bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards a Novel Classification of Table Types in Scholarly Publications
Authors: He Jilin , Borisova Ekaterina , Rehm Georg 
Published: August 2024

AbstractTables are one of the prevalent means of organising and representing structured data. They contain a wealth of valuable information that is challenging to extract automatically, yet can be leveraged for downstream tasks such as question answering and knowledge base construction. Table Type Classification (TTC) is one of the tasks which contributes to better semantic understanding and extraction of knowledge in tabular data. While multiple classification schemas exist, almost all of them are focused on web tables. Therefore, these classifications might overlook certain types which are common in other areas such as scientific research. This paper addresses this gap by introducing ten novel TTC taxonomies tailored towards tables used in scholarly publications. We also evaluate the applicability of taxonomies derived from web tables to scientific tables. Additionally, we propose a new dataset containing 13,000 annotated table images, called TD4CLTabs. Our results indicate that both existing and newly proposed taxonomies are suitable and effective for classifying scientific tables.
Scientific Software Citation Intent Classification Using Large Language Models
Authors: Istrate Ana-Maria , Fisher Joshua , Yang Xinyu , Moraw Kara , Li Kai , Li Donghui , Klein Martin 
Published: August 2024

AbstractSoftware has emerged as a crucial tool in the current research ecosystem, frequently referenced in academic papers for its application in studies or the introduction of new software systems. Despite its prevalence, there remains a significant gap in understanding how software is cited within the scientific literature. In this study, we offer a conceptual framework for studying software citation intent and explore the use of large language models, such as BERT-based models, GPT-3.5, and GPT-4 for this task. We compile a representative software-mention dataset by merging two existing gold standard software mentions datasets and annotating them to a common citation intent scheme. This new dataset makes it possible to analyze software citation intent at the sentence level. We observe that in a fine-tuning setting, large language models can generally achieve an accuracy of over 80% on software citation intent classification on unseen, challenging data. Our research paves the way for future empirical investigations into the realm of research software, establishing a foundational framework for exploring this under-examined area.
Towards bit threads in general gravitational spacetimes
Authors: Du Dong-Hui , Sun Jia-Rui 
Published: August 2024

Abstract
The concept of the generalized entanglement wedge was recently proposed by Bousso and Penington, which states that any bulk gravitational region a possesses an associated generalized entanglement wedge E(a) ⊃ a on a static Cauchy surface M in general gravitational spacetimes, where E(a) may contain an entanglement island I(a). It suggests that the fine-grained entropy for bulk region a is given by the generalized entropy Sgen(E(a)). Motivated by this proposal, we extend the quantum bit thread description to general gravitational spacetimes, no longer limited to the AdS spacetime. By utilizing the convex optimization techniques, a dual flow description for the generalized entropy Sgen(E(a)) of a bulk gravitational region a is established on the static Cauchy surface M, such that Sgen(E(a)) is equal to the maximum flux of any flow that starts from the boundary ∂M and ends at bulk region a, or equivalently, the maximum number of bit threads that connect the boundary ∂M to the bulk region a. In addition, the nesting property of flows is also proved. Thus the basic properties of the entropy for bulk regions, i.e. the monotonicity, subadditivity, Araki-Lieb inequality and strong subadditivity, can be verified from flow perspectives by using properties of flows, such as the nesting property. Moreover, in max thread configurations, we find that there exists some lower bounds on the bulk entanglement entropy of matter fields in the region E(a) \ a, particularly on an entanglement island region I(a) ⊂ (E(a) \ a), as required by the existence of a nontrivial generalized entanglement wedge. Our quantum bit thread formulation may provide a way to investigate more fine-grained entanglement structures in general spacetimes.
SU(2)L deconstruction and flavour (non)-universality
Authors: Capdevila Bernat , Crivellin Andreas , Lizana Javier M. , Pokorski Stefan 
Published: August 2024

Abstract
We study two-site deconstructions of the SU(2)L gauge group factor of the SM. Models based on this approach can explain the hierarchies of the quark masses and CKM mixing between third and light families if these fields are localised on different sites by the presence of hierarchical new physics scales. The model leads to an accidental global U(2)q × U(3)u × U(3)d flavour symmetry which prevents dangerously large effects in flavour observables, making a TeV extension of the SM possible. Given the structure of the PMNS matrix in the neutrino sector, we explore different possibilities for the arrangement of the leptons on the two sites, and consider different models with U(2)ℓ or U(3)ℓ flavour symmetries. The phenomenology of the models is mostly governed by a massive vector triplet of SU(2)L. We study the interesting interplay between LHC searches and precision observables. In particular, one of the models can give a sizeable lepton flavour universal effect in the Wilson coefficient C9 while naturally suppressing contributions to C10, as suggested by current b → sℓ+ℓ− data, predicting simultaneously a mild positive shift in the W boson mass.
Gravitational axiverse spectroscopy: seeing the forest for the axions
Authors: Dimastrogiovanni Ema , Fasiello Matteo , Leedom Jacob M. , Putti Margherita , Westphal Alexander 
Published: August 2024

Abstract
We consider inflationary models with multiple spectator axions coupled to dark gauge sectors via Chern-Simons (CS) terms. The energy injection into Abelian gauge fields from the axions engenders a multi-peak profile for scalar and tensor spectra. We highlight the constraining power of CMB spectral distortions on the scalar signal and discuss the conditions under which spectator sectors can account for the recently observed stochastic gravitational wave (GW) background in the nHz range. Given the tantalizing prospect of a multi-peak “GW forest” spanning several decades in frequency, we elaborate on possible ultraviolet origins of the spectator models from Type IIB orientifolds. String compactifications generically produce a multitude of axions, the “Axiverse”, from dimensional reduction of p-form gauge fields. The CS coupling of such axions to dark gauge fields in the worldvolume theory of D7-branes can be tuned via multiple brane wrappings and/or quantized gauge field strengths. If string axions coupled to Abelian gauge fields undergo slow-roll during inflation, they produce GW signals with peaked frequency distribution whose magnitude depends on the details of the compactification. We discuss the restrictions on spectator models from consistency and control requirements of the string compactification and thereby motivate models that may live in the string landscape as opposed to the swampland.
Generalised hydrodynamics of $$ \textrm{T}\overline{\textrm{T}} $$-deformed integrable quantum field theories
Authors: Travaglino Riccardo , Mazzoni Michele , Castro-Alvaredo Olalla A. 
Published: August 2024

Abstract
In this paper we evaluate the averages of conserved densities and currents associated to charges of generic spin in (1+1)-dimensional massive integrable Quantum Field Theories perturbed by the irrelevant $$ \textrm{T}\overline{\textrm{T}} $$
T

T
¯

operator. By making use of the Thermodynamic Bethe Ansatz approach and of the theory of Generalised Hydrodynamics, we study the non-equilibrium steady state averages of conserved densities and currents in a partitioning protocol. We show that, in particular limits, averages can be evaluated exactly in terms of quantities known from the unperturbed theory. In the massless limit we recover known results for the energy and momentum currents and generalise those to any higher spin conserved quantities. We extend some of our results to perturbations of the generalised $$ \textrm{T}\overline{\textrm{T}} $$
T

T
¯

type. For the massive free fermion theory, we find an analytic expression for the effective inverse temperature after at $$ \textrm{T}\overline{\textrm{T}} $$
T

T
¯

perturbation in terms of the bare inverse temperature by making use of Lambert’s W function.
Spinodal slowing down and scaling in a holographic model
Authors: Caddeo Alessio , Henriksson Oscar , Hoyos Carlos , Sanchez-Garitaonandia Mikel 
Published: August 2024

Abstract
The dynamics of first-order phase transitions in strongly coupled systems are relevant in a variety of systems, from heavy ion collisions to the early universe. Holographic theories can be used to model these systems, with fluctuations usually suppressed. In this case the system can come close to a spinodal point where theory and experiments indicate that the behaviour should be similar to a critical point of a second-order phase transition. We study this question using a simple holographic model and confirm that there is critical slowing down and scaling behaviour close to the spinodal point, with precise quantitative estimates. In addition, we determine the start of the scaling regime for the breakdown of quasistatic evolution when the temperature of a thermal bath is slowly decreased across the transition. We also extend the analysis to the dynamics of second-order phase transitions and strong crossovers.
Quantum gravity of the Heisenberg algebra
Authors: Almheiri Ahmed , Goel Akash , Hu Xu-Yao 
Published: August 2024

Abstract
We consider a simplified model of double scaled SYK (DSSYK) in which the Hamiltonian is the position operator of the Harmonic oscillator. This model captures the high temperature limit of DSSYK but could also be defined as a quantum theory in its own right. We study properties of the emergent geometry including its dynamics in response to inserting matter particles. In particular, we find that the model displays de Sitter-like properties such as that infalling matter reduces the rate of growth of geodesic slices between the two boundaries. The simplicity of the model allows us to compute the full generating functional for correlation functions of the length mode or any number of matter operators. We provide evidence that the effective action of the geodesic length between boundary points is non-local. Furthermore, we use the on-shell solution for the geodesic lengths between any two boundary points to reconstruct an effective bulk metric and reverse engineer the dilaton gravity theory that generates this metric as a solution.
Non-linear dynamics and critical phenomena in the holographic landscape of Weyl semimetals
Authors: Matsumoto Masataka , Mirjalali Mirmani , Vahedi Ali 
Published: August 2024

Abstract
This study presents a detailed analysis of critical phenomena in a holographic Weyl semi-metal (WSM) using the D3/D7 brane configuration. The research explores the non-linear response of the longitudinal current J when subjected to an external electric field E at both zero and finite temperatures. At zero temperature, the study identifies a potential quantum phase transition in the J-E relationship, driven by background parameters the particle mass, and axial gauge potential. This transition is characterized by a unique reconnection phenomenon resulting from the interplay between WSM-like and conventional nonlinear conducting behaviors, indicating a quantum phase transition.Additionally, at non-zero temperatures with dissipation, the system demonstrates first- and second-order phase transitions as the electric field and axial gauge potential are varied. The longitudinal conductivity is used as an order parameter to identify the current-driven phase transition. Numerical analysis reveals critical exponents in this non-equilibrium phase transition that show similarities to mean-field values observed in metallic systems.
Single-valuedness of the AdS Veneziano amplitude
Authors: Alday Luis F. , Hansen Tobias 
Published: August 2024

Abstract
We consider the Veneziano amplitude for the scattering of gluons in type IIB string theory on AdS5 × S5/ℤ2 in the presence of D7 branes. On general grounds curvature corrections around flat space can be thought of as arising from the extra insertion of soft gravitons. This naturally leads to an open string world-sheet representation with the extra insertion of single-valued functions evaluated on the real line. We check that the recently obtained first curvature correction is of this form and use this new constraint to compute the second curvature correction of the AdS Veneziano amplitude.
Anticancer potential of delphinidin and its derivatives: therapeutic and mechanistic insights
Authors: Iqbal Shabnoor , Omara Timothy , Kahwa Ivan , Khan Usman Mir 
Published: August 2024

AbstractAnthocyanins are water-soluble naturally occurring flavonoids present in fruits, flowers, leaves, and roots of fruit plants and vegetables. One of the important anthocyanidin components of red wine and berries is delphinidin (DP). This review provides an update on the potential of DP in cancer therapy, with a further understanding of the mechanisms involved. Delphinidin has been shown to elicit inhibitory effects on catabolizing enzymes of human granulocytes and parasites, TNF-induced COX-2 expression in mouse epidermal cells, and reduce oxidative stress. It also inhibited anchorage-independent growth and caused cell death in breast cancer cell lines. Delphinidin increased Nrf2 expression, increased HO-1 production, and promoted mRNA expression of mitochondrial biogenesis-related factors. Further, DP has anti-proliferative and pro-apoptotic effects in various cancer cell lines such as lung, breast, and ovarian cancer cells. The mTOR-related pathway is the most important signaling pathway in the activation of autophagy, and DP has been shown to exert its cytotoxic effects on cancer cell lines via activating protein kinases. Among DP derivatives, delphinidin-3-O-glucoside has the best anticancer activity because it is easily absorbed. However, the metabolism of DP and its bioavailability in biological systems need to be explored to fully understand its benefits.
Maternal peripheral blood telomere length and preterm birth in African American women: a pilot study
Authors: Huang Weiyi , Han Gang , Taylor Brandie DePaoli , Neal Gabriel , Kochan Kelli , Page Robin L. 
Published: August 2024

Abstract
Purpose
This study aimed to explore the association between preterm birth and telomere length of maternal peripheral blood in African American women.

Methods
78 African American women were recruited for this study between 2018 and 2023 from 2 prenatal clinics in central and east Texas. Participants provided blood samples and completed clinic questionnaires, with clinical data collected from their post-delivery medical records. Telomere length was measured using monochrome multiplex quantitative real-time polymerase chain reaction. Linear regression and multinomial logistic regression were used to analyze the association between telomere length and gestational length. Kruskal–Wallis’s test and Fisher’s exact test were used to compare preterm birth, early-term birth and full-term birth by telomere length, social-demographic characteristics, stress and discrimination.

Results
The rates of preterm birth was higher in pregnant women with shorter telomeres. After adjusting for confounders, for every 10-units increase in the relative telomere-to-single-copy gene (T/S) ratio, gestational days increased by 1.090 days (90% CI 0.182, 1.997), and for every 10-units decrease in the T/S ratio, the odds of preterm birth was 2.664 (90% CI 1.064, 6.673) times greater than the odds of full-term birth. No statistically significant associations were observed between stress, discrimination, and either preterm birth or telomere length.

Conclusions
Maternal peripheral blood telomere shortening is associated with preterm birth, providing support to further explore the clinical utility of maternal telomere testing for prediction and early intervention of preterm birth and the study of biological mechanisms of spontaneous preterm birth.
Clinical characterization of common pathogenic variants of SOD1-ALS in Germany
Authors: Wiesenfarth Maximilian , Forouhideh-Wiesenfarth Yalda , Elmas Zeynep , Parlak Özlem , Weiland Ulrike , Herrmann Christine , Schuster Joachim , Freischmidt Axel , Müller Kathrin , Siebert Reiner , Günther Kornelia , Fröhlich Elke , Knehr Antje , Simak Tatiana , Bachhuber Franziska , Regensburger Martin , Petri Susanne , Klopstock Thomas , Reilich Peter , Schöberl Florian , Schumann Peggy , Körtvélyessy Peter , Meyer Thomas , Ruf Wolfgang P. , Witzel Simon , Tumani Hayrettin , Brenner David , Dorst Johannes , Ludolph Albert C. 
Published: August 2024

AbstractPathogenic variants in the Cu/Zn superoxide dismutase (SOD1) gene can be detected in approximately 2% of sporadic and 11% of familial amyotrophic lateral sclerosis (ALS) patients in Europe. We analyzed the clinical phenotypes of 83 SOD1-ALS patients focusing on patients carrying the most frequent (likely) pathogenic variants (R116G, D91A, L145F) in Germany. Moreover, we describe the effect of tofersen treatment on ten patients carrying these variants. R116G patients showed the most aggressive course of disease with a median survival of 22.0 months compared to 198.0 months in D91A and 87.0 months in L145F patients (HR 7.71, 95% CI 2.89–20.58 vs. D91A; p < 0.001 and HR 4.25, 95% CI 1.55–11.67 vs. L145F; p = 0.02). Moreover, R116G patients had the fastest median ALSFRS-R progression rate with 0.12 (IQR 0.07–0.20) points lost per month. Median diagnostic delay was 10.0 months (IQR 5.5–11.5) and therefore shorter compared to 57.5 months (IQR 14.0–83.0) in D91A (p < 0.001) and 21.5 months (IQR 5.8–38.8) in L145F (p = 0.21) carriers. As opposed to D91A carriers (50.0%), 96.2% of R116G (p < 0.001) and 100.0% of L145F (p = 0.04) patients reported a positive family history. During tofersen treatment, all patients showed a reduction of neurofilament light chain (NfL) serum levels, independent of the SOD1 variant. Patients with SOD1-ALS carrying R116G, D91A, or L145F variants show commonalities, but also differences in their clinical phenotype, including a faster progression rate with shorter survival in R116G, and a comparatively benign disease course in D91A carriers.
Endoscopic repair of duodenal perforations, a scoping review
Authors: Williams Jennifer , Joshi Hansa , Schwartz Michael , Kalola Ami , Mercado Alvin , Saracco Benjamin , Adams Amanda , Chaaya Adib , Baik Daniel , Elfant Adam , Hong Young Ki 
Published: August 2024

Abstract
Background
There is a discrepancy in the surgical and endoscopic literature for managing duodenal perforations. Although often managed conservatively, surgical repair is the standard treatment for duodenal perforations. This contrasts with the gastroenterology literature, which now recommends endoscopic repair of duodenal perforations, which are more frequently iatrogenic from the growing field of advanced endoscopic procedures. This study aims to provide a scoping review to summarize the current literature content and quality on endoscopic repair of duodenal perforations.

Methods
The protocol for performing this scoping review was outlined by the Joanna Briggs Institute. All studies that reported primary outcomes of patients who had undergone endoscopic repair of duodenal perforations before February 2022, regardless of perforation etiology or repair type were reviewed, with studies after 1999 meeting inclusion criteria. The study excluded articles that did not report clinical outcomes of endoscopic repair, articles that did not describe where in the gastrointestinal tract the endoscopic repair occurred, pediatric patients, and animal studies.

Results
7606 abstracts were screened, with 474 full articles reviewed and 152 studies met inclusion criteria. 560 patients had duodenal perforations repaired endoscopically, with a technical success rate of 90.4% and a survival rate of 86.7%. Most of these perforations (74.5%) were iatrogenic from endoscopic procedures or surgery. Only one randomized control trial (RCT) was found, and 53% of studies were case reports.

Conclusion
These results suggest that endoscopic repair could emerge as a viable first-line treatment for duodenal perforation and highlight the need for more high-quality research in this topic.
Resistant starch reduces glycolysis by HK2 and suppresses high-fructose corn syrup-induced colon tumorigenesis
Authors: Zhang Ying , Shen Weiyi , Chen Zhehang , He Jiamin , Feng Lijun , Wang Lan , Chen Shujie 
Published: August 2024

Abstract
Background
The intake of high-fructose corn syrup (HFCS) may increase the risk of colorectal cancer (CRC). This study aimed to explore the potential effects and mechanisms of resistant starch (RS) in HFCS-induced colon tumorigenesis.

Methods
The azoxymethane/dextran sodium sulfate (AOM/DSS) and ApcMin/+ mice models were used to investigate the roles of HFCS and RS in CRC in vivo. An immunohistochemistry (IHC) staining analysis was used to detect the expression of proliferation-related proteins in tissues. 16S rRNA sequencing for microbial community, gas chromatography for short-chain fatty acids (SCFAs), and mass spectrometry analysis for glycolysis products in the intestines were performed. Furthermore, lactic acid assay kit was used to detect the glycolysis levels in vitro.

Results
RS suppressed HFCS-induced colon tumorigenesis through reshaping the microbial community. Mechanistically, the alteration of the microbial community after RS supplement increased the levels of intestinal SCFAs, especially butyrate, leading to the suppression of glycolysis and CRC cell proliferation by downregulating HK2.

Conclusions
Our study identified RS as a candidate of protective factors in CRC and may provide a potential target for HFCS-related CRC treatment.
Red and near-infrared light-activated photoelectrochemical nanobiosensors for biomedical target detection
Authors: Monsalve Yeison , Cruz-Pacheco Andrés F. , Orozco Jahir 
Published: August 2024

AbstractPhotoelectrochemical (PEC) nanobiosensors integrate molecular (bio)recognition elements with semiconductor/plasmonic photoactive nanomaterials to produce measurable signals after light-induced reactions. Recent advancements in PEC nanobiosensors, using light-matter interactions, have significantly improved sensitivity, specificity, and signal-to-noise ratio in detecting (bio)analytes. Tunable nanomaterials activated by a wide spectral radiation window coupled to electrochemical transduction platforms have further improved detection by stabilizing and amplifying electrical signals. This work reviews PEC biosensors based on nanomaterials like metal oxides, carbon nitrides, quantum dots, and transition metal chalcogenides (TMCs), showing their superior optoelectronic properties and analytical performance for the detection of clinically relevant biomarkers. Furthermore, it highlights the innovative role of red light and NIR-activated PEC nanobiosensors in enhancing charge transfer processes, protecting them from biomolecule photodamage in vitro and in vivo applications. Overall, advances in PEC detection systems have the potential to revolutionize rapid and accurate measurements in clinical diagnostic applications. Their integration into miniaturized devices also supports the development of portable, easy-to-use diagnostic tools, facilitating point-of-care (POC) testing solutions and real-time monitoring.