bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network Effects
Authors: Antony Alexander K , Thompson William R 
Published: July 2024

Abstract
This chapter looks into how network structures influence the creation of rivalry and positive peace relationships that form the constitutive elements of zones of peace. It discusses the importance of dyadic versus neighborhood attributes in driving patterns of rivalry and positive peace. From a theoretical perspective, neighborhood industrialization should both prevent the formation of local rivalries and facilitate the formation of positive peaceful ties. The chapter details how network analysis techniques are uniquely positioned to provide a way to assess the relative contribution of dyadic attributes, regional attributes, and network structure on relations between states. It considers the Exponential Random Graph Model (ERGM) as the most common and well-developed inferential network model.
Morphology, immunophenotype, and suggested diagnostic criteria of TCL1 family–negative T-prolymphocytic leukemia
Authors: Fang Hong , Wang Sa A , Beird Hannah C , Tang Zhenya , You M James , Li Shaoying , Xu Jie , Hu Shimin , Yin C Cameron , El Hussein Siba , Lin Pei , Jelloul Fatima Zahra , Vega Francisco , Medeiros L Jeffrey , Wang Wei 
Published: July 2024

Abstract

Objectives
We sought to investigate the morphologic and immunophenotypic characteristics of TCL1 family–negative T-cell prolymphocytic leukemia (T-PLL)

Methods
Twenty cases of TCL1 family–negative T-PLL were studied.

Results
The doubling time of leukemic cells ranged from less than 2 days to more than 5 years, with a median of 5.5 months. Leukemic cells were small to medium-sized, with round to irregular nuclei, variably condensed chromatin, and small amounts of agranular cytoplasm. A visible nucleolus was identified in 11 (55%) cases. Cytoplasmic blebs/protrusions were identified in all cases, but their occurrence was highly variable from case to case. Bone marrow biopsy showed an interstitial pattern in 90% of cases and a diffuse pattern in the remaining 10% of cases. Flow cytometric immunophenotypic analysis showed that the leukemic cells in all cases were CD4 positive; 3 (15%) also showed concurrent CD8 expression. All cases were positive for CD2 and CD5. Surface CD3 and CD7 were positive in 19 of 20 (95%) cases, and all CD3-positive cases expressed the T-cell receptor αβ. Compared with prototypic T-PLL cases, these 2 groups shared many immunophenotypic findings, except CD8 and CD26, both of which were more commonly expressed in prototypic T-PLL cases.

Conclusions
TCL1 family–negative T-PLL cases have morphologic and immunophenotypic features that are similar to prototypic T-PLL. They are characterized by neoplastic proliferation of small to medium-sized mature T cells with CD4-positive T-cell receptor αβ phenotype. Tumor cells frequently maintain pan-T antigen expression. Recognizing these morphologic and immunophenotypic features will aid in accurately diagnosing this rare subset of T-PLL.
SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network
Authors: Wang Yongjie , Zhou Fengfan , Guan Jinting 
Published: July 2024

Abstract

Motivation
The rise of single-cell RNA sequencing (scRNA-seq) technology presents new opportunities for constructing detailed cell type-specific gene regulatory networks (GRNs) to study cell heterogeneity. However, challenges caused by noises, technical errors, and dropout phenomena in scRNA-seq data pose significant obstacles to GRN inference, making the design of accurate GRN inference algorithms still essential. The recent growth of both single-cell and spatial transcriptomic sequencing data enables the development of supervised deep learning methods to infer GRNs on these diverse single-cell datasets.

Results
In this study, we introduce a novel deep learning framework based on shared factor neighborhood and integrated neural network (SFINN) for inferring potential interactions and causalities between transcription factors and target genes from single-cell and spatial transcriptomic data. SFINN utilizes shared factor neighborhood to construct cellular neighborhood network based on gene expression data and additionally integrates cellular network generated from spatial location information. Subsequently, the cell adjacency matrix and gene pair expression are fed into an integrated neural network framework consisting of a graph convolutional neural network and a fully-connected neural network to determine whether the genes interact. Performance evaluation in the tasks of gene interaction and causality prediction against the existing GRN reconstruction algorithms demonstrates the usability and competitiveness of SFINN across different kinds of data. SFINN can be applied to infer GRNs from conventional single-cell sequencing data and spatial transcriptomic data.

Availability and implementation
SFINN can be accessed at GitHub: https://github.com/JGuan-lab/SFINN.
Reproductive biology of Santolina ligustica Arrigoni, a rare narrow-ranged species: implications for conservation
Authors: Bonifazio Chiara , Guerrina Maria , Armanino Filippo , Casazza Gabriele , Galli Loris , Varaldo Lucia , Zappa Elena , Minuto Luigi 
Published: July 2024

Abstract
Santolina ligustica is a rare narrow-ranged species endemic to Liguria (Italy) for which a likely trend of decline has been recorded. For this reason, it would be important to assess the reproductive biology of this endemic species. In this study, we investigated the plant–pollinator interactions, the reproductive mode of the plant, and we evaluated both reproductive efficiency and seeds’ germination performances. Santolina ligustica is an obligate cross-pollinating species with a generalist pollination system. The most frequent insects are Coleoptera belonging to the genus Oedemera. Seed set is low, but the seeds germinate under a wide range of temperatures. Taken together, our results indicate that S. ligustica is an insect pollinated and self-incompatible plant, in which low visitation rate, secondary pollen presentation and/or lack of compatible mate may cause a low seed set per capitulum. Nevertheless, the high number of capitula per plant and the high percentage of germination may assure high number of seedlings. Thus, the survival of S. ligustica is probably threatened by other factors such as fragmented distribution and habitat reduction because of land-use change. Under this scenario, we proved that species’ decline is not directly related to reproductive failure and different studies are desirable to provide suggestions for the species conservation.
Surgical outcomes of hidradenitis suppurativa: evaluating factors influencing recurrence and complications after 284 complete excisions
Authors: Chang Tsung-Hsien , Sheen Yi-Shuan , Liao Yi-Hua 
Published: July 2024

Abstract

Background
Hidradenitis suppurativa (HS) is a chronic inflammatory disorder associated with tunnel formation and scarring. Surgical excision is a potential curative therapy for HS.

Objectives
To characterize the surgical outcomes of patients with HS undergoing complete excision and to identify the risk factors associated with postoperative recurrence.

Methods
This retrospective 16-year cohort study enrolled patients ≥ 20 years who underwent complete excision for HS lesions at the National Taiwan University Hospital. We assessed the rates of postsurgical recurrence and complications and estimated the odds ratio (ORs) with 95% confidence intervals (CIs) of their association with potential risk factors using generalized estimating equations.

Results
In total, 136 patients with HS and the 284 corresponding complete excisions were identified. Recurrence developed in 88 of 284 (31.0%) operations and complications occurred in 102 (35.9%). Common types of complications included wound dehiscence, hypertrophic scars and surgical-site infection. Clinical factors associated with a lower risk of recurrence were male sex [adjusted OR (aOR) 0.48, 95% CI 0.23–0.98], surgery at atypical body sites (aOR 0.28, 95% CI 0.08–0.99) and wound repair by split-thickness skin graft (aOR 0.31, 95% CI 0.12–0.77). Wound dehiscence was associated with an increased risk of recurrence (aOR 2.55, 95% CI 1.21–5.42). No independent factors were identified as being associated with composite postoperative complications.

Conclusions
Complete excision alone can be effective in curing HS in Asian populations. Recurrence developed in about one-third of the complete excisions performed for HS. Sex, surgical body sites, methods of wound repair and wound dehiscence were major determinants for recurrence.
Conversion or Reversion of Interferon γ Release Assays for Mycobacterium tuberculosis Infection: A Systematic Review and Meta-analysis
Authors: Wang Mao-Shui , Li-Hunnam Jarrod , Chen Ya-Li , Gilmour Beth , Alene Kefyalew Addis , Zhang Yan-An , Nicol Mark P 
Published: July 2024

Abstract

Background
Interferon γ release assays (IGRAs) are widely used for diagnosis of latent tuberculosis infection. However, with repeated testing, IGRA transformation (conversion or reversion) may be detected and is challenging to interpret. We reviewed the frequency of and risk factors for IGRA transformation.

Methods
We screened public databases for studies of human participants that reported the frequency of IGRA transformation. We extracted study and participant characteristics, details of IGRA testing and results. We calculated the pooled frequency of IGRA transformation (and transient transformation) and examined associated risk factors.

Results
The pooled frequency of IGRA conversion or reversion from 244 studies was estimated at 7.3% (95% confidence interval [CI], 6.1%–8.5%) or 22.8% (20.1%–25.7%), respectively. Transient conversion or reversion were estimated at 46.0% (95% CI, 35.7%–56.4%) or 19.6% (9.2%–31.7%) of conversion or reversion events respectively. Indeterminate results seldom reverted to positive (1.2% [95% CI, .1%–3.5%]). IGRA results in the borderline-positive or borderline-negative range were associated with increased risk of conversion or reversion (pooled odds ratio [OR] for conversion, 4.15 [95% CI, 3.00–5.30]; pooled OR for reversion, 4.06 [3.07–5.06]). BCG vaccination was associated with decreased risk of conversion (OR, 0.70 [95% CI, .56–.84]), cigarette smoking with decreased risk of reversion (0.44 [.06–.82]), and female sex with decreased risk of either conversion or reversion (OR for conversion, 0.66 [.58–.75]; OR for reversion, 0.46 [.31–.61]).

Conclusions
IGRA conversion is less common than reversion, and frequently transient. Research is needed to determine whether individuals with reversion would benefit from tuberculosis-preventive treatment. Retesting of people with indeterminate results is probably not indicated, because indeterminate results seldom revert to positive.
The cytidine deaminase APOBEC3C has unique sequence and genome feature preferences
Authors: Brown Grant W 
Published: July 2024

Abstract
APOBEC proteins are cytidine deaminases that restrict the replication of viruses and transposable elements. Several members of the APOBEC3 family, APOBEC3A, APOBEC3B, and APOBEC3H-I, can access the nucleus and cause what is thought to be indiscriminate deamination of the genome, resulting in mutagenesis and genome instability. Although APOBEC3C is also present in the nucleus, the full scope of its deamination target preferences is unknown. By expressing human APOBEC3C in a yeast model system, I have defined the APOBEC3C mutation signature, as well as the preferred genome features of APOBEC3C targets. The APOBEC3C mutation signature is distinct from those of the known cancer genome mutators APOBEC3A and APOBEC3B. APOBEC3C produces DNA strand-coordinated mutation clusters, and APOBEC3C mutations are enriched near the transcription start sites of active genes. Surprisingly, APOBEC3C lacks the bias for the lagging strand of DNA replication that is seen for APOBEC3A and APOBEC3B. The unique preferences of APOBEC3C constitute a mutation profile that will be useful in defining sites of APOBEC3C mutagenesis in human genomes.
SE(3) Synchronization by eigenvectors of dual quaternion matrices
Authors: Hadi Ido , Bendory Tamir , Sharon Nir 
Published: July 2024

Abstract
In synchronization problems, the goal is to estimate elements of a group from noisy measurements of their ratios. A popular estimation method for synchronization is the spectral method. It extracts the group elements from eigenvectors of a block matrix formed from the measurements. The eigenvectors must be projected, or ‘rounded’, onto the group. The rounding procedures are constructed ad hoc and increasingly so when applied to synchronization problems over non-compact groups. In this paper, we develop a spectral approach to synchronization over the non-compact group $\mathrm{SE}(3)$, the group of rigid motions of $\mathbb{R}^{3}$. We based our method on embedding $\mathrm{SE}(3)$ into the algebra of dual quaternions, which has deep algebraic connections with the group $\mathrm{SE}(3)$. These connections suggest a natural rounding procedure considerably more straightforward than the current state of the art for spectral $\mathrm{SE}(3)$ synchronization, which uses a matrix embedding of $\mathrm{SE}(3)$. We show by numerical experiments that our approach yields comparable results with the current state of the art in $\mathrm{SE}(3)$ synchronization via the spectral method. Thus, our approach reaps the benefits of the dual quaternion embedding of $\mathrm{SE}(3)$ while yielding estimators of similar quality.
Use of the DMAIC Lean Six Sigma quality improvement framework to improve beta-lactam antibiotic adequacy in the critically ill
Authors: Wessel Rebecca J , Rivera Christina G , Ausman Sara E , Martin Nathaniel , Braga Shienna A , Hagy Natalie T , Moreland-Head Lindsay N , Abu Saleh Omar M , Gajic Ognjen , Jannetto Paul J , Barreto Erin F 
Published: July 2024

Abstract
Beta-lactam antibiotics are widely used in the intensive care unit due to their favorable effectiveness and safety profiles. Beta-lactams given to patients with sepsis must be delivered as soon as possible after infection recognition (early), treat the suspected organism (appropriate), and be administered at a dose that eradicates the infection (adequate). Early and appropriate antibiotic delivery occurs in &gt;90% of patients, but less than half of patients with sepsis achieve adequate antibiotic exposure. This project aimed to address this quality gap and improve beta-lactam adequacy using the Define, Measure, Analyze, Improve, and Control Lean Six Sigma quality improvement framework. A multidisciplinary steering committee was formed, which completed a stakeholder analysis to define the gap in practice. An Ishikawa cause and effect (Fishbone) diagram was used to identify the root causes and an impact/effort grid facilitated prioritization of interventions. An intervention that included bundled education with the use of therapeutic drug monitoring (TDM; i.e. drug-level testing) was projected to have the highest impact relative to the amount of effort and selected to address beta-lactam inadequacy in the critically ill. The education and TDM intervention were deployed through a Plan, Do, Study, Act cycle. In the 3 months after “go-live,” 54 episodes of beta-lactam TDM occurred in 41 unique intensive care unit patients. The primary quality metric of beta-lactam adequacy was achieved in 94% of individuals after the intervention. Ninety-four percent of clinicians gauged the education provided as sufficient. The primary counterbalance of antimicrobial days of therapy, a core antimicrobial stewardship metric, was unchanged over time (favorable result; P = .73). Application of the Define, Measure, Analyze, Improve, and Control Lean Six Sigma quality improvement framework effectively improved beta-lactam adequacy in critically ill patients. The approach taken in this quality improvement project is widely generalizable to other drugs, drug classes, or settings to increase the adequacy of drug exposure.
Asymmetric relations and systemic misperceptions: Why and how Australia and China talk past each other
Authors: Pan Guangyi 
Published: July 2024

Abstract
Caught by conflicts, both Australia and China exhibited confused attitudes towards each other’s motives. For China, despite the common interests of strong economic and trade complementarities, Australia acts as a vassal state of the USA, campaigning against China for no reason. For Canberra, it has been frustrated by China’s ignorance of Australia’s independent position and concerns. This article explores the fundamental cause behind this misperception, arguing that asymmetric relationships lead two countries to put their attention on different levels, generating misinterpretations from both sides. As a great power, China concentrates on worldwide competition with the USA and prioritizes its global strategy while underplaying concerns of Australia. However, in Australia’s agenda, regional security and China’s expansion deepened its anxiety, so its over-attention spotlighted Beijing’s moves in a sensitive scenario. The asymmetry exacerbates each other’s threats. The article provides a systematic explanation of the China–Australia tension and clarifies the mechanism behind asymmetric relations.
The first step is the hardest: pitfalls of representing and tokenizing temporal data for large language models
Authors: Spathis Dimitris , Kawsar Fahim 
Published: July 2024

Abstract

Objectives
Large language models (LLMs) have demonstrated remarkable generalization and across diverse tasks, leading individuals to increasingly use them as personal assistants due to their emerging reasoning capabilities. Nevertheless, a notable obstacle emerges when including numerical/temporal data into these prompts, such as data sourced from wearables or electronic health records. LLMs employ tokenizers in their input that break down text into smaller units. However, tokenizers are not designed to represent numerical values and might struggle to understand repetitive patterns and context, treating consecutive values as separate tokens and disregarding their temporal relationships. This article discusses the challenges of representing and tokenizing temporal data. It argues that naively passing timeseries to LLMs can be ineffective due to the modality gap between numbers and text.

Materials and methods
We conduct a case study by tokenizing a sample mobile sensing dataset using the OpenAI tokenizer. We also review recent works that feed timeseries data into LLMs for human-centric tasks, outlining common experimental setups like zero-shot prompting and few-shot learning.

Results
The case study shows that popular LLMs split timestamps and sensor values into multiple nonmeaningful tokens, indicating they struggle with temporal data. We find that preliminary works rely heavily on prompt engineering and timeseries aggregation to “ground” LLMs, hinting that the “modality gap” hampers progress. The literature was critically analyzed through the lens of models optimizing for expressiveness versus parameter efficiency. On one end of the spectrum, training large domain-specific models from scratch is expressive but not parameter-efficient. On the other end, zero-shot prompting of LLMs is parameter-efficient but lacks expressiveness for temporal data.

Discussion
We argue tokenizers are not optimized for numerical data, while the scarcity of timeseries examples in training corpora exacerbates difficulties. We advocate balancing model expressiveness and computational efficiency when integrating temporal data. Prompt tuning, model grafting, and improved tokenizers are highlighted as promising directions.

Conclusion
We underscore that despite promising capabilities, LLMs cannot meaningfully process temporal data unless the input representation is addressed. We argue that this paradigm shift in how we leverage pretrained models will particularly affect the area of biomedical signals, given the lack of modality-specific foundation models.
Mutation of mpv17 results in loss of iridophores due to mitochondrial dysfunction in tilapia
Authors: Xu Jia , Li Peng , Xu Mengmeng , Wang Chenxu , Kocher Thomas D , Wang Deshou 
Published: July 2024

Abstract
Mpv17 (mitochondrial inner membrane protein MPV17) deficiency causes severe mitochondrial DNA depletion syndrome in mammals and loss of pigmentation of iridophores and a significant decrease of melanophores in zebrafish. The reasons for this are still unclear. In this study, we established an mpv17 homozygous mutant line in Nile tilapia. The developing mutants are transparent due to the loss of iridophores and aggregation of pigment granules in the melanophores and disappearance of the vertical pigment bars on the side of the fish. Transcriptome analysis using the skin of fish at 30 dpf (days post fertilization) revealed that the genes related to purine (especially pnp4a) and melanin synthesis were significantly downregulated. However, administration of guanine diets failed to rescue the phenotype of the mutants. In addition, no obvious apoptosis signals were observed in the iris of the mutants by TUNEL staining. Significant downregulation of genes related to iridophore differentiation was detected by qPCR. Insufficient ATP, as revealed by ATP assay, α-MSH treatment, and adcy5 mutational analysis, might account for the defects of melanophores in mpv17 mutants. Several tissues displayed less mtDNA and decreased ATP levels. Taken together, these results indicated that mutation of mpv17 led to mitochondrial dTMP deficiency, followed by impaired mtDNA content and mitochondrial function, which in turn, led to loss of iridophores and a transparent body color in tilapia.
Research on the mechanism of TWSG1 in the malignant progression of glioma cells and tumor-associated macrophage infiltration
Authors: Feng Kuan , Ye Gengfan , Wang Hongcai , Li Shiwei , Wen Xuebin , Chen Maosong 
Published: July 2024

Abstract
Gliomas are malignant tumors of the central nervous system; current treatment methods have low efficacy. Twisted gastrulation BMP signaling modulator 1 (TWSG1) has been shown to play a role in gliomas but it is not known whether TWSG1 participates in glioma pathogenesis and macrophage immune regulation. This study identified a total of 24 differentially expressed genes with survival differences in gliomas using bioinformatics analysis. Among them, TWSG1 exhibited the strongest correlation with gliomas and was positively correlated with macrophage enrichment. The results showed that TWSG1 was highly expressed in various glioma cell lines, with the highest expression observed in the A172 cell line. Silencing TWSG1 significantly decreased the viability, migration, and invasion of A172 cells in vitro and tumor growth in a mouse xenograft model in vivo. It also reduced the expression of the matrix metalloproteinases MMP2 and MMP9 both in vivo and in vitro. Silencing TWSG1 significantly reduced the expression of M2 macrophage makers and upregulated the expression of M1 macrophage markers in A172 cells and tumor tissues. These data suggest that interference with TWSG1 suppressed the progression of A172 glioma cells and regulated immune infiltration.