bluuebunny/crossref_metadata_2025 huggingface dataset:
An Efficient and Exact Algorithm for Locally
h
-Clique Densest Subgraph Discovery
Authors: Xu Xiaojia , Liu Haoyu , Lv Xiaowei , Wang Yongcai , Li Deying
Published: December 2024

Detecting locally, non-overlapping, near-clique densest subgraphs is a crucial problem for community search in social networks. As a vertex may be involved in multiple overlapped local cliques, detecting locally densest sub-structures considering
h
-clique density, i.e.,
locally h-clique densest subgraph (LhCDS)
attracts great interests. This paper investigates the L
h
CDS detection problem and proposes an efficient and exact algorithm to list the top-
k
non-overlapping, locally
h
-clique dense, and compact subgraphs. We in particular jointly consider
h
-clique compact number and L
h
CDS and design a new ''Iterative Propose-Prune-and-Verify'' pipeline
(IPPV)
for top-
k
L
h
CDS detection. (1) In the proposal part, we derive initial bounds for
h
-clique compact numbers; prove the validity, and extend a convex programming method to tighten the bounds for proposing L
h
CDS candidates without missing any. (2) Then a tentative graph decomposition method is proposed to solve the challenging case where a clique spans multiple subgraphs in graph decomposition. (3) To deal with the verification difficulty, both a basic and a fast verification method are proposed, where the fast method constructs a smaller-scale flow network to improve efficiency while preserving the verification correctness. The verified L
h
CDSes are returned, while the candidates that remained unsure reenter the
IPPV
pipeline. (4) We further extend the proposed methods to locally more general pattern densest subgraph detection problems. We prove the exactness and low complexity of the proposed algorithm. Extensive experiments on real datasets show the effectiveness and high efficiency of
IPPV.
Codes are available at: https://github.com/Elssky/IPPV
Buffered Persistence in B+ Trees
Authors: Du Mingzhe , Scott Michael L.
Published: December 2024

Non-volatile Memory (NVM) offers the opportunity to build large, durable B+ trees with markedly higher performance and faster post-crash recovery than is possible with traditional disk- or flash-based persistence. Unfortunately, cache flush and fence instructions, required for crash consistency and failure atomicity on many machines, introduce substantial overhead not present in non-persistent trees, and force additional NVM reads and writes. The overhead is particularly pronounced in workloads that benefit from cache reuse due to good temporal locality or small working sets---traits commonly observed in real-world applications.

In this paper, we propose a buffered durable B+ tree (BD+Tree) that improves performance and reduces NVM traffic via
relaxed
persistence. Execution of a BD+Tree is divided into
epochs
of a few milliseconds each; if a crash occurs in epoch
e,
the tree recovers to its state as of the end of epoch
e
-2. (The persistence boundary can always be made current with an explicit sync operation, which quickly advances the epoch by 2.) NVM writes within an epoch are aggregated for delayed persistence, thereby increasing cache reuse and reducing traffic to NVM.

In comparison to state-of-the-art persistent B+ trees, our micro-benchmark experiments show that BD+Tree can improve throughput by up to 2.4x and reduce NVM writes by up to 90% when working sets are small or workloads exhibit strong temporal locality. On real-world workloads that benefit from cache reuse, BD+Tree realizes throughput improvements of 1.1--2.4x and up to a 99% decrease in NVM writes. Even on uniform workloads, with working sets that significantly exceed cache capacity, BD+Tree still improves throughput by 1--1.3x. The performance advantage of BD+Tree increases with larger caches, suggesting ongoing benefits as CPUs evolve toward gigabyte cache capacities.
Connectivity-Oriented Property Graph Partitioning for Distributed Graph Pattern Query Processing
Authors: Shi Min , Peng Peng , Zhou Xu , Liu Jiayu , Xiao Guoqing , Li Kenli
Published: December 2024

Graph pattern query is a powerful tool for extracting crucial information from property graphs. With the exponential growth of sizes, property graphs are typically divided into multiple subgraphs (referred to as
partitions
) and stored across various sites in distributed environments. Existing graph partitioning methods have not been efficiently optimized for pattern queries, resulting in numerous query matches across multiple partitions, called
crossing matches.
Identifying these matches requires much inter-partition communication, which is the primary performance bottleneck in distributed query processing. To address this issue, this paper introduces a novel connectivity-oriented relationship-disjoint partitioning method, namely RCP (Relationship Connectivity Partitioning), aimed at enhancing the efficiency of graph pattern query processing by reducing crossing matches. By employing each weakly connected component of the subgraph, which is induced by different relationship labels, as a basic unit of partition, RCP ensures that matches for both
variable-length path
and
labeled graph pattern
queries are not crossing matches. Here,
variable-length path
and
labeled graph pattern
are two common components in graph pattern queries to identify paths meeting specific label constraints and retrieve subgraphs with consistent relationship types, respectively. Moreover, in the query processing phase, we further demonstrate that all graph pattern queries, belonging to these two basic queries or their extensions, can be executed independently under RCP, thereby avoiding crossing matches. In experiments, we implemented two prototype distributed property graph systems based on Neo4j and JanusGraph, which use declarative and functional query language, respectively. Experimental results on billion-scale datasets demonstrate that our approach brings a performance improvement of nearly two orders of magnitude over state-of-the-art partitioning methods.
Constant-time Connectivity Querying in Dynamic Graphs
Authors: Xu Lantian , Wen Dong , Qin Lu , Li Ronghua , Zhang Ying , Lin Xuemin
Published: December 2024

Connectivity query processing is a fundamental problem in graph processing. Given an undirected graph and two query vertices, the problem aims to identify whether they are connected via a path. Given frequent edge updates in real graph applications, in this paper, we study connectivity query processing in fully dynamic graphs, where edges are frequently inserted or deleted. A recent solution, called D-tree, maintains a spanning tree for each connected component and applies several heuristics to reduce the depth of the tree. To improve the efficiency, we propose a new spanning-tree-based solution by maintaining a disjoint-set tree simultaneously. By combining the advantages of two trees, we achieve the constant query time complexity and also significantly improve the theoretical running time in both edge insertion and edge deletion. Our performance studies on real large datasets show considerable improvement of our algorithms.
DPconv: Super-Polynomially Faster Join Ordering
Authors: Stoian Mihail , Kipf Andreas
Published: December 2024

We revisit the join ordering problem in query optimization. The standard exact algorithm, DPccp, has a worst-case running time of O(3
n
). This is prohibitively expensive for large queries, which are not that uncommon anymore. We develop a new algorithmic framework based on subset convolution. DPconv achieves a super-polynomial speedup over DPccp, breaking the O(3
n
) time-barrier for the first time. We show that the framework instantiation for the C
max
cost function is up to 30x faster than DPccp for large clique queries.
GIDCL: A Graph-Enhanced Interpretable Data Cleaning Framework with Large Language Models
Authors: Yan Mengyi , Wang Yaoshu , Wang Yue , Miao Xiaoye , Li Jianxin
Published: December 2024

Data quality is critical across many applications. The utility of data is undermined by various errors, making rigorous data cleaning a necessity. Traditional data cleaning systems depend heavily on predefined rules and constraints, which necessitate significant domain knowledge and manual effort. Moreover, while configuration-free approaches and deep learning methods have been explored, they struggle with complex error patterns, lacking interpretability, requiring extensive feature engineering or labeled data. This paper introduces GIDCL (
G
raph-enhanced
I
nterpretable
D
ata
C
leaning with
L
arge language models), a pioneering framework that harnesses the capabilities of Large Language Models (LLMs) alongside Graph Neural Network (GNN) to address the challenges of traditional and machine learning-based data cleaning methods. By converting relational tables into graph structures, GIDCL utilizes GNN to effectively capture and leverage structural correlations among data, enhancing the model's ability to understand and rectify complex dependencies and errors. The framework's creator-critic workflow innovatively employs LLMs to automatically generate interpretable data cleaning rules and tailor feature engineering with minimal labeled data. This process includes the iterative refinement of error detection and correction models through few-shot learning, significantly reducing the need for extensive manual configuration. GIDCL not only improves the precision and efficiency of data cleaning but also enhances its interpretability, making it accessible and practical for non-expert users. Our extensive experiments demonstrate that GIDCL significantly outperforms existing methods, improving F1-scores by 10% on average while requiring only 20 labeled tuples.
Provenance-Enabled Explainable AI
Authors: Zhang Jiachi , Zhou Wenchao , Ujcich Benjamin E.
Published: December 2024

Machine learning (ML) algorithms have advanced significantly in recent years, progressively evolving into artificial intelligence (AI) agents capable of solving complex, human-like intellectual challenges. Despite the advancements, the interpretability of these sophisticated models lags behind, with many ML architectures remaining "black boxes" that are too intricate and expansive for human interpretation. Recognizing this issue, there has been a revived interest in the field of explainable AI (XAI) aimed at explaining these opaque ML models. However, XAI tools often suffer from being tightly coupled with the underlying ML models and are inefficient due to redundant computations. We introduce provenance-enabled explainable AI (PXAI). PXAI decouples XAI computation from ML models through a provenance graph that tracks the creation and transformation of all data within the model. PXAI improves XAI computational efficiency by excluding irrelevant and insignificant variables and computation in the provenance graph. Through various case studies, we demonstrate how PXAI enhances computational efficiency when interpreting complex ML models, confirming its potential as a valuable tool in the field of XAI.
Towards a Converged Relational-Graph Optimization Framework
Authors: Lou Yunkai , Lai Longbin , Lyu Bingqing , Yang Yufan , Zhou XiaoLi , Yu Wenyuan , Zhang Ying , Zhou Jingren
Published: December 2024

The recent ISO SQL:2023 standard adopts SQL/PGQ (Property Graph Queries), facilitating graph-like querying within relational databases. This advancement, however, underscores a significant gap in how to effectively optimize SQL/PGQ queries within relational database systems. To address this gap, we extend the foundational SPJ (Select-Project-Join) queries to SPJM queries, which include an additional matching operator for representing graph pattern matching in SQL/PGQ. Although SPJM queries can be converted to SPJ queries and optimized using existing relational query optimizers, our analysis shows that such a graph-agnostic method fails to benefit from graph-specific optimization techniques found in the literature. To address this issue, we develop a converged relational-graph optimization framework called RelGo for optimizing SPJM queries, leveraging joint efforts from both relational and graph query optimizations. Using DuckDB as the underlying relational execution engine, our experiments show that RelGo can generate efficient execution plans for SPJM queries. On well-established benchmarks, these plans exhibit an average speedup of 21.90x compared to those produced by the graph-agnostic optimizer.
Understanding and Reusing Test Suites Across Database Systems
Authors: Zhong Suyang , Rigger Manuel
Published: December 2024

Database Management System (DBMS) developers have implemented extensive test suites to test their DBMSs. For example, the SQLite test suites contain over 92 million lines of code. Despite these extensive efforts, test suites are not systematically reused across DBMSs, leading to wasted effort. Integration is challenging, as test suites use various test case formats and rely on unstandardized test runner features. We present a unified test suite, SQuaLity, in which we integrated test cases from three widely-used DBMSs, SQLite, PostgreSQL, and DuckDB. In addition, we present an empirical study to determine the potential of reusing these systems' test suites. Our results indicate that reusing test suites is challenging: First, test formats and test runner commands vary widely; for example, SQLite has 4 test runner commands, while MySQL has 112 commands with additional features, to, for example, execute file operations or interact with a shell. Second, while some test suites contain mostly standard-compliant statements (e.g., 99% in SQLite), other test suites mostly test non-standardized functionality (e.g., 31% of statements in the PostgreSQL test suite are nonstandardized). Third, test reuse is complicated by various explicit and implicit dependencies, such as the need to set variables and configurations, certain test cases requiring extensions not present by default, and query results depending on specific clients. Despite the above findings, we have identified 3 crashes, 3 hangs, and multiple compatibility issues across four different DBMSs by executing test suites across DBMSs, indicating the benefits of reuse. Overall, this work represents the first step towards test-case reuse in the context of DBMSs, and we hope that it will inspire follow-up work on this important topic.
Automating Vectorized Distributed Graph Computation
Authors: Zhao Wenyue , Cao Yang , Buneman Peter , Li Jia , Ntarmos Nikos
Published: December 2024

Multi-instance graph algorithms interleave the evaluation of multiple instances of the same algorithm with different inputs over the same graph. They have been shown to be significantly faster than traditional serial and batch evaluation, by sharing computation across instances. However, writing correct multi-instance algorithms is challenging; and in this work, we describe AutoMI, a framework for automatically converting vertex-centric graph algorithms into their vectorized multi-instance versions. We also develop an algebraic characterization of algorithms that can benefit best from multi-instance computation with simpler and faster streamlined vectorization. This allows users to decide when to use such optimization and instruct AutoMI to make the best use of SIMD vectorization. Using 6 real-life graphs, we show that AutoMI-converted multi-instance algorithms are 9.6 to 29.5 times faster than serial evaluation, 7.1 to 26.4 times faster than batch evaluation, and are even 2.6 to 4.6 times faster than existing highly optimized handcrafted multi-instance algorithms without vectorization.
Cylinder Lottery
Authors: Shasha Dennis
Published: December 2024

Sifting the mix.
Ubiquitous and Low-Overhead Floor Identification with Limited Cellular Information
Authors: Mostafa Sherif , Youssef Moustafa , Harras Khaled A.
Published: December 2024

Floor identification has gained much attention due to the increasing demand for indoor location-based services, especially prompt emergency response services. Leveraging cellular signals for floor identification has recently been of interest due to the pervasiveness of cellular technology. However, all current systems require information from multiple cell towers concurrently, which is inaccessible in most phones and thus severely limits their deployability.

We propose
UniCellular
, a ubiquitous and deployable floor identification system.
UniCellular
is the first system to meet the regulatory agencies’ accuracy requirements using received signal strength information from only the serving cell tower.
UniCellular
relies on a sequence of signal measurements to overcome the limited information available when using only the serving tower. Our system handles multiple challenges affecting accuracy and deployability, including noisy cellular data, overfitting, data collection overhead, and suitability for mobile device deployment. Moreover,
UniCellular
employs recent advances in deep generative models to improve the system’s robustness to unseen noisy data and reduce data collection overhead. Our extensive experiments verify
UniCellular
’s effectiveness in multiple real testbeds, where it correctly estimates the user’s exact floor up to 98.7% of the time using only the serving tower, an improvement up to 310% compared to the state-of-the-art cellular-based system. Furthermore,
UniCellular
can remain regulatory-compliant with up to 70% reduction in available training data.
UniCellular
achieves these improvements with over an order of magnitude reduction in the model size compared to the state-of-the-art. This shows
UniCellular
’s superior performance while providing a ubiquitous, efficient, and practical solution that meets regulatory requirements.
From Representation to Response: Assessing the Alignment of Large Language Models with Human Judgment Patterns
Authors: Hrytsyna Anastasiia , Alves Rodrigo
Published: December 2024

Large language models (LLMs) are sophisticated artificial intelligence systems designed to process and understand natural language at a complex level. The recent progress of these models, culminating in chat-based LLMs, has democratized the accessibility of these sophisticated intelligent systems, showcasing how machine learning methods can help humans in daily tasks. This research addresses the growing interest in understanding the mechanisms of LLMs and in evaluating their alignment with human cognition. We introduce an innovative alignment assessment strategy in the realm of LLMs that diverges from traditional approaches, utilizing the odd-one-out triplet-based task to investigate the alignment of LLMs’ representations with human object concept mental organization. Our methodology, which incorporates image captioning and zero/few-shot learning accuracy scoring, is designed to evaluate language models’ ability to predict similarities and differences in object concepts. A comprehensive experimental evaluation was conducted, involving four captioning strategies, twenty-four LLMs across eight model families, and three scoring procedures, utilizing a significantly large dataset for enhanced understanding of LLM comprehensibility. Finally, our study explores the impact of object description comprehensiveness on model-human representation alignment and analyzes a subset of randomly selected triplets to assess how LLMs are able to represent different levels of human judgment patterns.
Antiplatelet Effects of a Combination of Sappan Wood (Caesalpinia sappan L.) and Red Ginger (Zingiber officinale var. Rubrum) Extracts in a High‐Fat Diet‐Induced Rat Model
Authors: Puteri Meidi Utami , Afifah Nur , Mathriul Anisa Qisti , Wicaksono Farhan Mahmudi , Sugiarti Mellynia Tri , Izzatinisa Raihana , Kato Mitsuyasu , Saputri Fadlina Chany
Published: December 2024

Background: Antithrombotic medications, including antiplatelet agents, are standard treatments for patients with hyperlipidemia who have a high risk of developing cardiovascular disease (CVD). The ongoing exploration of new antiplatelet agents with minimal bleeding effects is crucial, including the investigation of potential compounds derived from natural products. This study intended to evaluate the antiplatelet effects of a combined extract of sappan wood (Caesalpinia sappan L.) and red ginger (Zingiber officinale var. Rubrum) in high‐fat diet‐(HFD)‐induced rats.

Methods: Eighteen male Wistar rats were grouped into six groups (n = 3): control, negative, positive, and three groups of various combinations of extracts. All groups, excluding the control group, were fed an HFD for 8 weeks. In the eighth week, the control and negative groups were given carboxyl methyl cellulose (CMC) 0.5%, the positive control group was administered aspirin, and the other three groups were administered the combination extract of sappan wood and red ginger at various doses for 2 weeks. Blood samples were collected to assess the levels of hyperlipidemia and platelet hyperactivity markers by enzyme‐linked immunosorbent assay (ELISA). The physiological effects of platelet hyperactivity were evaluated using the tail bleeding assay.

Results: HFD‐induced hypertriglyceridemia and hypercholesterolemia synergistically enhanced platelet hyperactivity after 8 weeks of induction. Interestingly, administration of all doses of the combined extract for 2 weeks significantly decreased the platelet activation markers P‐selectin, RANTES, and PCSK9 in a dose‐dependent manner compared with the negative control. In addition, the combination of sappan wood and red ginger extract at dose 3 (sappan wood:red ginger: 200:800 mg/200 bw/day) significantly extended the bleeding time of rats (p < 0.05) compared to the negative control.

Conclusion: Collectively, our results highlight the antiplatelet effect of a combination of sappan wood and red ginger extract in HFD‐fed rats.
A Review on the Application of Traditional to Modern Approaches of Chinese Herbal Veterinary Medicines: Current Status and Challenges
Authors: Xu Fangbing , Yao Yecheng , Li Yifan , Wang Weiming , Wu Zhiyong
Published: December 2024

Chinese herbal medicine, a cornerstone of traditional medical practices, possesses the potential to make a significant impact on international veterinary care. For these ancient therapeutic methods to be seamlessly integrated into contemporary healthcare, they must undergo thorough research and stringent validation. The rapid advancements in the biotechnology field have propelled the modernization of the Chinese medicine industry, leading to remarkable progress and innovation. This study aims to dissect the distinctions and intersections in the utilization of Chinese herbal medicine between the veterinary and human healthcare sectors. It seeks to understand how these applications can be adapted to enhance veterinary practices on an international scale. The findings of this review underscore the disparities and synergies between Chinese herbal medicine in veterinary and human medicine. It brings to light the unique challenges and opportunities that arise from the adaptation of these treatments in a veterinary context. To sum up, this article emphasizes the application prospect of Chinese veterinary medicine and challenges and puts forward the strategy to cope with the complexity of the strategic direction and development. It advocates for an interdisciplinary approach and the adoption of novel technologies to further the field.
Inquisition of the Phytochemistry, Antioxidants, and Hemolytic and Antimicrobial Potential of Polar Extracts of Moringa oleifera Leaves Indigenously Grown in Pakistan
Authors: Jamal Adil , Arif Amina , Kiran Shumaila , Shahid Muhammad Naveed , Hossain Md. Belal
Published: December 2024

Phytochemicals and metabolites make Moringa oleifera (MO) a very nutritious vegetable tree with therapeutic properties. MO leaves contain phytochemicals that have anticarcinogenic, antidiabetic, antioxidant, and antibacterial abilities. This study investigates the antibacterial, antioxidant, total phenolic, total flavonoid , and hemolytic and antimicrobial activities of MO leaf (MoLe) extracts grown indigenously in Pakistan. Phytochemical study utilizing qualitative chemical tests revealed the presence of key phytochemical components such as alkaloids, saponins, flavonoids, tannins, coumarins, quinones, and terpenoids in organic solvents. Antioxidant (SOD, POD, and CAT) activities in the MoLe aqueous extract vary dose‐dependently. Acetic acid extract endured the highest total phenolic content (TPC) and total flavonoid content (TFC), followed by n‐hexane, chloroform, and butanol solvents. The current investigation suggests that all extracts have the ability, to varying extents, to function as radical scavengers because of the presence of polyphenolics. 2,2‐Diphenyl‐1‐picrylhydrazyl (DPPH) activity was observed to be significantly varied in all solvents, with the highest activity observed in acetic acid, methanol, and n‐butanol. Maximum ZOI (mm) in Streptococcus pneumoniae (13 ± 1.24) and Staphylococcus aureus (17 ± 1.26) was marked by an aqueous solvent; likewise, Escherichia coli (13 ± 1.24) and Pseudomonas aeruginosa (15 ± 1.69) showed maximum ZOI by acetic acid and methanol, respectively. Additionally, the acetic acid extract showed significant inhibitory activity (ZOI, mm) against fungal pathogens Aspergillus fumigatus (22 ± 1.24), A. flavus (24 ± 1.24). Maximum hemolytic was documented by aqueous (0.51 ± 0.001) followed by acetic acid (0.38 + 0.003), whereas minimum one was exhibited by n‐hexane (0.3 ± 0.002). Overall, the results indicated that MoLe is an excellent selection for elevated antioxidants, DPPH activity, and biological control of bacterial and fungal pathogens.
Supplemental Figure S2 from Precision Patient Navigation to Improve Rates of Follow-up Colonoscopy, An Individual Randomized Effectiveness Trial
Authors: Coronado Gloria D. , Rawlings Andreea M. , Petrik Amanda F. , Slaughter Matthew , Johnson Eric S. , Hannon Peggy A. , Cole Allison , Vu Thuy , Mummadi Rajasekhara R.
Published: December 2024

Supplemental Figure S2
Supplemental Figure S1 from Precision Patient Navigation to Improve Rates of Follow-up Colonoscopy, An Individual Randomized Effectiveness Trial
Authors: Coronado Gloria D. , Rawlings Andreea M. , Petrik Amanda F. , Slaughter Matthew , Johnson Eric S. , Hannon Peggy A. , Cole Allison , Vu Thuy , Mummadi Rajasekhara R.
Published: December 2024

Supplemental Figure S1
Figure 2 from Nuclear Focal Adhesion Kinase Protects against Cisplatin Stress in Ovarian Carcinoma
Authors: Zhang Yichi , Ojalill Marjaana , Boyer Antonia , Chen Xiao Lei , Tahon Elise , Thivolle Lioux Gaëtan , Xia Marvin , Abbas Maryam , Soylu Halime Meryem , Flieder Douglas B. , Connolly Denise C. , Molinolo Alfredo A. , McHale Michael T. , Stupack Dwayne G. , Schlaepfer David D.
Published: December 2024

Nuclear FAK accumulation occurs upon cisplatin treatment of human and murine ovarian tumor cells. A, Nuclear and cytoplasmic cell fractionation of human OVCAR4 cells treated with DMSO (control) or cisplatin (1 μmol/L) for 12 hours followed by immunoblotting for FAK pY397, total FAK, β-tubulin (cytoplasmic marker), and histone H3 (nuclear marker). B, Schematic of GFP fusion to FAK denoting N-terminal band 4.1, ezrin, radixin, moesin homology (FERM), kinase, and focal adhesion targeting (FAT) domains. FAK FERM arginine R177 and R178 to alanine mutational changes prevent FAK nuclear localization. C, Stable reexpression of GFP-FAK-WT (WT) and GFP-FAK-NLS− (NLS−) in KMF FAK KO murine ovarian tumor cells as analyzed by FAK, pY397 FAK, and β-actin immunoblotting. D, KMF FAK-WT and KMF FAK-NLS− cells treated with DMSO (control) or cisplatin (20 μmol/L) for 1 hour and immunoblotting for FAK pY397 and total FAK. E, Confocal immunofluorescence imaging was used to visualize GFP-FAK and DAPI stain in FAK-WT and FAK-NLS− cells treated with DMSO (control) or cisplatin (20 μmol/L) for 12 hours. Shown are representative images of GFP-FAK (images shown at midline of Z-stack), nucleus, and merged images. Scale bar, 10 μm. F, Nuclear and cytoplasmic fractionation of FAK-WT and FAK-NLS− cells treated with cisplatin (20 μmol/L) for 0, 12, or 24 hours followed by immunoblotting for FAK, β-tubulin, and histone H3. G, Representative images of GFP-FAK-WT and FAK-NLS− expressing (images shown at midline of Z-stack) and DAPI-stained cells treated with leptomycin B (50 nmol/L) for 6 hours. Scale bar, 10 μm. Cyto, cytoplasmic.
Figure 1 from Nuclear Focal Adhesion Kinase Protects against Cisplatin Stress in Ovarian Carcinoma
Authors: Zhang Yichi , Ojalill Marjaana , Boyer Antonia , Chen Xiao Lei , Tahon Elise , Thivolle Lioux Gaëtan , Xia Marvin , Abbas Maryam , Soylu Halime Meryem , Flieder Douglas B. , Connolly Denise C. , Molinolo Alfredo A. , McHale Michael T. , Stupack Dwayne G. , Schlaepfer David D.
Published: December 2024

Active FAK staining increases in the nucleus of HGSOC patient tumors after neoadjuvant chemotherapy. A, IHC staining of paraffin-embedded serial initial tumor biopsy sections (patient 1014109 and patient 3000276) and corresponding tumor resection after neoadjuvant chemotherapy treatment. Samples were stained with H&E and phosphospecific antibodies to the FAK activation loop Y576 (pY576) within the kinase domain. Scale is 100 μm (inset scale is 25 μm). B, Image quantification of percent of tumor cell area exhibiting FAK pY576 staining. Paired tumor samples (n = 8) from initial biopsy (blue circles) and from surgical tumor debulking after neoadjuvant chemotherapy (red circles). Dotted lines connect paired patient tumor samples collected prior to and after neoadjuvant chemotherapy (***, P < 0.001). Chemo, chemotherapy; H&E, hematoxylin and eosin; NeoAdj, neoadjuvant.
Data from Nuclear Focal Adhesion Kinase Protects against Cisplatin Stress in Ovarian Carcinoma
Authors: Zhang Yichi , Ojalill Marjaana , Boyer Antonia , Chen Xiao Lei , Tahon Elise , Thivolle Lioux Gaëtan , Xia Marvin , Abbas Maryam , Soylu Halime Meryem , Flieder Douglas B. , Connolly Denise C. , Molinolo Alfredo A. , McHale Michael T. , Stupack Dwayne G. , Schlaepfer David D.
Published: December 2024

Abstract
Tumor chemotherapy resistance arises frequently and limits high-grade serous ovarian cancer (HGSOC) patient survival. Focal adhesion kinase (FAK) is an intracellular protein–tyrosine kinase encoded by PTK2, a gene that is often gained in HGSOC. Canonically, FAK functions at the cell periphery. However, FAK also transits to the nucleus to modulate gene expression. We find that FAK is tyrosine-phosphorylated and nuclear-localized in tumors of patients with HGSOC surviving neoadjuvant platinum–paclitaxel chemotherapy and that FAK nuclear accumulation occurs upon subcytotoxic cisplatin exposure to ovarian tumor cells in vitro. FAK nuclear localization sequence (NLS) mutational inactivation resulted in tumor cell sensitization to cisplatin in vitro and in vivo relative to wild-type FAK-reconstituted ovarian tumor cells. Cisplatin cytotoxicity was associated with elevated ERK MAPK activation in FAK NLS− cells, cisplatin-stimulated ERK activation was also enhanced upon loss of FAK activity or expression, and cisplatin-stimulated cell death was prevented by an inhibitor of ERK signaling. MAPK phosphastase-1 (MKP1) negatively regulates ERK signaling, and cisplatin-induced MKP1 levels were significantly elevated in wild-type FAK compared with FAK NLS− ovarian tumor cells. Notably, small-molecule MKP1 inhibition enhanced both cisplatin-stimulated ERK phosphorylation and ovarian tumor cell death. Together, our results show that FAK expression, activity, and nuclear localization limit cisplatin cytotoxicity in part by regulating MKP1 levels and preventing noncanonical ERK/MAPK activation.
Significance:
FAK inhibitors are in combinatorial clinical testing with agents that prevent Ras–Raf–MAPK pathway activation in various cancers. This study suggests that nuclear FAK limits ERK/MAPK activation in supporting HGSOC cell survival to cisplatin stress. Overall, it is likely that targets of FAK-mediated survival signaling may be tumor type– and context-dependent.
Multilevel Mediators on the Associations of Neighborhood Social Environmental Factors and Severity of Metabolic Syndrome: The Jackson Heart Study
Authors: Moniruzzaman Mohammad , Reid Lauren A. , Jones Kelly K. , Zenk Shannon N. , Vega Gloria L. , Grundy Scott M. , Sims Mario , Powell‐Wiley Tiffany M. , Tamura Kosuke
Published: December 2024

Background

Neighborhood characteristics serve as risk factors for metabolic syndrome (MetS). However, the intermediary factors linking this relationship remain understudied. Thus, we investigated the sex‐specific mediating role of C‐reactive protein, physical activity (PA), and perceived stress in the associations of perceived neighborhood social environment (PNSE) with MetS severity among Black adults.

Methods and Results

This cross‐sectional study included 3185 adults (64% women) from exam 1 (2000–2004) of the Jackson Heart Study. MetS severity
Z
scores were calculated based on the Adult Treatment Panel III criteria formula. PNSE included neighborhood violence, problems, and social cohesion. Men and women were analyzed separately. A bootstrap resampling technique with 95% bias‐corrected CI (95% BC CI) was used to evaluate whether C‐reactive protein, PA, and perceived stress mediated the association between each PNSE and MetS severity, adjusting for covariates. All PNSE factors were directly related to MetS severity in women but not in men. In women, neighborhood problems were indirectly associated with MetS severity mediated through PA (β=0.02 [95% BC CI, 0.00–0.05]). In men, neighborhood violence, problems, and social cohesion were indirectly associated with MetS severity mediated through PA (β=0.05 [95% BC CI, 0.01–0.10]; β=0.03 [95% BC CI, 0.00–0.06]; and β=−0.04 [95% BC CI, −0.09 to −0.01], respectively). Neither C‐reactive protein nor perceived stress mediated such associations in either women or men.

Conclusions

All PNSEs (violence, problems, and social cohesion) were directly related to MetS severity in women only. PA mediated the relationship between each PNSE and MetS in a sex‐specific manner. Efforts focusing on local conditions are needed to better understand why such disparities exist for at‐risk minoritized groups.
Susanna Clarke’s Cautionary Tale of Re-enchantment
Authors: Clarkson Joy Marie
Published: December 2024

This article offers a reading of Susannah Clarke’s 2020 award-winning novel Piranesi in relation to theories of enchantment. Clarke’s novel has often been read as an affirmation of re-enchantment, but this article will show that Piranesi acts more as a cautionary tale, pointing out the inherent tensions in projects of re-enchantment which often reinforce rather than dissolve the boundaries between inner and outer world which characterize disenchantment. Clarke’s critique of re-enchantment is largely indebted to Owen Barfield’s distinctive and complex account of modernity through his notion of the evolution of consciousness and his affirmation of anthroposophy, which has often been overlooked in contemporary scholarship of enchantment. Thus, this article both brings to light Barfield’s influence on Clarke, but also highlights how Clarke and Barfield might be drawn upon as resources for diagnosing and describing the phenomenon of disenchantment, and even perhaps constructing alternative modernities.
Toward a Holistic and Integrative Pedagogy
Authors: Coulter Dale , Yong Amos
Published: December 2024

We wish to express our thanks to our interlocutors and to the editors of Pneuma for facilitating this exchange as part of an issue on higher education within Pentecostalism. It is a humbling experience to have our work digested by seasoned administrators long at work in pentecostal higher educational spheres who share with us the calling and task of forging a Christ-formed and Spirit-infused life of the mind. Maybe the best way to hand off our dialogue is simply to reiterate Mark Cartledge’s point, in his lead essay in this issue of the journal, of the attempt to capture in the phrase “head, heart, and hands” a holistic and transformational approach to personal and spiritual formation. Come Holy Spirit, inspire our collaborative conversation and educational efforts.
Sighs and Signs of the Spirit
Authors: Asamoah-Gyadu Kwabena
Published: December 2024

This article explores the importance of Spirit-empowered scholarship for theological education. It argues that given the overwhelming presence of Christianity in such non-Western contexts as Africa and the options in these new heartlands of Christianity for theological scholarship and education that accounts for the experience of the Spirit, it is appropriate for theological education to pay attention to these developments. This is imperative for the African context in which Pentecostalism with its emphasis on the experience of the Spirit is influencing virtually every area of Christian life including what is meant by theology and theological education.
On Sensibilities and Shamsy’s “Rediscovering”
Authors: Rafudeen Auwais
Published: December 2024

While Shamsy’s Rediscovering the Islamic Classics importantly traces the events and individuals involved in the rise of print culture in the Arab world, particularly in an Egyptian context, and, even more tellingly, throws light on how Muslim reformers used this culture to reintroduce long forgotten classical Islamic works – a process which they deemed crucial in view of what they felt was a very problematic postclassical status quo and through which they substantially transformed the then hegemonic intellectual tradition – one is left with a lingering sense that a vital dimension of this transformation, namely the underlying change in sensibilities with which this transformation is associated, needs to be more thoroughly scrutinised. These sensibilities speak to new notions of time, the nature of knowledge and the purpose of life engendered by modernity, which cannot be extricated from the intellectual transformations being discussed.
“God Is Not in the Habit”
Authors: Africa Obakeng
Published: December 2024

This article examines Steve Biko’s theology of human and divine agency, centred on his remark, “God is not in the habit of coming down from heaven to solve people’s problems on earth.” Engaging John D. Caputo’s radical theology and its relational model of the chiasm, it explores the interdependence of divine insistence and human responsibility. Highlighting Biko’s critique of apartheid-era Christianity and his call for Black self-liberation, the article emphasises his theology as a call to responsibility. The dialogue with Caputo’s framework opens a deeper understanding of Biko’s theological vision, offering a relational approach to agency that redefines divine-human interaction in the struggle for justice and liberation.
L’interprétation ricœurienne de Fichte : une lecture commune du primat kantien de la raison pratique
Authors: Renzi Angela
Published: December 2024

Cette contribution se propose d’établir un lien critique entre Ricœur et Fichte afin de déterminer deux objectifs. Le premier objectif consiste à analyser la réception complexe de Fichte par Ricœur, qui constitue à mon avis une approche interprétative intéressante de la philosophie transcendantale. Ricœur souligne la richesse inexplorée de la philosophie fichtéenne, qui se trouve précisément dans la philosophie transcendantale et dans le sentiment d’être en tant qu’affirmation éthique et point de départ de la réflexion elle-même et affirme vouloir rechercher une origine éthique. Le second objectif est souligner la fécondité de l’interprétation de Ricœur, qui oriente la lecture de la morale kantienne et la primauté de la raison pratique. On peut identifier la même direction critique entre les deux philosophes, dans laquelle la vision du sujet est orientée vers une perspective éthique intersubjective et intérieure.
Je est une autre
Authors: Muller Justine
Published: December 2024

Cet article s’interroge sur la façon dont le roman autobiographique L’Invitée traduit, par le biais du personnage de Françoise, la tension de Beauvoir au départ de sa relation avec Sartre entre sa tendance à la dépendance et sa volonté d’acquérir une autonomie personnelle et littéraire. La consécration de cette autonomie se marque par le déploiement d’une esthétique qui ne repose pas sur celle de Sartre, mais qui s’inspire des techniques de divers auteurs anglo-saxons afin de dévoiler une subjectivité féminine.
La philosophie morale comme exercice de démystification dans L’Amérique au jour le jour
Authors: Tribotté Julien
Published: December 2024

L’Amérique au jour le jour de Simone de Beauvoir est un ouvrage philosophique important, mais souvent négligé par la critique anglaise en raison de choix de traduction. Les premières traductions en anglais ont occulté la dette de Beauvoir à l’égard des écrits de Richard Wright ainsi que le concept de « mystification », au cœur de son cadre philosophique. Cet article examine l’effort de Beauvoir pour dévoiler les réalités sociales de l’Amérique depuis le point de vue d’une personne issue d’un autre pays. En analysant la cohérence du livre de Beauvoir et en soulignant l’importance de la « mystification », cette étude vise à élucider son projet novateur de rendre la philosophie morale accessible par le biais de l’expérience vécue.
A new brown lacewing species of the genus Pseudonotherobius Makarkin, 2024 (Neuroptera: Hemerobiidae) from the Eocene Baltic amber
Authors: CHEN ZU-LUAN , GAO YU-HE , LIU XING-YUE
Published: December 2024

A new species of the lacewing family Hemerobiidae, Pseudonotherobius fenestromaculatus sp. nov., is described from the Eocene Baltic amber. The new species is assigned to Pseudonotherobius based on the following characters: the forewing RP with three ORBs, the ORB1 and CuP deeply forked, and the presence of dark brown coloration. The species can be distinguished from Pseudonotherobius kohlsi Makarkin, 2024 by the forewing membrane medially with a large dark marking from costal margin to M vein along third gradate series, and distally with a broad dark marking covering whole wing apex. Our finding provides new evidence for understanding the palaeodiversity of brown lacewings from the Tertiary.
A new species of Treintamilun (Odonata: Frenguelliidae) from the early Eocene of Laguna del Hunco, Patagonia, Argentina
Authors: PETRULEVIČIUS JULIÁN F.
Published: December 2024

The Frenguelliidae Petrulevičius & Nel, 2003 is an endemic family of Odonata recorded from the Eocene of Patagonia, Argentina. They are only present in the lower Eocene (52 Ma) of Laguna del Hunco, the middle Eocene (47 Ma) of Río Pichileufú, and Arroyo Chacay (no absolute dating). The family consists of four genera and six species, namely Frenguellia patagonica Petrulevičius and Nel, 2003, F. iglesiasi Petrulevičius and Nel, 2013, Treintamilun vuelvenlucha Petrulevičius, 2017, Nelala chori Petrulevičius, 2019, N. chacay Petrulevičius, 2023, and Chacayala campeona Petrulevičius, 2022.
Swarming behaviour and pollination by Cretaceous thrips (Insecta: Thysanoptera)
Authors: PEÑA-KAIRATH CONSTANZA , PEÑALVER ENRIQUE , PERIS DAVID , DELCLÒS XAVIER
Published: December 2024

Direct biotic interactions fossilize in low probability and are difficult to be recognized. This is because they normally occur over a brief time span and the conditions required for their fossilization are exceptional. Swarm behaviour in Thysanoptera (thrips) is a phenomenon that is not yet fully understood but is crucial for the survival and success of representatives of this order of insects. Moreover, the role of thrips as pollinators of gymnosperms had not gained significant attention until the Recent decline in insect populations, particularly pollinators, and the consequent impact on the flora that relies on them. Here we describe a thrips assemblage in Cenomanian Kachin amber (Myanmar, ca. 99 Ma), composed of both, females and males of the new species Burmathrips engeli gen. et sp. nov., belonging to the family Stenurothripidae, that has been interpreted as a swarm. These specimens have Cycadopites-type pollen grains attached to their bodies, with additional associated grains, most likely detached, being abundant in the same amber flow, throughout the amber piece. Nowadays, hexapod aggregations are related to different activities like mating and courtship, but identifying this type of behaviour in the fossil record is difficult. This finding demonstrates the antiquity of mating-related swarming behaviour in thrips, which is consistent with that of their extant counterparts. It also provides direct evidence that gregariousness facilitated the prominent role of thrips as gymnosperm pollinators during the Cretaceous.
Tropical cyclone genesis potential using a ventilated potential intensity
Authors: Chavas Daniel R. , Camargo Suzana J. , Tippett Michael K.
Published: December 2024

Genesis potential indices (GPIs) are widely used to understand the climatology of tropical cyclones (TCs). However, the sign of projected future changes depends on how they incorporate environmental moisture. Recent theory combines potential intensity and mid-tropospheric moisture into a single quantity called the ventilated potential intensity, which removes this ambiguity. This work proposes a new GPI (GPIv) that is proportional to the product of the ventilated potential intensity and the absolute vorticity raised to a power. This power is estimated to be approximately 5 by fitting observed tropical cyclone best-track and ECMWF Reanalysis v5 (ERA5) data. Fitting the model with separate exponents yields nearly identical values, indicating that their product likely constitutes a single joint parameter. Likewise, results are nearly identical for a Poisson model as for the power law. GPIv performs comparably well to existing indices in reproducing the climatological distribution of tropical cyclone genesis and its covariability with El Niño-Southern Oscillation, while only requiring a single fitting exponent. When applied to Coupled Model Intercomparison Project Phase 6 (CMIP6) projections, GPIv predicts that environments globally will become gradually more favorable for TC genesis with warming, consistent with prior work based on the normalized entropy deficit, though significant changes emerge only at higher latitudes under relatively strong warming. GPIv helps resolve the debate over the treatment of the moisture term and its implication for changes in TC genesis favorability with warming, and its clearer physical interpretation may offer a step forward towards a theory for genesis across climate states.
Legacies of the War on Poverty
Authors: Bahk Sung Ah , Moffitt Robert , Smeeding Timothy M.
Published: December 2024

We extend the work of Haveman et al., a comprehensive analysis of the U.S. social welfare system’s evolution from the start of the War on Poverty through 2012. Their work chronicled changes in the welfare system and in poverty measurement and analyzed poverty levels and trends. We extend the analysis through 2022, finding that the poverty rate declined from 2012 to 2019 mostly because of improvements in the economy and not from changes in the transfer system; in the 2019 to 2022 pandemic period, though, the opposite occurred, as changes in poverty rates were mostly driven by changes in government relief programs. The decline in poverty from 2012 to 2022 followed a run-up in poverty from 2000 to 2012, leaving the nation with no improvement in poverty rates from the economy since 2000. We conclude that significant future reductions in poverty will likely require further improvements in the safety net.