bluuebunny/crossref_metadata_2025_split huggingface dataset:
inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples
Authors: Juzenas Simonas , Goda Karolis , Kiseliovas Vaidotas , Zvirblyte Justina , Quintinal-Villalonga Alvaro , Siurkus Juozas , Nainys Juozas , Mazutis Linas 
Published: January 2025

Abstract
The expansion of single-cell analytical techniques has empowered the exploration of diverse biological questions at the individual cells. Droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly widely used due to their high-throughput capabilities and small reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, their relatively high cost limits the ability to profile large numbers of cells and samples. Moreover, as the scale of single-cell sequencing continues to expand, accommodating diverse workflows and cost-effective multi-biospecimen profiling becomes more critical. Herein, we present inDrops-2, an open-source scRNA-seq technology designed to profile live or preserved cells with a sensitivity matching that of state-of-the-art commercial systems but at a 6-fold lower cost. We demonstrate the flexibility of inDrops-2, by implementing two prominent scRNA-seq protocols, based on exponential and linear amplification of barcoded-complementary DNA, and provide useful insights into the advantages and disadvantages inherent to each approach. We applied inDrops-2 to simultaneously profile multiple human lung carcinoma samples that had been subjected to cell preservation, long-term storage and multiplexing to obtain a multiregional cellular profile of the tumor microenvironment. The scalability, sensitivity and cost efficiency make inDrops-2 stand out among other droplet-based scRNA-seq methods, ideal for large-scale studies on rare cell molecular signatures.
Novel archaeal ribosome dimerization factor facilitating unique 30S–30S dimerization
Authors: Hassan Ahmed H , Pinkas Matyas , Yaeshima Chiaki , Ishino Sonoko , Uchiumi Toshio , Ito Kosuke , Demo Gabriel 
Published: January 2025

Abstract
Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various ribosome-interacting proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms to adapt to stress. Despite extensive studies on bacteria and eukaryotes, understanding factor-mediated ribosome dimerization or anti-association in archaea remains elusive. Here, we present cryo-electron microscopy structures of an archaeal 30S dimer complexed with an archaeal ribosome dimerization factor (designated aRDF), from Pyrococcus furiosus, resolved at a resolution of 3.2 Å. The complex features two 30S subunits stabilized by aRDF homodimers in a unique head-to-body architecture, which differs from the disome architecture observed during hibernation in bacteria and eukaryotes. aRDF interacts directly with eS32 ribosomal protein, which is essential for subunit association. The binding mode of aRDF elucidates its anti-association properties, which prevent the assembly of archaeal 70S ribosomes.
Realization of a cold atom gyroscope in space
Authors: Li Jinting , Chen Xi , Zhang Danfang , Wang Wenzhang , Zhou Yang , He Meng , Fang Jie , Zhou Lin , He Chuan , Jiang Junjie , Sun Huanyao , Chen Qunfeng , Qin Lei , Li Xiao , Wang Yibo , Zhang Xiaowei , Zhong Jiaqi , Li Runbing , An Meizhen , Zhang Long , Wang Shuquan , Li Zongfeng , Wang Jin , Zhan Mingsheng 
Published: January 2025

Abstract
High-precision gyroscopes in space are essential for fundamental physics research and navigation. Due to its potential high precision, the cold atom gyroscope is expected to be the next generation of gyroscopes in space. Here, we report the first realization of a cold atom gyroscope, which was demonstrated by the atom interferometer installed in the China Space Station (CSS) as a payload. By compensating for CSS's high dynamic rotation rate using a built-in piezoelectric mirror, spatial interference fringes in the interferometer are successfully obtained. Then, the optimized ratio of the Raman laser's angles is derived, the coefficients of the piezoelectric mirror are self-calibrated in orbit, and various systemic effects are corrected. We achieve a rotation measurement resolution of 50 μrad/s for a single shot and 17 μrad/s for an average number of 32. The measured rotation is -1142±29 μrad/s and is compatible with that recorded by the classical gyroscope of the CSS. This study paves the way for developing high-precision cold atom gyroscopes in space.
Meta-Analysis of Palmitoylethanolamide in Pain Management: Addressing Literature Gaps and Enhancing Understanding
Authors: Viña Isabel , López-Moreno Miguel 
Published: January 2025

Abstract

Context
Chronic pain is a debilitating condition that affects a significant proportion of the population. Palmitoylethanolamide (PEA), a naturally occurring fatty acid amide derived from omega-7 fatty acids, has emerged as a safe and effective alternative for pain management and exerts its effects by interacting with the endocannabinoid system, modulating inflammation, and regulating immune responses.

Objective
A comprehensive meta-analysis was conducted to evaluate the efficacy of PEA in alleviating pain across various pathologies, considering the nociceptive, neuropathic, or nociplastic nature of pain.

Data Sources
A systematic search was conducted of 4 databases: PubMed, Embase, Scopus, and Cochrane Collaboration Library.

Data Extraction
Randomized clinical trials were selected for analysis. This meta-analysis included 18 studies involving 1196 patients.

Data Analysis
Continuous variables were assessed using a standard mean difference (SMD). Heterogeneity was evaluated using the χ2 test and I2 statistics. Pain was significantly reduced in the PEA group at 6 weeks (SMD, –0.9; 95% CI, –1.60 to –0.31), 8 weeks (SMD, –0.98; 95% CI, –1.61 to –0.36), and 24-26 weeks (SMD, –1.16; 95% CI, –2.15 to –0.17). Quality of life, including pain-related items, was significantly higher in the PEA group (SMD, –0.61; 95% CI, –0.93 to –0.30). Significant differences in favor of PEA were observed at 4 (SMD, –0.36; 95% CI, –0.65 to –0.07) and 8 weeks (SMD, –0.66; 95% CI, –1.15 to –0.17). Palmitoylethanolamide was effective for all pain types: nociceptive (SMD, –0.74; 95% CI, –1.42 to –0.06), neuropathic (SMD, –0.97; 95% CI, –1.54 to –0.39), and nociplastic (SMD, –0.59; 95% CI, –1.15 to –0.03).

Conclusions
This meta-analysis confirmed that PEA effectively reduces pain and enhances quality of life, with significant benefits observed within 4-6 weeks of treatment. Palmitoylethanolamide is a promising alternative to chronic opioid analgesics, potentially reducing the risk of opioid abuse and dependency.

Systematic Review Registration
PROSPERO registration no. CRD42024550546.
The MADS-RIPENING INHIBITOR–DIVARICATA1 module regulates carotenoid biosynthesis in nonclimacteric Capsicum fruits
Authors: Wang Yinggang , Li Xinhui , Qiu Huixia , Chen Ruting , Xiong Aisheng , Xu Zhisheng , Miao Wu , Chen Rugang , Wang Peizhi , Hou Xilin , Yu Huiyang , Yang Bozhi , Yang Sha , Suo Huan , Zou Xuexiao , Liu Zhoubin , Ou Lijun 
Published: January 2025

Abstract
Carotenoids play indispensable roles in the ripening process of fleshy fruits. Capsanthin is a widely distributed and utilized natural red carotenoid. However, the regulatory genes involved in capsanthin biosynthesis remain insufficient. Here, we identified the MADS-box transcription factor RIPENING INHIBITOR (MADS-RIN) in pepper (Capsicum annuum), which regulates ripening in climacteric tomato (Solanum lycopersicum) fruits, using weighted gene co-expression network analysis. We found MADS-RIN can directly bind to the promoters of carotenoid biosynthetic genes phytoene synthase 1 (PSY1) and capsanthin/capsorubin synthase (CCS) and the promoter of DIVARICATA1 to activate their expression, thereby regulating carotenoid biosynthesis directly or indirectly. The physical interaction between MADS-RIN and DIVARICATA1 enhances the transactivation effect on PSY1 and CCS. The self-transactivation of MADS-RIN demonstrates its capability to expedite the above process under specific conditions. Interestingly, chromatin immunoprecipitation sequencing assays revealed consistency and divergence of potential targets of MADS-RIN in climacteric tomato and nonclimacteric pepper fruits, suggesting potential conservation and variation of MADS-RIN in regulating ripening and carotenoid metabolism. The present study illustrates the regulatory mechanism of the MADS-RIN–DIVARICATA1 module in capsanthin biosynthesis in pepper, providing targets for breeding high-quality peppers. These findings enrich our understanding of the regulatory network of carotenoid biosynthesis and offer insights into the complex mechanisms of MADS-RIN in climacteric/nonclimacteric fruit ripening and carotenoid biosynthesis.
Effect of abnormal placental cord insertion on hemodynamic change of umbilical cord in a tertiary center: a prospective cohort study
Authors: Wu Xiu-Qin , Miao Ying , Yang Xiao-Feng , Hong Yong-Qiang , Wang Liang-Cheng , Chiu Wei-Hsiu 
Published: January 2025

Abstract

Background
Our study aims to evaluate the umbilical vein (UV) hemodynamic change in the prenatal cohort of pregnancies diagnosed with abnormal placental cord insertion (aPCI).

Methods
From January 2022 to December 2022, the fetal umbilical cord insertion site was sonographically examined in singleton fetuses, and umbilical cord blood flow was calculated. The umbilical artery and UV Doppler flow indexes were assessed in cases of normal and abnormal cord insertion.

Results
Among 570 singleton fetuses between 18 + 0 and 40 + 6 weeks of gestation in the final study, the umbilical vein blood flow (UVBF) in the 3 groups of normal umbilical cord insertions, marginal umbilical cord insertions, and velamentous umbilical cord insertions was 145.39 ml/min, 146.18 ml/min, and 93.96 ml/min, respectively. UVBF was significantly lower in the velamentous cord insertion (VCI) group than in the other groups (P &lt; 0.05). Compared with the normal cord insertions group, lower birth weight (2820 ± 527 g vs. 3144 ± 577 g, P &lt; 0.05), delivery at an earlier gestational age (38.0 ± 1.55 weeks vs. 38.8 ± 2.34 weeks, P &lt; 0.05), higher bicarbonate (25.08 ± 1.72 mmol/L vs. 22.66 ± 4.05 mmol/L, P &lt; 0.05), and higher standard base excess (−1.14 ± 1.50 mmol/L vs. −3.30 ± 3.22 mmol/L, P &lt; 0.05) were found in the VCI group.

Conclusions
We observed lower UVBF volume with aPCI. Hence, we propose UVBF analysis to evaluate fetal aPCI according to UV hemodynamics as an advisory in prenatal care. This would be useful and improve obstetricians’ clinical explanation about the potential prenatal consequences so that parents can opt for future prenatal care during pregnancy.
Higher dietary zinc intake increases the risk of autoimmune thyroiditis
Authors: Chen Lijun , Yan Changjian , Huang Chunling , Jiang Zhengrong , Lin Ruhai , Wu Xiaohong , Huang Huibin 
Published: January 2025

Abstract

Background
Autoimmune thyroiditis (AIT), encompassing Hashimoto’s thyroiditis (HT), is a prevalent chronic autoimmune disorder characterized by lymphocytic infiltration and the presence of anti-thyroid antibodies. It is the primary cause of primary hypothyroidism and affects women more frequently than men. Nearly 95% of individuals with HT exhibit thyroid peroxidase antibodies or thyroglobulin antibodies. Dietary factors, including vitamins and trace elements such as zinc, play a significant role in thyroid health; yet, clinical guidelines lack explicit dietary recommendations for AIT.

Methods
This study investigates the relationship between dietary zinc intake (Zinc) and AIT using data from the 2007–2008 National Health and Nutrition Examination Survey. A total of 5467 participants were analyzed, including 273 individuals with AIT and 5194 without AIT. Clinical characteristics, dietary Zinc, and other relevant variables were assessed. Multivariate logistic bidirectional stepwise regression analysis was conducted to identify independent risk factors for AIT, and a risk prediction model was developed.

Results
The prevalence of AIT was 5%. Individuals with AIT were older, had a higher proportion of females, and showed elevated levels of various biomarkers, including zinc. Dietary Zinc was significantly higher in the AIT group (22.6 mg vs. 15.3 mg, P &lt; .001). The regression analysis identified dietary Zinc, along with other factors, as an independent risk factor for AIT. The risk prediction model, including zinc, demonstrated a better performance (area under the curve = 0.8) compared to the model without zinc.

Conclusion
The findings indicate that higher dietary Zinc is positively correlated with the risk of AIT and serves as an independent risk factor. Excessive Zinc may disrupt immune balance, potentially increasing the risk of autoimmune diseases. These results suggest that dietary Zinc should be carefully considered in the management of AIT, and further research is needed to explore the causal relationship and determine safe zinc consumption levels to avoid increasing the risk of autoimmune diseases.
Assessing the Implementation of ARPA Coronavirus State and Local Fiscal Recovery Funds: The View from City Officials
Authors: Ke Laiyang , Kwon Eunjoo , Hong Minji , Jimenez Benedict 
Published: January 2025

Abstract
The 2021 American Rescue Plan Act created the Coronavirus State and Local Fiscal Recovery Funds (SLFRF), which provided $350 billion for state and local governments to aid with pandemic recovery efforts. This research examines the local implementation of SLFRF from the point of view of city officials. We assess the effectiveness of grant implementation on two dimensions: funding allocation (the ease or difficulty of selecting and prioritizing projects to be funded) and project management (the ability to complete projects on time and within budget). Our research focuses on the contributions of three general groups of factors on grant implementation performance: federal control and oversight, local capacities, and the role of local political actors. We conducted a national survey of cities that received SLFRF grants and gathered information from city officials responsible for administering the grant on different aspects of SLFRF implementation. Using ordinary least squares and ordered logit regressions to analyze the survey data, the empirical results uncover some consistent patterns. Specifically, local management discretion, perceived clarity of federal rules, a centralized local grant administration structure, and mayoral involvement are positively associated with grant implementation effectiveness.
Adjuvant effect of green tea intake on treatment of patients with acute venous thromboembolism
Authors: Xiong Wei , Deng Zhenzhong , Song Xiaoyang , Cheng Yi , Yao Qihuan , Qu Jianmin , Xu Mei , Luo Yong , Guo Xuejun , Han Fengfeng 
Published: January 2025

Abstract

Background
Although there have been reports that green tea intake has a thromboprophylactic effect, it was still unknown whether it had adjuvant effect on the basis of conventional anticoagulation for patients diagnosed with venous thromboembolism (VTE).

Methods
VTE patients were retrospectively classified into green tea group and no green tea group in a 1:1 ratio using propensity score matching, based on whether they drank green tea during the 3 months’ period after VTE diagnosis. Primary outcomes were VTE recurrence at 3 months after VTE diagnosis and VTE-related death during 3 months after VTE diagnosis. Secondary outcomes were all-cause death and major bleeding during 3 months after VTE diagnosis. The primary and secondary outcomes were compared between the green tea and no green tea groups, in all patients, PE patients, and patients with cancer-associated VTE, respectively.

Results
The VTE recurrence at 3-month after VTE diagnosis occurred less in the green tea group (N = 1102) than in the no green tea group (N = 1102) (19 [1.7%] vs 55 [5.0%], P &lt; 0.001). The VTE-related mortality during 3 months after VTE diagnosis occurred similarly between the two groups (13 [1.2%] vs 21 [1.9%], P = 0.187). The all-cause mortality (82 [7.4%] vs 78 [7.1%], P = 0.682) and major bleeding (55 [5.0%] vs 40 [3.6%], P = 0.142) during 3 months after VTE diagnosis both occurred similarly between the two groups. The results of VTE recurrence analysis in PE and cancer-associated VTE subgroups were both consistent with the main findings.

Conclusions
Green tea intake on the basis of conventional anticoagulation can lead to a lower short-term VTE recurrence rate without safety concern, compared with isolated conventional anticoagulation.
Poor prognostic factors and unmet needs in rheumatoid arthritis
Authors: Smolen Josef S 
Published: January 2025

Abstract
Prognostic factors in rheumatoid arthritis relate to several aspects, such as prediction of joint damage and loss of function or prediction of response to a particular therapy. For many decades it has been well established that high disease activity, especially exemplified by swollen joint counts and acute phase reactants, is associated with progression of joint damage. In addition, rheumatoid factor (RF) positive patients, but not patients with anti-citrullinated peptide antibodies (ACPA) are particularly prone to high disease activity and joint destruction. Newer studies have looked at molecular markers, but they have either not shown better results than those seen with the long-established ones or have not been sufficiently validated. Most recent insights suggest that high C-reactive protein levels may predict a particularly good response to IL-6 blockade, but not to other therapies, and that high RF-levels may be associated with better responses to Fc-free monoclonal antibodies than molecules containing an Fc-region. It is hoped, however, that with newer techniques and better insight into RA pathogenesis research may come up with even better molecular markers than currently available to predict responses to specific drugs in the not-too-distant future.
Anti-C1q antibodies in IgG4-related disease are common and associated with renal involvement and cutaneous small-vessel vasculitis
Authors: Martín-Nares Eduardo , Nuñez-Álvarez Carlos A , Hernández-Molina Gabriela 
Published: January 2025

Abstract

Objectives
To evaluate the prevalence and clinical associations of anti-C1q antibodies in IgG4-related disease (IgG4-RD), focusing on renal involvement and cutaneous small-vessel vasculitis (CSVV).

Methods
We enrolled patients who met the revised 2020 Comprehensive Diagnostic Criteria and/or the 2019 ACR/EULAR Classification Criteria for IgG4-RD. Variables included demographics, organ involvement, clinical phenotypes, disease activity, serum biomarkers, follow-up duration, remission and relapses. Anti-C1q antibodies were measured using a quantitative enzyme-linked immunosorbent assay (cut-off &lt;10 U/ml).

Results
Seventy patients with a mean age of 52.1 years were included. Thirty-four patients (48.6%) were male. Anti-C1q antibodies were positive in 74.3%, with a median level of 19.8 U/ml. Patients with active disease had higher anti-C1q antibody levels than inactive patients (P = 0.03). Renal involvement was more frequent in anti-C1q positive patients (P = 0.01). Six patients (8.6%) had CSVV, and all had positive anti-C1q levels. All exhibited palpable purpura and one patient had urticarial-like lesions. These patients had multi-organ involvement, and most had high IgG, IgG1, IgG4 and hypocomplementemia. Skin biopsies in three patients showed leukocytoclastic vasculitis with lymphocytic and eosinophilic infiltrates. Anti-C1q antibody levels correlated negatively with levels of C3 and C4, and positively with levels of IgG1, IgG4, and serum free light chains. Anti-C1q positivity did not predict relapse-free survival.

Conclusions
This study is the first to evaluate anti-C1q antibodies in IgG4-RD, finding a high prevalence, particularly in patients with renal involvement and CSVV. The results support the hypothesis that immune complex-mediated complement activation contributes to IgG4-RD pathogenesis.
Competing frames of STI policy: uncovering ‘fragmented cohesion’ in reorganization of public research funding
Authors: Vase Susanna 
Published: January 2025

Abstract
Despite variation across Science, Technology, and Innovation (STI) policies, project-based public research funding allocation models, characterized by a complexity of policy objectives, are becoming increasingly prevalent. This article examines the emergence of such a development within a specific context through a case study on the policy process leading to the establishment of Finland’s Strategic Research funding instrument. Drawing on the policy proposal, organizational responses, and interviews, it explores five frames for and against the proposal and its development into a decision. Based on the empirical analysis, I propose the notion of ‘fragmented cohesion’ to characterize how several stakeholder organizations employed framing as an argumentative tool to valorize the proposal’s objectives, while selectively justifying and opposing the proposed methods of achieving them. I argue that this dynamic increased the likelihood of policymakers embracing one-size-fits-all models across diverse sectors, as originally outlined, rather than case-by-case consideration.
Diurnal fluctuations of subthalamic nucleus local field potentials follow naturalistic sleep-wake behavior in Parkinson’s disease
Authors: Baumgartner Alexander J , Hirt Lisa , Amara Amy W , Kern Drew S , Thompson John A 
Published: January 2025

Abstract

Study Objectives
Deep brain stimulation (DBS) of the subthalamic nucleus (STN) may improve sleep dysfunction, a common non-motor symptom of Parkinson’s disease (PD). Improvement in motor symptoms correlates with DBS-suppressed local field potential (LFP) activity, particularly in the beta frequency (13–30 Hz). Although well-characterized in the short term, little is known about the innate progression of these oscillations across the sleep–wake cycle. We sought to characterize LFP fluctuations over several days and nights in the home setting in patients chronically treated with DBS.

Methods
LFPs in the beta and alpha frequency range were recorded from the STN in 13 PD subjects (18 hemispheres) over 14.6 (interquartile range 4) days. Sleep and wake were determined by validated actigraphy. We calculated the mean difference between sleep and wakefulness in LFP power (µVp), probability density functions of normalized LFP, and the fraction of overlap between probability density histograms.

Results
STN LFPs showed a consistent fluctuation based on behavioral state. LFP power was higher during wakefulness than during sleep, with little overlap in the magnitude of LFP power between these two states. Delineation of subject activity patterns revealed that LFP variance by time of day was more strongly correlated at night.

Conclusions
STN LFP fluctuations represent a useful measure to distinguish between sleep and wakefulness in PD. These fluctuations can be detected in the home setting using commercially available devices, including in patients who have been treated with DBS for years. This technology may lead to opportunities for closed-loop DBS therapy.