bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of atmospheric water locks and water lock solutions in tight sandstone gas reservoirs in the Ordos Basin
Authors: Zheng Sen , Wang Ruifei , Shou Qianru , Zhao Jia , Zhang Yixuan 
Published: February 2025

Abstract
The target layer of the tight sandstone gas reservoir in Area J of the Ordos Basin is the Lower Shihezi Formation, and the well depth is greater than 3,000 meters. The porosity of the reservoir ranges from 4% to 16%, and the permeability ranges from (0.1 to 3.0) × 10−3μm2. It is a low-porosity and low-permeability reservoir with developed micro-fractures, high clay mineral content, high bound water saturation, and high capillary forces under the dual medium of pores and micro-fractures. It is extremely vulnerable to water lock damage during development. Based on the geological characteristics of the study area, water-lock experiments using the saturating displacement method and the imbibition method, as well as water-lock release experiments using the reverse injection of nitrogen and the reverse injection of methanol were carried out to compare the degree of water-lock damage and the degree of water-lock recovery using different methods. The research found that the water-lock damage under the saturating displacement method was 67.15%, and the water-lock damage under the imbibition method was slightly higher at 69.63%, both of which showed significant water-lock damage. The reverse injection of nitrogen to relieve water locks has a high rate of permeability recovery; the reverse injection of methanol to relieve water locks has the second-highest rate of permeability recovery. The lower the permeability, the higher the water lock damage rate and the rate of permeability recovery. A deeper understanding of the water lock mechanism in tight sandstone gas reservoirs and the improvement of water lock evaluation and water lock relief methods are of great significance for the efficient development of tight sandstone gas reservoirs.
Epoxide modification for enhancing chemical and suspension stability of cerium oxide polishing abrasives
Authors: Gao Bo , Wu Shuming , Shen Hui , Li Simin , Zhang Fan 
Published: February 2025

Abstract
In order to address the significant challenges presented by ultra-precision machining technology, conventional cerium oxide (CeO2) polishing materials are incorporated into the polishing fluid as a means of resolving this issue. However, traditional CeO2 exhibits drawbacks such as low dispersion, susceptibility to aggregation, and limited suspension stability, all of which have a negative impact on the uniformity of the polishing process. A preparation method of CeO2 polishing fluid modified by epoxy carboxylic acid was presented. A series of modified epoxy-cerium oxide abrasives with different types and contents of surface ligands were obtained by surface modification of the precursor abrasives of CeO2 polishing powders using different kinds and proportions of epoxy-carboxylic acids. By adding stabilizer and pH regulator to prepare the polishing liquid, the chemical and physical properties of the modified epoxy-cerium oxide abrasive can be optimized, and its reactivity and removal rate in the chemical mechanical polishing process can be improved, thus effectively enhancing the polishing efficiency. By optimizing the reaction conditions, the sample with the best ratio is selected as 50CeO2-EPO2-@NH3. The modified CeO2 was tested by SEM and TEM, its XRD pattern was collected, and thermogravimetric analysis (TGA) was performed. The results showed that the surface modification strategy was successfully realized. The surface functionalization strategy enhanced the suspension of CeO2 abrasive in an aqueous solution. Compared with the modified epoxy-cerium oxide polishing liquid before modification, the cutting ability and removal rate did not decrease significantly, and the modified epoxy-cerium oxide polishing liquid had stronger chemical stability and suspension in the solution. It is worth noting that the local structure and surface environment of the CeO2 surface are precisely regulated by the presence of surface epoxide carboxylic acid, which enhances the suspension property (T50) of modified CeO2 in water for up to two months. This study expands the scope of considerations for the development of cerium oxide polishing fluid.
Study on coagulation treatment and floc settling rate of alcohol and oil containing wastewater
Authors: Dong Yue , Wang Zhenyu , Zhang Le , Hu Haijie , Han Lei 
Published: February 2025

Abstract
Methanol, as a new type of energy, is becoming increasingly widely used in society. However, how to efficiently utilize and recover methanol has become a major challenge. In order to improve the methanol recovery efficiency of the methanol distillation tower, this paper applied the chemical oxidation coagulation method to pretreat the high alcohol and oil containing wastewater entering the methanol distillation tower. The results showed that the transmittance of the supernatant of the treated water could reach 97.76%, and the removal rates of suspended solids, oil, and iron were 99.71%, 98.62%, and 98.61%, respectively. This can meet the inlet water index of the methanol distillation tower in Yanchang Oilfield Gas Production Plant 2, indirectly improving the methanol recovery efficiency in the methanol distillation tower. By examining the settling velocity of flocs, it was found that the maximum settling velocity of flocs was 0.848mm/s when the methanol content was 40%. The settling velocity of flocs decreased with the increase of the ratio of condensate oil/suspended solids content. When the ratio of condensate oil/suspended solids content was greater than 5.88, flocs would float up and the optimal coagulation formula would no longer be applicable.
Tribus: Semi-automated discovery of cell identities and phenotypes from multiplexed imaging and proteomic data
Authors: Kang Ziqi , Szabo Angela , Farago Teodora , Perez-Villatoro Fernando , Junquera Ada , Saundarya Shah , Launonen Inga-Maria , Anttila Ella , Casado Julia , Elias Kevin , Virtanen Anni , Haltia Ulla-Maija , Färkkilä Anniina 
Published: February 2025

Abstract

Motivation
Multiplexed imaging and single-cell analysis are increasingly applied to investigate the tissue spatial ecosystems in cancer and other complex diseases. Accurate single-cell phenotyping based on marker combinations is a critical but challenging task due to (i) low reproducibility across experiments with manual thresholding, and, (ii) labor-intensive ground-truth expert annotation required for learning-based methods.

Results
We developed Tribus, an interactive knowledge-based classifier for multiplexed images and proteomic datasets that avoids hard-set thresholds and manual labeling. We demonstrated that Tribus recovers fine-grained cell types, matching the gold standard annotations by human experts. Additionally, Tribus can target ambiguous populations and discover phenotypically distinct cell subtypes. Through benchmarking against three similar methods in four public datasets with ground truth labels, we show that Tribus outperforms other methods in accuracy and computational efficiency, reducing runtime by an order of magnitude. Finally, we demonstrate the performance of Tribus in rapid and precise cell phenotyping with two large in-house whole-slide imaging datasets.

Availability
Tribus is available at https://github.com/farkkilab/tribus as an open-source Python package.

Supplementary information
Supplementary data are available at Bioinformatics online.
Disruption of oocyte SUMOylation impacts critical regulatory processes during folliculogenesis in mice
Authors: Liao Zian , Steenwinkel Tessa E , Moscoso Bruno , Salas Ernesto , Patton Bethany K , Rodriguez Amanda , Malovannaya Anna , Pangas Stephanie A 
Published: February 2025

Abstract
The conjugation of small ubiquitin-like modifiers (SUMO) to target proteins, known as SUMOylation, plays a crucial role in regulating protein homeostasis, activity, interaction with other proteins, and subcellular localization. Loss of SUMOylation in non-growing oocytes by conditional deletion of the E2 sumo conjugating enzyme, Ube2i, at the primordial follicle stage leads to female sterility due to complex changes in oocyte development, including altered folliculogenesis, defective meiotic progression, and premature loss of the ovarian reserve. In this study, proteomics was used to compare control and Ube2i conditional knockout ovaries during the first wave of folliculogenesis to identify key differences that may drive the premature follicle loss phenotype. Data are available via ProteomeXchange with identifier PXD055913. Label-free mass spectrometry results showed that 238 proteins were significantly altered more than 2-fold (P &lt; 0.05). Proteins upregulated in the Ube2i conditional knockout ovaries included those involved in mRNA splicing and WNT signaling, while those downregulated were related to metabolism, mitochondria, and the maternal effect proteins NLRP2 and NLRP9B. The majority of differentially expressed proteins showed no change by transcriptome analysis, indicating protein level regulation and revealing potential SUMOylation targets with necessary roles in oocyte and follicle development.
High-dimensional Factor Analysis for Network-linked data
Authors: Li Jinming , Xu Gongjun , Zhu Ji 
Published: February 2025

Abstract
Factor analysis is a widely used statistical tool in many scientific disciplines, such as psychology, economics, and sociology. As observations linked by networks become increasingly common, incorporating network structures into factor analysis remains an open problem. In this paper, we focus on high-dimensional factor analysis involving network-connected observations, and propose a generalized factor model with latent factors that account for both the network structure and the dependence structure among high-dimensional variables. These latent factors can be shared by the high-dimensional variables and the network, or exclusively applied to either of them. We develop a computationally efficient estimation procedure and establish asymptotic inferential theories. Notably, we show that by borrowing information from the network, the proposed estimator of the factor loading matrix achieves optimal asymptotic variance under much milder identifiability constraints than existing literature. Furthermore, we develop a hypothesis testing procedure to tackle the challenge of discerning the shared and individual latent factors’ structure. The finite sample performance of the proposed method is demonstrated through simulation studies and a real-world dataset involving a statistician co-authorship network.
Minimally invasive resection is associated with decreased occurrence of early delayed gastric conduit emptying after Ivor-Lewis esophagectomy
Authors: Rompen Ingmar F , Yilmazcelik Batuhan , Crnovrsanin Nerma , Schiefer Sabine , Jorek Nicolas , Kantowski Marcus , Al-Saeedi Mohammed , Michalski Christoph W , Sisic Leila , Schmidt Thomas , Müller-Stich Beat P , Nienhüser Henrik 
Published: February 2025

Summary
Early delayed gastric conduit emptying (DGCE) is a frequent complication after Ivor-Lewis esophagectomy (ILE). Despite its relevance, few studies are published using the international consensus criteria. Therefore, we aimed to assess predictors and clinical consequences of DGCE in patients after ILE. This analysis represents a retrospective, single-center cohort study of patients who underwent ILE (2016–2021). DGCE was assessed by the international consensus criteria. Univariable and a multivariable penalized LASSO logistic regression model was applied to identify predictors of DGCE, whereas postoperative outcomes were assessed by group comparisons. The incidence of early DGCE was 15.6% (46/294 included patients). Of all tested preoperatively known and treatment related factors, only minimally invasive surgery was associated with lower odds for the occurrence of DGCE (OR 0.33, 95%CI:0.12–0.77, P = 0.017) when compared to open surgery. When DGCE occurred, the impact on major postoperative morbidity was limited (DGCE 39.1% vs. non-DGCE 33.1%, P = 0.425), especially there were no differences in starting adjuvant treatment (DGCE 50% vs. non-DGCE 46%; P = 0.615) or overall survival (Log-Rank P = 0.995). The results of this study suggest that the impact of DGCE might have been overestimated in the past. The only factor found to be significantly associated with decreased DGCE was minimally invasive surgery. Therefore, individual patient selection for preventive interventions is difficult and routine preventive interventions only seem justified when they can be performed with low adverse outcomes and at low cost. Higher evidence from randomized controlled trials is needed to assess the optimal strategy to prevent and treat DGCE.
Added predictive value of childhood physical fitness to traditional risk factors for adult cardiovascular disease
Authors: Fraser Brooklyn J , Blizzard Leigh , Tomkinson Grant R , Dwyer Terence , Venn Alison J , Magnussen Costan G 
Published: February 2025

Abstract

Aim
Childhood physical fitness is a predictor of cardiovascular (CV) health but is underutilised in health surveillance. This study determined the predictive utility of child physical fitness levels on obesity, hypertension, dyslipidaemia, and the metabolic syndrome (MetS) in adulthood over traditional CV risk factors in childhood.

Methods
A longitudinal cohort study of Childhood Determinants of Adult Health Study participants who had their fitness (cardiorespiratory fitness (CRF): 1.6 km run/walk, physical work capacity at 170 beats per minute; muscular fitness: dominant handgrip strength, standing long jump) measured as children and their CV health assessed as children and adults (mean follow-up=27 years). Participants had their body mass index (BMI), waist circumference, blood pressure, fasting blood sample (lipids, glucose), and smoking status assessed as children in 1985 and in early adulthood (2004-06, 26-36 years) and/or middle adulthood (2014-19, 36-49 years) where obesity, hypertension, dyslipidaemia, and MetS were defined. Logistic regression was used to model associations (N range=578-5049).

Results
Additionally considering childhood CRF or muscular fitness improved the ability to discriminate and fit models to predict adult obesity, low HDL-C and MetS when added to demographics (age, sex) and the corresponding measure in childhood (BMI, HDL-C, CV risk score), as reflected by increments in area under the curve (Δrange=0.003-0.022), net reclassification index (range=0.026-0.149), integrated discrimination index (range=0.003-0.027), reductions in deviance and Brier scores, and statistically significant likelihood ratio tests.

Conclusion
CRF and muscular fitness are independent health indicators that could complement other risk factors in childhood to identify individuals at increased long-term CV risk.
‘Diagnose & Adios’: Multi-Perspective Insights on Formal Service Use in Dementia Family Caregivers
Authors: Falzarano Francesca , Greenfield Annabelle , Osso Francesco , Bumbalova Katerina , Bloom Rachel F 
Published: February 2025

Abstract

Background and Objectives
Dementia family caregiving is a complex role that becomes increasingly intense and demanding over time. The utilization of home and community-based services (HCBS) can provide knowledge and skills to foster preparedness, which may protect against adverse caregiving outcomes; yet actual uptake of services remains low. The current study aims to gather multi-perspective insights underlying the disconnect between caregivers' need for - versus utilization of - HCBS using Pearlin et al.’s (1990) stress process model as a guiding theoretical framework.

Research Design and Methods
Five focus groups of 4-8 participants each were conducted with dementia family caregivers (n=13) and Subject Matter Experts (n=17). A deductive-inductive thematic approach was used for data analysis.

Results
Three overarching concepts were identified: “Pathways to Preparedness'', “Multi-Level Barriers”, and “Bridging the Gap.” Findings reflected caregivers’ need for support in four core areas: 1) Dementia-specific education/training; 2) Competent mental health support; 3) Financial/legal navigation, and 4) Emergency readiness. Results revealed cross-dimensional barriers across individual-, provider-, and systemic-contexts impeding HCBS access and utilization. Personalized caregiving navigation and technology were deemed potential solutions to facilitate clearer clinical pathways between unmet needs and relevant services.

Discussion and Implications
Results underscore the complexity of the HCBS system in the United States and highlight the multidimensional barriers disrupting the pipeline connecting caregivers to HCBS. Findings can inform web-based behavioral interventions aiming to enhance family caregivers’ knowledge of, access to, and utilization of formal services in community settings.
Single-Cell Transcriptomic Profile of Innate Cell Populations in Mesenteric Lymph Nodes of Inflammatory Bowel Disease Patients
Authors: Wils Pauline , Habibi Kavashkohie Mohammad Reza , Sélos Guerra Fabiana , Landais Séverine , Rubio Manuel , Mehta Heena , Sarfati Marika , Chapuy Laurence 
Published: February 2025

Abstract

Background and Aims
Innate immune cells, including dendritic cells (DCs), monocytes (Mono), macrophages (Mac), natural killer (NK), and innate lymphoid cells (ILC), contribute to chronic inflammation in lymphoid tissues. Here, we characterized the innate immune cell landscape in inflamed mesenteric lymph nodes (MLNs) of patients with inflammatory bowel diseases (IBD) at the single-cell level.

Methods
Surgically resected colonic MLNs were obtained from patients with Crohn’s disease (CD; n = 3), ulcerative colitis (UC; n = 3), non-inflamed UC (n = 1), and non-IBD (n = 2). CD45+CD3−CD19− non-T/non-B cells were FACS-sorted to capture rare innate immune cells. Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) was performed on the BD Rhapsody platform alongside multiparameter flow cytometry staining.

Results
CITE-seq analysis unveiled the molecular signature of 11 Mono/Mac/DC (MMDC) and 7 NK/ILC enriched clusters in human MLNs. DC clusters included 3 newly characterized DC clusters such as CD1c/CD163/VCAN/CD64-expressing DC3; AXL-expressing DCs; and a CD103+ DC subset, expressing LTB, S100B, and IL22RA2 (encoding IL22BP). Mono/Mac clusters comprised inflammatory monocytes, which accumulated in IBD compared to non-IBD MLNs. Among NK/ILC clusters, we identified a cytotoxic ILC subset (IL7R, KLRD1, GNLY), previously not reported in MLNs, reminiscent of cytotoxic ILC1-like cells found in inflamed gut mucosa.

Conclusion
CITE-seq and flow-cytometry analyses of colonic MLNs from patients with active IBD reveal the molecular signature and cell distribution of previously uncharacterized DC and ILC subpopulations in human MLNs. These findings expand our understanding of immune responses during chronic inflammation in IBD.
Serum IgG1 and IgG3 antibody responses to Chlamydia trachomatis Pgp3 and Hsp60 in tubal factor infertility
Authors: Holster Tiina , Joki-Korpela Päivi , Yu Hong , Brunham Robert C , Tiitinen Aila , Paavonen Jorma , Puolakkainen Mirja 
Published: February 2025

Abstract

Purpose
Our goal was to investigate IgG1 and IgG3 antibody responses to Chlamydia trachomatis proteins Pgp3 and Hsp60 in women with tubal factor infertility (TFI). Our goal was to determine the role of these biomarkers in the diagnosis of C. trachomatis-associated TFI, and assess their sensitivity and specificity for detecting tubal pathology.

Methods
Serum samples were collected from 258 subfertile women, and 34 women positive for C. trachomatis by nucleic acid amplification test (NAAT). IgG1 and IgG3 antibodies to Pgp3 and Hsp60 were measured using enzyme immune assays (EIA).

Results
Pgp3 IgG1 antibodies were detected in 68.2% of TFI cases and 31.8% of controls (non-TFI), while Hsp60 IgG1 antibodies were found in 36.4% of TFI cases. Pgp3 IgG1 had the highest sensitivity for TFI (68.2%, 95% CI [45.1–86.1]), while Hsp60 IgG3 was the most specific (93.6%, 95% CI [89.7–96.4]). Antibody levels increased with tubal damage severity. Among the 34 NAAT-positive women, 78.8% were positive for Pgp3 IgG1.

Conclusions
Pgp3 IgG1 antibody was a sensitive marker for detecting C. trachomatis-related TFI, while Hsp60 IgG3 antibody was highly specific. These findings suggest that Pgp3 and Hsp60 antibodies and antibody subclass testing may be useful diagnostic tools for assessing TFI.
Automated surrogate-assisted particle swarm optimizer with an adaptive parental guidance strategy for expensive engineering optimization problems
Authors: Dai Rui , Jie Jing , Wang Zheng , Zheng Hui , Wang Wanliang 
Published: February 2025

Abstract
Surrogate-assisted evolutionary algorithms (SAEAs) have emerged as powerful tools for addressing complex engineering optimization problems, but their implementation often involves extensive manual intervention. To reduce the subjectivity of human design and lower computational costs, this paper proposes a generalized framework of automated surrogate-assisted optimization inspired by ensemble learning. Within this framework, we develop the AutoSAPSO algorithm, which integrates model and algorithm adaptation at the control layer. The algorithm employs an adaptive parental guidance strategy (APGS) to dynamically adjust optimizer selection based on population diversity and convergence trends, an automated parameter control strategy (APCS) to fine-tune key algorithm parameters during optimization, and an ensemble model dynamic selection (EMDS) strategy to enhance surrogate model accuracy by leveraging problem-specific characteristics. Additionally, an interactive cooperative optimization strategy (ICOS) is introduced to improve generalization ability and prediction accuracy by enabling dynamic interactions between the metamodel and objective function. The performance of AutoSAPSO is evaluated using 20 benchmark functions and verified with three real-world engineering optimization problems. Results demonstrate that AutoSAPSO significantly outperforms state-of-the-art approaches regarding convergence accuracy and robustness, confirming its potential as a general-purpose optimization tool for expensive engineering optimization problems.
Phototherapeutic keratectomy for calcific band keratopathy secondary to multiple myeloma
Authors: Tardão Gonçalo , Moraes Filipe , Barros Sandra R , Cardoso Ana , Campos Nuno 
Published: February 2025

Abstract
To report a case of calcific band keratopathy (CBK) secondary to multiple myeloma (MM) successfully treated with phototherapeutic keratectomy (PTK). An 80-year-old woman presented with progressive vision loss in her left eye with a best corrected visual acuity (BCVA) of 4/10 in the left eye (OS). Slit-lamp examination revealed a central band-like corneal opacification indicative of CBK. Anterior segment optical coherence tomography (AS-OCT) showed a subepithelial hyper reflective layer. Further evaluation confirmed an indolent IgAk MM, with no indication for systemic therapy. PTK was performed using the Technolas® TENEO™ 317 M2 excimer laser, resulting in corneal surface regularization and BCVA improvement. At 1-year follow-up, the patient was asymptomatic, had a clear cornea, normal topography, and a BCVA of 10/10. CBK can be associated with systemic conditions. PTK is an effective and safe procedure for managing CBK, and can provide complete visual rehabilitation.