bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of tokenization on transformers for biological sequences
Authors: Dotan Edo , Jaschek Gal , Pupko Tal , Belinkov Yonatan 
Published: April 2024

Abstract

Motivation
Deep-learning models are transforming biological research, including many bioinformatics and comparative genomics algorithms, such as sequence alignments, phylogenetic tree inference, and automatic classification of protein functions. Among these deep-learning algorithms, models for processing natural languages, developed in the natural language processing (NLP) community, were recently applied to biological sequences. However, biological sequences are different from natural languages, such as English, and French, in which segmentation of the text to separate words is relatively straightforward. Moreover, biological sequences are characterized by extremely long sentences, which hamper their processing by current machine-learning models, notably the transformer architecture. In NLP, one of the first processing steps is to transform the raw text to a list of tokens. Deep-learning applications to biological sequence data mostly segment proteins and DNA to single characters. In this work, we study the effect of alternative tokenization algorithms on eight different tasks in biology, from predicting the function of proteins and their stability, through nucleotide sequence alignment, to classifying proteins to specific families.

Results
We demonstrate that applying alternative tokenization algorithms can increase accuracy and at the same time, substantially reduce the input length compared to the trivial tokenizer in which each character is a token. Furthermore, applying these tokenization algorithms allows interpreting trained models, taking into account dependencies among positions. Finally, we trained these tokenizers on a large dataset of protein sequences containing more than 400 billion amino acids, which resulted in over a 3-fold decrease in the number of tokens. We then tested these tokenizers trained on large-scale data on the above specific tasks and showed that for some tasks it is highly beneficial to train database-specific tokenizers. Our study suggests that tokenizers are likely to be a critical component in future deep-network analysis of biological sequence data.

Availability and implementation
Code, data, and trained tokenizers are available on https://github.com/technion-cs-nlp/BiologicalTokenizers.
Supramolecular salicylic acid combined with niacinamide in chloasma: a randomized controlled trial
Authors: Xiong Ying , Jiang Xian , Lai Wei , Gao Xinghua , You Yan , Huang Yongmei , Li Xueli , Zhang Junling , Tao Shiqin , Chen Jin , Zhang Wei , Yu Nan , Xu Nan , Liu Chunling , Zeng Weihui , Lv Shichao , Wang Gang 
Published: April 2024

Abstract

Background
Chloasma is a common skin hyperpigmentation condition, with treatment options ranging from topical agents to advanced interventions such as chemical peels and laser therapy. Salicylic acid, including its supramolecular form (SSA), has shown promise in managing chloasma. However, to date, no multicentre randomized controlled trial of SSA for chloasma is available.

Objectives
The purpose of this study was to assess the efficacy and safety of 30% SSA combined with 10% niacinamide in treating ­chloasma.

Methods
This multicentre (n = 15), randomized, double-blind, parallel placebo-controlled trial (Clinical trial registration number: ChiCTR2200065346) enrolled and randomized 300 participants (1 : 1) to either 30% SSA treatment or placebo, with 150 allocated to treatment and 150 to placebo in the full analysis set, and 144 to treatment and 147 to placebo in the per-protocol set. A Visia® Skin Analysis System was used at each visit to assess the degree of improvement in chloasma lesions. The primary endpoint was the effective rate after 16 weeks, assessed using the modified Melasma Area and Severity Index (mMASI) score [(pretreatment score − post-treatment score)/pretreatment score × 100%].

Results
The total mMASI score, overall score on the Griffiths 10-point scale, and Griffiths 10 score for the left and the right sides of the face were significantly lower in the 30% SSA group than in the placebo group (all P &lt; 0.001). One study of drug-related adverse events (AEs) and one study of drug-unrelated AEs were reported in the 30% SSA group. No AE was reported in the placebo group.

Conclusions
Among our patients, 30% SSA combined with 10% niacinamide was shown to be effective and safe for treating chloasma.
How conspecific and allospecific eggs and larvae drive oviposition preference in Drosophila
Authors: Moreira-Soto Rolando D , Khallaf Mohammed A , Hansson Bill S , Knaden Markus 
Published: April 2024

Abstract
Where to lay the eggs is a crucial decision for females as it influences the success of their offspring. Female flies prefer to lay eggs on food already occupied and consumed by larvae, which facilitates social feeding, but potentially could also lead to detrimental interactions between species. Whether females can modulate their attraction to cues associated with different species is unknown. Here, we analyzed the chemical profiles of eggs and larvae of 16 Drosophila species, and tested whether Drosophila flies would be attracted to larvae-treated food or food with eggs from 6 different Drosophila species. The chemical analyses revealed that larval profiles from different species are strongly overlapping, while egg profiles exhibit significant species specificity. Correspondingly, female flies preferred to lay eggs where they detected whatever species’ larval cues, while we found a significant oviposition preference only for eggs of some species but not others. Our findings suggest that both larval and egg cues present at a given substrate can drive oviposition preference in female flies.
GNN-Based Multimodal Named Entity Recognition
Authors: Gong Yunchao , Lv Xueqiang , Yuan Zhu , You Xindong , Hu Feng , Chen Yuzhong 
Published: April 2024

Abstract
The Multimodal Named Entity Recognition (MNER) task enhances the text representations and improves the accuracy and robustness of named entity recognition by leveraging visual information from images. However, previous methods have two limitations: (i) the semantic mismatch between text and image modalities makes it challenging to establish accurate internal connections between words and visual representations. Besides, the limited number of characters in social media posts leads to semantic and contextual ambiguity, further exacerbating the semantic mismatch between modalities. (ii) Existing methods employ cross-modal attention mechanisms to facilitate interaction and fusion between different modalities, overlooking fine-grained correspondences between semantic units of text and images. To alleviate these issues, we propose a graph neural network approach for MNER (GNN-MNER), which promotes fine-grained alignment and interaction between semantic units of different modalities. Specifically, to mitigate the issue of semantic mismatch between modalities, we construct corresponding graph structures for text and images, and leverage graph convolutional networks to augment text and visual representations. For the second issue, we propose a multimodal interaction graph to explicitly represent the fine-grained semantic correspondences between text and visual objects. Based on this graph, we implement deep-level feature fusion between modalities utilizing graph attention networks. Compared with existing methods, our approach is the first to extend graph deep learning throughout the MNER task. Extensive experiments on the Twitter multimodal datasets validate the effectiveness of our GNN-MNER.
Twenty-five years’ experience with isolated bicuspid aortic valve repair: impact of commissural orientation
Authors: Ehrlich Tristan , Abeln Karen B , Froede Lennart , Schmitt Flora , Giebels Christian , Schäfers Hans-Joachim 
Published: April 2024

Abstract

OBJECTIVES
Repair of the bicuspid aortic valve (BAV) has evolved in the past 25 years. The aim of this study was to review and analyse the long-term durability of isolated BAV repair with particular focus on commissural orientation (CO).

METHODS
All patients who underwent BAV repair for severe aortic regurgitation between October 1998 and December 2022 were included. The study group consists of all patients operated after 2009, i.e. since CO modification. The control group includes patients who were operated before 2009. CO was classified as symmetric, asymmetric and very asymmetric.

RESULTS
Overall, 594 adult patients (93% male; mean age 42 years) were included. At 15 years, survival was 94.8% [standard deviation (SD): 2.2]; freedom from reoperation was 86.8% (SD: 2.3). Freedom from aortic insufficiency ≥II was 70.8% (SD: 4.7) at 15 years. Modification of CO by sinus plication was performed in 200 (33.7%) instances. Using competing risks analysis, the absence of effective height measurement (P = 0.018), very asymmetric CO (P = 0.028), the presence of calcification (P &lt; 0.001), the use of pericardial patch (P &lt; 0.001), the use of subcommissural sutures (P &lt; 0.001) and preoperative endocarditis (P = 0.005) were identified as independent predictors for reoperation. Follow-up was 97% complete (4228 patient-years); mean follow-up was 7 years (SD: 5).

CONCLUSIONS
Isolated BAV repair leads to good survival and durability in all morphologic types if cusp repair is guided by effective height, suture annuloplasty is performed, and CO is modified using sinus plication in asymmetrical valves. Very asymmetrical valves may should be treated with a lower threshold for replacement.
Ischaemic stroke in women with atrial fibrillation: temporal trends and clinical implications
Authors: Teppo Konsta , Airaksinen K E Juhani , Jaakkola Jussi , Halminen Olli , Salmela Birgitta , Kouki Elis , Haukka Jari , Putaala Jukka , Linna Miika , Aro Aapo L , Mustonen Pirjo , Hartikainen Juha , Lip Gregory Y H , Lehto Mika 
Published: April 2024

Abstract

Background and Aims
Female sex has been linked with higher risk of ischaemic stroke (IS) in atrial fibrillation (AF), but no prior study has examined temporal trends in the IS risk associated with female sex.

Methods
The registry-linkage Finnish AntiCoagulation in Atrial Fibrillation (FinACAF) study included all patients with AF in Finland from 2007 to 2018. Ischaemic stroke rates and rate ratios were computed.

Results
Overall, 229 565 patients with new-onset AF were identified (50.0% women; mean age 72.7 years). The crude IS incidence was higher in women than in men across the entire study period (21.1 vs. 14.9 events per 1000 patient-years, P &lt; .001), and the incidence decreased both in men and women. In 2007–08, female sex was independently associated with a 20%–30% higher IS rate in the adjusted analyses, but this association attenuated and became statistically non-significant by the end of the observation period. Similar trends were observed when time with and without oral anticoagulant (OAC) treatment was analysed, as well as when only time without OAC use was considered. The decrease in IS rate was driven by patients with high IS risk, whereas in patients with low or moderate IS risk, female sex was not associated with a higher IS rate.

Conclusions
The association between female sex and IS rate has decreased and become non-significant over the course of the study period from 2007 to 2018, suggesting that female sex could be omitted as a factor when estimating expected IS rates and the need for OAC therapy in patients with AF.
Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations
Authors: Vogel Anjela L , Thompson Katharine J , Straub Daniel , Musat Florin , Gutierrez Tony , Kleindienst Sara 
Published: April 2024

Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g. those encoding ring-hydroxylating dioxygenases (RHDs)] has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help to monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L−1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. By contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.
Enhancing xylose-fermentation capacity of engineered Saccharomyces cerevisiae by multistep evolutionary engineering in inhibitor-rich lignocellulose hydrolysate
Authors: Demeke Mekonnen M , Echemendia Dannele , Belo Edgard , Foulquié-Moreno María R , Thevelein Johan M 
Published: April 2024

Abstract
Major progress in developing Saccharomyces cerevisiae strains that utilize the pentose sugar xylose has been achieved. However, the high inhibitor content of lignocellulose hydrolysates still hinders efficient xylose fermentation, which remains a major obstacle for commercially viable second-generation bioethanol production. Further improvement of xylose utilization in inhibitor-rich lignocellulose hydrolysates remains highly challenging. In this work, we have developed a robust industrial S. cerevisiae strain able to efficiently ferment xylose in concentrated undetoxified lignocellulose hydrolysates. This was accomplished with novel multistep evolutionary engineering. First, a tetraploid strain was generated and evolved in xylose-enriched pretreated spruce biomass. The best evolved strain was sporulated to obtain a genetically diverse diploid population. The diploid strains were then screened in industrially relevant conditions. The best performing strain, MDS130, showed superior fermentation performance in three different lignocellulose hydrolysates. In concentrated corncob hydrolysate, with initial cell density of 1 g DW/l, at 35°C, MDS130 completely coconsumed glucose and xylose, producing ± 7% v/v ethanol with a yield of 91% of the maximum theoretical value and an overall productivity of 1.22 g/l/h. MDS130 has been developed from previous industrial yeast strains without applying external mutagenesis, minimizing the risk of negative side-effects on other commercially important properties and maximizing its potential for industrial application.
The Dual Role of Code-Switching in Alejandro Morales’s Reto en el paraíso
Authors: Montes-Alcalá Cecilia 
Published: April 2024

ABSTRACT
Although most contemporary Chicano authors tend to write exclusively in one language, English or Spanish, they have a range of linguistic options available to them – as would any member of a bilingual community – including code-switching. Code-switching in US literature dates back to the Mexican–American War and has been employed to establish aesthetic or stylistic credibility and to communicate biculturalism or ethnic identity. This article examines the dual role of code-switching in Alejandro Morales’s only bilingual novel, Reto en el paraíso. It explores how code-switching serves as a narrative technique to develop character identity in a bilingual and bicultural context, while also performing some of the socio-pragmatic and communicative functions commonly attested in natural bilingual discourse. Morales’s linguistic choices exemplify how Chicano writers living between two cultures may, and often must, use both languages to depict accurately the intricate cultural and linguistic realities of their characters.
A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait
Authors: Chan Yuan-Fu , Lu Chia-Wei , Kuo Hao-Chih , Hung Chih-Ming 
Published: April 2024

Abstract
The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations. Understanding the genetic mechanism underpinned feathered-foot development in wild birds is still in its infancy. Here, we assembled a chromosome-level genome of the Asian house martin (Delichon dasypus) using the long-read High Fidelity sequencing approach to initiate the search for genes associated with its feathered feet. We employed the whole-genome alignment of D. dasypus with other swallow species to identify high-SNP regions and chromosomal inversions in the D. dasypus genome. After filtering out variations unrelated to D. dasypus evolution, we found six genes related to feather development near the high-SNP regions. We also detected three feather development genes in chromosomal inversions between the Asian house martin and the barn swallow genomes. We discussed their association with the wingless/integrated (WNT), bone morphogenetic protein, and fibroblast growth factor pathways and their potential roles in feathered-foot development. Future studies are encouraged to utilize the D. dasypus genome to explore the evolutionary process of the feathered-foot trait in avian species. This endeavor will shed light on the evolutionary path of feathers in birds.
The Cluster Complex for Cluster Poisson Varieties and Representations of Acyclic Quivers
Authors: Melo Carolina , Nájera Chávez Alfredo 
Published: April 2024

Abstract
Let $\mathcal{X}$ be a skew-symmetrizable cluster Poisson variety. The cluster complex $\Delta ^{+}(\mathcal{X})$ was introduced in [ 12]. It codifies the theta functions on $\mathcal{X}$ that restrict to a character of a seed torus. Every seed $\textbf{s}$ for $\mathcal{X}$ determines a fan realization $\underline{\Delta ^{+}_{\textbf{s}}(\mathcal{X})}$ of $\Delta ^{+}(\mathcal{X})$. For every $\textbf{s}$ we provide a simple and explicit description of the cones of $\underline{\Delta ^{+}_{\textbf{s}}(\mathcal{X})}$ and their facets using c-vectors. Moreover, we give formulas for the theta functions parametrized by the integral points of $\underline{\Delta ^{+}_{\textbf{s}}(\mathcal{X})}$ in terms of $F$-polynomials. In case $\mathcal{X}$ is skew-symmetric and the quiver $Q$ associated to $\textbf{s}$ is acyclic, we describe the normal vectors of the supporting hyperplanes of the cones of $\underline{\Delta ^{+}_{\textbf{s}}(\mathcal{X})}$ using g-vectors of (non-necessarily rigid) objects in $\textsf{K}^{\textrm{b}}(\textrm{proj} \; kQ)$.
Measuring interpersonal firearm violence: natural language processing methods to address limitations in criminal charge data
Authors: Kafka Julie M , Schleimer Julia P , Toomet Ott , Chen Kaidi , Ellyson Alice , Rowhani-Rahbar Ali 
Published: April 2024

Abstract

Objective
Firearm violence constitutes a public health crisis in the United States, but comprehensive data infrastructure is lacking to study this problem. To address this challenge, we used natural language processing (NLP) to classify court record documents from alleged violent crimes as firearm-related or non-firearm-related.

Materials and Methods
We accessed and digitized court records from the state of Washington (n = 1468). Human review established a gold standard label for firearm involvement (yes/no). We developed a key term search and trained supervised machine learning classifiers for this labeling task. Results were evaluated in a held-out test set.

Results
The decision tree performed best (F1 score: 0.82). The key term list had perfect recall (1.0) and a modest F1 score (0.65).

Discussion and Conclusion
This case report highlights the accuracy, feasibility, and potential time-saved by using NLP to identify firearm involvement in alleged violent crimes based on digitized narratives from court documents.
Incidentality of the civilian harm in international humanitarian law and its Contra Legem antonyms in recent discourses on the laws of war
Authors: Daniele Luigi 
Published: April 2024

Abstract
This article develops an interpretative effort to clarify the meaning of the notion of incidentality of the civilian harm in international humanitarian law (IHL), with particular concern to the role of this concept as normative cornerstone for a systematic reading, and coherent implementation, of the law of targeting. The article begins with a critical analysis of recent discourses on the laws of war, focusing on the emergence and growth of contra legem uses of the concept of ‘collateral damage’. These discourses revolve around proportionality in attacks, commonly re-translating this rule by removing incidentality as legal qualifier of the civilian harm susceptible of proportionality assessments. The article shows that proportionality misconceptions neglecting incidentality have become so common and accepted as to be often confused with structural features of IHL. On the contrary, the analysis highlights the collisions between these conceptions, on the one hand, and IHL targeting prescriptions, their interplay and protective functions, on the other, unveiling how the former result in promoting unlimited expansions of the entity of civilian harm that can be object of proportionality assessments, even when this civilian harm constitutes the largely preponderant, main anticipated result of a given attack. Within a background of unequal relativization of international humanitarian law (IHL) parameters, minimalist understandings of incidentality have also been the basis of questionable orientations about attacks on residential tower buildings, reproducing exponential ‘militarizations’ of civilian objects (and at times of the protected persons therein) for proximity with lawful targets. Cumulatively, these discourses and scholarly orientations contributing to depriving proportionality of its incidentality requirement continue to produce dramatic consequences for civilian protection worldwide and provide aggressive military powers with arguments functional to circumvent the prohibitions of disproportionate and indiscriminate attacks. Against these tendencies, it is proposed that the notion of incidentality of the civilian harm, in homage to letter, object, and protective purpose of IHL, and understood with the interpretative help of mens rea categories, should be strictly construed and urgently re-centralized by laws of war scholars as a fundamental conditio sine qua non for proportionality assessments and as main dividing line between the operative spheres of distinction and proportionality.