective study of adults diagnosed with HIV between January 2006 and December 2019.

Methods:

The impact of SUDs on SVS was assessed using generalized linear mixed model. Potential confounders included age, sex, chronic diseases history, etc. Stepwise selection was performed to decide the confounders included in the final model, and the optimal correlation structure was determined by Akaike information criterion.

Results:

Of the 9412 eligible participants, 7481 (79.48%) had reached SVS status during their follow-up periods. SUDs related to alcohol (adjusted odds ratio (AOR) = 1.70, 95% confidence interval (CI): 1.46–1.98), cannabis (AOR = 1.62, 95% CI: 1.35–1.95), cocaine (AOR = 1.95, 95% CI: 1.60–2.37), opioid (AOR = 1.91, 95% CI: 1.13–3.23), and tobacco (AOR = 1.80, 95% CI: 1.69–1.92) were negatively associated with SVS. Individuals with chronic conditions such as cardiovascular disease (AOR=0.31, 95% CI: 0.29–0.33), diabetes (AOR=0.49, 95% CI: 0.41–0.59), and cancer (AOR=0.47, 95% CI: 0.38–0.58) showed a higher likelihood of maintaining SVS.

Conclusion:

This large cohort study of PWH with extended follow-up highlights the negative impact of SUDs on maintaining SVS. Long-term strategies for reducing substance use could support SVS in HIV patients.
Genome-based reclassification of Spiroplasma atrichopogonis Koerber et al. 2005 as a later heterotypic synonym of Spiroplasma mirum Tully et al. 1982
Authors: Bhargava Vatsal , Lahon Darshana , Gupta Sonal , Kaur Jasvinder , Lata Pushp
Published: November 2024

The present study was carried out to clarify the taxonomic assignment of two closely related Spiroplasma species. Genomic information for 26 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Spiroplasma atrichopogonis (Koerber et al. 2005) and Spiroplasma mirum (Tully et al. 1982), are conspecific. The 16S rRNA gene sequences of the two species possess 99.78% sequence similarity. Furthermore, whole-genome sequence comparisons showed that S. atrichopogonis GNAT3597T (CP011855.1) GCA 001029245.1 and S. mirum ATCC 29335T (CP002082.1) GCA 000517365.1 shared 99.99% average nucleotide identity, 99.99% average amino acid identity and 100% digital DNA–DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Furthermore, the phylogenomic analysis based on the core proteome of the strains under study confirmed that S. atrichopogonis GNAT3597T (CP011855.1) GCA 001029245.1 and S. mirum ATCC 29335T (CP002082.1) GCA 000517365.1 formed a monophyletic clade. Based on this evidence, we propose the reclassification of S. atrichopogonis Koerber et al. 2005 as a later heterotypic synonym of S. mirum Tully et al. 1982.
Effects of spatial sampling on network alterations in idiopathic generalized epilepsy – can routine EEG be enough?
Authors: Stier Christina , Loose Markus , Loew Carmen , Oropeza Marysol Segovia , Baek Sangyeob , Lerche Holger , Focke Niels K.
Published: November 2024

Objective

Idiopathic generalized epilepsy (IGE) is characterized by marked brain network alterations as assessed using electrophysiology. The clinical application of high-density EEG or MEG is often hindered by logistical challenges and the need for a volumetric MRI. This study investigates how EEG channel density and the head model influence brain metrics in individuals with IGE versus controls ranging from 256-channel high-density EEG to 19-channel routine EEG.

Methods

Resting-state EEG data from 35 individuals with IGE and 54 healthy controls were collected using a 256-channel setup. Data were analyzed at full density and then iteratively down-sampled to lower densities. Source reconstruction was performed either using individual MRI data or a standard brain template. We assessed EEG power and connectivity group differences at all channel compositions, head model types, and parcellations (cortical vertices, anatomical and network parcellations). Additionally, a clinical sample recorded with 19 channels was analyzed to validate findings in a real epilepsy monitoring scenario (71 patients, 43 controls).

Results

Lower-density arrays reliably identified global group differences for both power and connectivity and in frequency bands for which the strongest effects were observed. The spatial similarity of the results for the 256 channels set and those with less channels were good to moderate for power (rspin~0.97 to 0.33), but dropped for connectivity with less than 64 channels (rspin~0.78 to −0.12). Comparing individual and canonical head models revealed consistent effects (rspin~0.77 to 0.5), with coarser brain parcellations increasing stability for low-density maps.

Significance

Low-density EEG arrays suffice for detecting global alterations in IGE, particularly in signal power. For precision-critical contexts and complex metrics such as connectivity, high-density setups are beneficial. Canonical head models are a viable alternative if no individual MRI is available, especially for regional-or network-level assessments.

Highlights

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Averaged EEG power and connectivity alterations in IGE are detectable with low-density EEG

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High-density EEG improves spatial accuracy of connectivity estimates

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Individual and canonical head models produce comparable group effects on EEG metrics, especially when using anatomical and network parcellations

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Our findings advocate for leveraging clinical EEG for network analyses in IGE while emphasizing the need for high-density coverage if spatial precision is needed
Sustainable Development Goals and Health Sector Strategic Indicators Assessment in Cameroon: A Retrospective Analysis at Regional and National Levels
Authors: Cheuyem Fabrice Zobel Lekeumo , Ajong Brian Ngongheh , Amani Adidja , Boukeng Lionel Berthold Keubou , Ngos Christelle Sandrine , Nkongo Florence Kissougle , Tsafack Martine Golda Mekouzou , Mvondo Esther Andriane Bitye Bi , Nloga Guy Stephane , Nouko Ariane , Edzamba Michel Franck , Nyonga Denetria Ngati , Fouda Fernande Murielle Mba , Kam Yollande Ngo , Mouangue Christian
Published: November 2024

Background

Cameroon has developed a Health Sector Strategy (HSS) that aims at fostering a healthy and productive human capital. To achieve this objective, key health indicators have been defined to track progress towards the goal. This study was conducted to provide evidence on the current situation and assess progress towards achieving the HSS and other key health indicators in the Centre Region and in Cameroon.

Methods

Data were collected in April 2023 through a through a comprehensive review of online documents and databases. They were collected retrospectively till 2022. Data were retrieved from the national database using DHIS2 version 2.40 and checked for completeness. Additional data were gathered from online surveys and reports available including Demographic and Health Survey, Multiple Indicators Cluster Survey, National Statistical Institute report for the Centre Region.

Results

At national level, the highest performance was observed in the proportion of HIV-positive pregnant women receiving ART (99%), while the lowest performance was observed in the reduction of the prevalence of chronic malnutrition among children under five, with 63% of the target achieved. In the Centre Region, the national target of reducing the prevalence of chronic malnutrition to 11% was achieved. The lowest performance was observed in the proportion of children under five sleeping under long-lasting insecticidal nets. The density of health facilities was above target at national level (2.3 per 10,000 population) but below target at regional level (1.4 per 10,000 population). Coverage of tracer antigens (Penta 3, BCG) decreased over the five-year study period, falling below the national target of 95% in 2022. However, coverage remained above the national average throughout the study period. Coverage of pregnant women attending four or more antenatal clinics and receiving at least three doses of intermittent preventive treatment (IPT) remained low from 2018 to 2022.

Conclusions

Significant progress has been made in strengthening the healthcare system and fostering a healthy, productive workforce. Nevertheless, further efforts are required to prevent malaria transmission, promote antenatal care utilization among pregnant women, and address nutritional insecurity in certain Regions.
D-glucuronyl C5-epimerase binds to EGFR to suppress kidney fibrosis
Authors: Jing Xiaoqi , Wu Jun , Ning Jingru , Ding Xiaoyu , Du Zhenyun , Wang Xiaojiang , Huang Lulin , Wang Ran , Mei Changlin , Ding Kan
Published: November 2024

Renal tubular cells may actively participate in fibrosis processes leading to end-stage renal failure. However, which molecule play pivotal role in the fibrogenesis is still vague. Glucuronyl C5-epimerase (Hsepi, gene name,Glce) is a key enzyme that catalyzes biosynthesis of Heparan sulfate (HS) chains attached to HS proteoglycan which are ubiquitously located on cell membrane. HomozygousGlce-/- mice may cause embryonic lethality and multi-organ defects. However, whetherGlceplays a key role in kidney fibrosis is unknown. Here, we show thatGlceexpression is significant attenuated in kidneys of patients with renal fibrosis and the animal models. Further study shows that renal tubular-specificGlcedeletion in mice exacerbate kidney fibrosis while AAV-mediated overexpressing ofGlcein UUO-treated mice may ameliorate kidney fibrosis associated with epithelial-mesenchymal transition (EMT) progress via the TGF-β/Smad2/3 signaling pathway. Mechanism study demonstrates thatGlceprotein may bind to EGFR to inactivate EGFR/ERK signaling and further impede TGF-β/Smad-driven EMT and renal fibrosis in Glce-/- and the wild type mice. Interestingly, the anti-fibrosis function is independent ofGlceenzymatic activation.

These data uncover a novel function forGlcewhich plays a key role in kidney tissues against fibrosis.
NoButter: An R package for reducing transcript dispersion in CosMx Spatial Molecular Imaging Data
Authors: O’Hora Béibhinn , Laddach Roman , Nuamah Rosamond , Alberts Elena , Wall Isobelle , Bell Joseph , Johnston David A , James Sonya , Norman Jeanette , Jones Mark G. , Chiappini Ciro , Grigoriadis Anita , Quist Jelmar
Published: November 2024

Motivation

Advances in spatial transcriptomics technologies at single-cell resolution have high-lighted the need for innovative quality assessment approaches and improved analytical tools. Imaging-based spatial transcriptomics technologies, such as the CosMx Spatial Molecular Imager (SMI), provide the location and abundance of transcripts through multifocal imaging. Optical sections (or Z-slices) form a Z-stack that represents the tissue depth. Transcript dispersion can be observed across these Z-slice and introduce considerable levels of technical noise to the data that can negatively impact downstream analysis.

Package Functionality

NoButter is an R package designed to evaluate transcript dispersion in CosMx SMI spatial transcriptomics data. Using the raw data, the transcript distribution is assessed for each Z-slice of a Z-stack across multiple fields of views (FOVs). To systematically identify transcript dispersion, the percentage of transcripts located outside cell boundaries is calculated. Z-slices exhibiting high levels of transcript dispersion can be excluded, while high-confidence transcripts are preserved.

Usage Scenario

To demonstrate the functionalities of NoButter, spatial transcriptomics data was generated using the CosMx SMI for lymph node tissue, a lung sample, and two triple-negative breast cancers (TNBCs). Use cases illustrate substantial transcript dispersion in optical planes closer to the glass slide. In these Z-slices, on average, an additional 10% of the transcripts were discarded using NoButter. Cleaning such Z-slices with high dispersion rates reduces technical noise and improves the overall quality of the spatial transcriptomics data.

Availability

The package can be accessed athttps://github.com/cancerbioinformatics/NoButter.
Nitrogen enrichment alters selection on rhizobial genes
Authors: Hill Caleb A. , McMullen John G. , Lennon Jay T.
Published: November 2024

1

Mutualisms evolve over time when individuals belonging to different species derive fitness benefits through the exchange of resources and services. Although prevalent in natural and managed ecosystems, mutualisms can be destabilized by environmental fluctuations that alter the costs and benefits of maintaining the symbiosis. In the rhizobia-legume mutualism, bacteria provide reduced nitrogen to the host plant in exchange for photosynthates that support bacterial metabolism. However, this relationship can be disrupted by the addition of external nitrogen sources to the soil, such as fertilizers. While the molecular mechanisms underpinning the rhizobia-legume symbiosis are well-characterized, the genome-wide fitness effects of nitrogen enrichment on symbiotic rhizobia are less clear. Here, we inoculated a randomly barcoded transposon-site sequencing (RB-TnSeq) library of the bacteriumEnsifer(Sinorhizobium)melilotiinto soils containing a host plant, alfalfa (Medicago sativa), under conditions of low and high nitrogen availability. Although plant performance remained robust to fertilization, nitrogen enrichment altered gene fitness for specific traits and functions in the rhizobial partner. Genes involved in carbohydrate metabolism showed increased fitness irrespective of soil nutrient content, whereas fitness gains in quorum-sensing genes were only observed in high-nitrogen environments. We also documented reductions in the fitness of nucleotide metabolism and cell-growth genes, while genes from oxidative phosphorylation and various amino-acid biosynthesis pathways were detrimental to fitness under elevated soil nitrogen, underscoring the complex trade-offs in rhizobial responses to nutrient enrichment. Our experimental functional genomics approach identified gene functions and pathways across allE. melilotireplicons that may be associated with the disruption of an agronomically important mutualism.

2

Importance

Understanding the evolutionary dynamics of the rhizobia-legume mutualism is important for elucidating how plant-soil-microbe interactions operate in natural and managed ecosystems. Legumes constitute a significant portion of global food production and generate 25% of all terrestrially fixed nitrogen. The application of chemical fertilizers can disrupt the mutualism by altering the selective pressures experienced by symbiotic rhizobia, potentially affecting gene fitness throughout the microbial genome and leading to the evolution of less productive or cooperative mutualists. To investigate how exogenous nitrogen inputs influence gene fitness during the complex rhizobial lifecycle, we used a barcoded genome-wide mutagenesis screen to quantify gene-level fitness across the rhizobial genome during symbiosis and identify metabolic functions affected by nitrogen enrichment. Our findings provide genomic insight into potential eco-evolutionary mechanisms by which symbioses are maintained or degraded over time in response to changing environmental conditions.
Advanced Bioprinting of Hydrogels with Controlled Mineral Gradients for Regenerative Engineering of the Osteochondral Interface
Authors: Zhao Xiao , Wang Weiwei , Yu Xiaojun , Kalyon Dilhan M , Erisken Cevat
Published: November 2024

The osteochondral (OC) interface exhibits a mineral gradient in the subchondral bone and articular cartilage interface, varying in thickness by several hundred micrometers across different species. Disruptions to this interface can cause severe damage to OC tissues, leading to osteoarthritis (OA), a debilitating and irreversible condition. Regenerative engineering approaches hold promise for addressing this issue by replicating the natural architecture and composition of native OC interface within a biomaterial scaffold. This study introduces a novel one-step bioprinting process using a twin-screw extruder that facilitates the fabrication of a unitary synthetic graft (USG), which mimics the native OC interface’s mineral concentration gradient.

The newly developed USG is composed of an agarose-based cartilage layer and a bone layer, which consists of agarose enriched with 20% hydroxyapatite (w/vol). The USG features a gradient interface with the mineral concentration seamlessly transitioning from 0 to 20wt% from the cartilage to the bone layer. The mineral gradients in the USG and the native tissue were documented using thermogravimetric analysis (TGA), micro-CT, and energy dispersive x-ray (EDX). TGA revealed that the gradient transition length in the graft (647±21μm) compared well to that of native OC tissue (633±124μm) harvested from bovine knee. The strain sweep and frequency sweep tests in oscillatory shear evaluated the linear viscoelastic properties of the grafts, indicating a dominant storage modulus over loss modulus similar to that of native OC tissues. Additionally, the compressive and stress relaxation behaviors of the USGs were quantified using multi-extensional tests, highlighting the grafts’ ability to maintain structural integrity under mechanical stress. Furthermore, viability assays performed after bioprinting showed that chondrocytes and human fetal osteoblast cells successfully integrated and survived within their designated regions of the graft. The USGs engineered in this study exhibit properties that make them promising candidates for regenerating OC defects and restoring knee joint functionality.
Accelerating whole-genome alignment in the age of complete genome assemblies
Authors: Chandra Ghanshyam , Vasimuddin Md. , Misra Sanchit , Jain Chirag
Published: November 2024

Recent advancements in long-read sequencing and assembly methods have ushered in an era of high-quality genome assemblies. Modern assemblies commonly feature megabase-long sequences frequently spanning entire chromosomes. The increase in the assembly contiguity and the reduced number of assembly contigs also implies that whole-genome alignment is no longer an embarrassingly parallel problem. The conventional method of aligning sequences of the query genome in parallel is to utilize a single thread per sequence. This results in poor CPU utilization and long runtimes. In this work, we designed optimizations to accelerate whole-genome alignment on multi-core processors and implemented them in a commonly used aligner, minimap2. Our improvements include a fine-grained parallel chaining method and a fast mechanism for differentiating primary and secondary chains. Our approach accelerates alignment of human, plant, and primate genomes by 1.6×to 7.2×without compromising accuracy.
Expanding the genetic landscape of endometriosis: Integrative -omics analyses uncover key pathways from a multi-ancestry study of over 900,000 women
Authors: Guare Lindsay A , Das Jagyashila , Caruth Lannawill , Rajagopalan Ananya , Akerele Alexis T. , Brumpton Ben M , Chen Tzu-Ting , Kottyan Leah , Lin Yen-Feng , Moreno Elisa , Mulford Ashley J , Rovite Vita , Sanders Alan R , Dombrovska Marija Simona , Elhadad Noemie , Hill Andrew , Jarvik Gail , Jaworski James , Luo Yuan , Namba Shinichi , Okada Yukinori , Shi Yue , Shirai Yuya , Shortt Jonathan , Wei Wei-Qi , Weng Chunhua , Yamamoto Yuji , Chapman Sinead , Zhou Wei , Velez Edwards Digna R. , Setia-Verma Shefali
Published: November 2024

We report the findings of a genome-wide association study (GWAS) meta-analysis of endometriosis consisting of a large portion (31%) of non-European samples across 14 biobanks worldwide as part of the Global Biobank Meta-Analysis Initiative (GBMI). We identified 45 significant loci using a wide phenotype definition, seven of which are previously unreported and detected first genome-wide significant locus (POLR2M) among only African-ancestry. Our narrow phenotypes and surgically confirmed case definitions for endometriosis analyses replicated the known loci nearCDC42,SKAP1, andGREB1. Through this large ancestry stratified analyses, we document heritability estimates in range of 10-12% for all ancestral groups. Thirty-eight loci had at least one variant in the credible set after fine-mapping. An imputed transcriptome-wide association study (TWAS) identified 11 associated genes (two previously unreported), while the proteome-wide association study (PWAS) suggests significant association of R-spondin 3 (RSPO3) with wide endometriosis, which plays a crucial role in modulating the Wnt signaling pathway. Our diverse, comprehensive GWAS, coupled with integrative -omics analysis, identifies critical roles of immunopathogenesis, Wnt signaling, and balance between proliferation, differentiation, and migration of endometrial cells as hallmarks for endometriosis. These interconnected pathways and risk factors underscore a complex, multi-faceted etiology of endometriosis, suggesting multiple targets for precise and effective therapeutic interventions.
Advanced HIV Disease Burden in Selected Health Facilities in Mozambique, October–December 2023
Authors: Nguimfack Alexandre , Filipe Eudoxia , Filimao Dercio , Mizela José , Bila Erica , Matsinhe Mercia , Tomo de Deus Maria Inês , Gaspar Irenio , Ruano Maria , Armando Luis , Tiberi Orrin
Published: November 2024

Introduction

Advanced HIV Disease (AHD) is a remaining hurdle in the care and treatment cascade in Mozambique and has the potential to delay Mozambique’s progress towards the UNAIDS 95-95-95 goals for 2025. An improved understanding of the prevalence and demographics of AHD is critical to understanding this important condition.

Methods

Data from October to December 2023 were reviewed from the 79 health facilities implementing the AHD diagnosis and treatment package at the national level.

Results

Overall, 36% (7.811/21.452) of people living with HIV (PLHIV) newly initiated or reinitiated on treatment had a CD4 test, of which 1.986 were diagnosed with AHD. Most diagnosed cases were in the newly initiated PLHIV (1.814) versus reinitiated (179).

Conclusion

Low CD4 testing uptake means that AHD remains a serious challenge in Mozambique’s path towards the elimination of HIV as a public health threat.
Learning latent profiles via cognitive growth charting in psychosis: design and rationale for the PRECOGNITION project
Authors: Marquand Andre F. , Bučková Barbora Rehák , Cattaranusi Giulia , Flaaten Camilla , Busch Cecilie , Lemvigh Cecilie K. , Gupta Veenu , Fraza Charlotte , Westlye Lars T. , Andreassen Ole A. , Hlinka Jaroslav , Ebdrup Bjørn H. , Shiers David , Ueland Torill , Dazzan Paola
Published: November 2024

Cognitive impairments are a core feature of psychosis that are often evident before illness onset and have substantial impact on both clinical and real-world functional outcomes. Therefore, these are an excellent target for stratification and early detection in order to facilitate early intervention. While many studies have aimed to characterise the effects of cognition at the group level and others have aimed to detect individual differences by referencing subjects against existing norms, these studies have limited generalisability across clinical populations, demographic backgrounds and instruments and also do not fully account for the inter-individual heterogeneity inherent in psychosis. Here, we outline the rationale, design and analysis plan for the PRECOGNITION project which aims to address these challenges. This project is a collaboration between partners in five European countries, that aims to (i) translate normative modelling approaches that have been pioneered in brain imaging to psychosis data, to yield ‘cognitive growth charts’ for longitudinal tracking and prediction at the individual level (ii) develop machine learning models for harmonising and stratifying cohorts on the basis of these models; (iii) provide comprehensive reference models that provide broad sociodemographic coverage including different languages and distinct norms for individuals with psychosis and unaffected individuals and (iv) stratification models and predictions for functional outcome measures in psychosis cohorts. Crucially, this project will be guided throughout by experts with lived experience.
What does it cost to expand two-way texting for post-operative follow-up? A cost analysis in routine voluntary medical male circumcision settings in South Africa
Authors: Unsworth Molly , Fabens Isabella , Setswe Geoffrey , Moyo Khumbulani , Pienaar Jacqueline , Makhele Calsile , Phohole Motshana , Igaba Nelson , Hlongwane Sizwe , Sardini Maria , Dong Tracy , Sharma Monisha , Tweya Hannock , Ndebele Felex , Holec Marrianne , Feldacker Caryl
Published: November 2024

Up to 98% of adult voluntary medical male circumcision (VMMC) clients heal without adverse events (AEs) in South Africa and in the sub-Saharan Africa (SSA) region, yet all clients in South Africa (SA) are still required to attend in-person reviews, creating added work for providers and barriers for clients. A randomized controlled trial (RCT) using our fee-free, open-source, two-way texting (2wT) approach showed that males could independently monitor their healing with support from VMMC nurse-led telehealth and that 2wT was more cost-effective than routine visits for quality post-operative monitoring. The objectives of this costing activity were to assess the additive cost of 2wT vs. SoC during a stepped wedge design (SWD) expansion trial; costing an augmentation of 2wT with dedicated personnel during peak VMMC periods; and estimate the cost savings of 2wT from the payer perspective if scaled in routine VMMC settings. Data was collected from routine financial reports and complemented by previous RCT time-motion estimates. We conducted activity-based costing of SWD and peak season periods; sensitivity analysis estimated 2wT costs at scale. We included data from 6,842 males, with 2,586 (38%) opting for 2wT. 2wT participants attended an average of zero visits; SoC males had an average of 2 visits. Under 2wT, quality care markers improved and AE ascertainment increased while loss to follow-up (LTFU) decreased. Given a VMMC population of 10,000 adults, scenario analysis suggests that: 1) 2wT becomes cost neutral with 45% 2wT enrollment; 2) 2wT saves $0.29/client with 60% 2wT enrollment; and 3) 2wT saves $0.46/client with 80% 2wT enrollment. When implemented at scale, 2wT appears to significantly reduce costs to the healthcare system while improving the quality of post-operative care and requiring no additional client costs. 2wT should be expanded for eligible males across VMMC and other post-operative contexts in South Africa.
Influence of Genetic Ancestry on Gene-Environment Interactions of Polygenic Risk and Sociocultural Factors: Results from the Hispanic Community Health Study/Study of Latinos
Authors: Sharma Jayati , McArdle Cristin E. , Graff Mariaelisa , Cordero Christina , Daviglus Martha , Gallo Linda C. , Isasi Carmen R. , Kelly Tanika N. , Perreira Krista M. , Talavera Gregory A. , Cai Jianwen , North Kari E. , Fernández-Rhodes Lindsay , Wojcik Genevieve L.
Published: November 2024

Background

Many present analyses of Hispanic/Latino populations in epidemiologic research aggregate all members of this ethnic group, despite immense diversity in genetic backgrounds, environment, and culture between and across Hispanic/Latino background groups. Using the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), we examined the role of self-identified background group and genetic ancestry proportions in gene-environment interactions influencing the relationship between body mass index (BMI) and a polygenic score for BMI (PGSBMI).

Methods

Weighted univariate and multivariable generalized linear models were executed to compare the effects of environmental variables identifieda prioriby McArdle et al. 2021. Both Amerindigenous (AME) ancestry proportion and background group identity were statistically modeled as confounders both through stratified and joint analyses to understand their influence on the relationship between BMI and PGSBMI, while incorporating gene-environment interactions of PGS x diet and PGS x age-at-immigration.

Results

After complex survey weighting, 7,075 participants remained in the analytic sample, representing individuals of six background groups: Central American, Cuban, Dominican, Mexican, Puerto Rican, and South American. The distributions of key environmental and sociocultural variables were heterogeneous between Hispanic/Latino background groups. Associations of these variables with AME ancestry were similarly heterogeneous upon stratification, indicating confounding by background group. In a predictive model for BMI incorporating health, immigration, and environmental variables, PGSBMIperformance decreased with increasing AME ancestry proportion. In this model, most statistically significant GxE interactions lost significance after ancestry and background stratification, except for PGS x age-at-immigration interactions in some strata: Mexican background individuals born in the US compared to those >=21 years old at migration (β=1.33, p<0.01), Dominican background individuals 6-12 years old at migration compared to those >=21 years old at migration (β=4.38, p<0.001), and Cuban background individuals 0-5 years old at migration compared to those >=21 years old at migration (β=2.20, p=0.015), where US-born includes individuals born in the US 50 states/DC.

Conclusions

Controlling for self-identified background group identity and genetic ancestry did not eliminate statistically significant differences in interactions between AME ancestry and environmental variables in certain strata of AME ancestry among some Hispanic/Latino background groups in HCHS/SOL.
NIR-SC-UFES: A portable NIR spectral dataset to skin cancer in vivo
Authors: da Cunha Pedro Henrique P. , Zanoni Madson P. , Santos Francine D. , Nascimento Isadora Tavares , Rezende Isabella , Canuto Tania R. P. , de Paula Vieira Luciana , Rossoni Renan , Santos Maria C. S. , Romão Wanderson , Frasson Patricia H. L. , Krohling Renato A. , Filgueiras Paulo R.
Published: November 2024

In recent years, significant progress has been made in computer-aided diagnostics (CAD) for skin lesions, primarily using images and metadata. However, these methods have limitations, particularly in revealing the molecular structure of lesions. NIR spectroscopy offers additional data, capturing information not visible to the naked eye, which can improve automated CAD for skin lesions. Skin cancer remains a major cause of death, making early diagnosis crucial. A key challenge in applying machine and deep learning (MDL) techniques to spectroscopy is the lack of publicly available datasets. Previously, no public dataset of portable NIR spectral data for skin lesions existed. In collaboration with the Programa de Assistência Dermatológica (PAD) at UFES, we developed a new dataset, NIR-SC-UFES, for skin cancer diagnosis. This dataset includes portable NIR spectral data for six lesion skin, with 714 spectra captured between 900 and 1700 nm. The dataset is available atdata.mendeley.com/datasets/j9773cyr3k/1.

Graphical abstract

Specifications Table