bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis of Galactoacrylamide and Study of Stimuli‐Responsive Fluorescent Hierarchical Self‐Assembly‐Promoted Specific Interactions with Proteins
Authors: Ajish Juby K. , Ajish Kumar K. S. 
Published: October 2023

AbstractA new sugar based acrylamide, 6‐N‐acrylamido‐D‐galactopyranose (Gal‐acryl) was synthesized from D‐galactose in 6 steps. A solution of Gal‐acryl at basic pH exhibited concentration dependent fractal type assembly formation upon solvent evaporation as revealed by the microscopic images. The fractal dimensions calculated point towards Diffusion Limited Aggregation mode of aggregate formation. The critical aggregation concentration (CAC) of Gal‐acryl in water was found to be 49.3 μM. The increase in fluorescence intensity accompanied by blue shift in emission maxima of coumarin 153 suggests increase in non‐polar environment with Gal‐acryl concentration. The I1/I3ratio of pyrene emission confirmed more non‐polar microenvironment at acidic pH and vice versa at basic pH. Self‐assembly allows Gal‐acryl to exhibit specificity to lectin RCA120 as is demonstrated by fluorescence study further supported by turbidimetric assay. The fluorescence quenching studies with FITC‐RCA120 afforded the Ka value as 6.34×105 M−1, which is much higher than Ka values observed for small galactose derivatives. The present study may help in designing different fractal like glycomaterials with potential applications in drug delivery, bio‐sensing, tissue engineering, and as ligands to asialoglycoprotein receptors that are exclusively expressed by liver cells.
K3v2(Po4)3/C as a New High‐Voltage Cathode Material for Calcium‐Ion Batteries with a Water‐In‐Salt Electrolyte
Authors: Qiao Fan , Wang Junjun , Yu Ruohan , Pi Yuqiang , Huang Meng , Cui Lianmeng , Liu Ziang , An Qinyou 
Published: October 2023

AbstractAqueous Ca‐ion batteries (ACIBs) attract immense attention due to its high safety and the high abundance of calcium. However, the development of ACIBs is hindered by the lack of high voltage cathode materials to host the large radius and divalent Ca2+. Herein, polyanionic phosphate K3V2(PO4)3/C (KVP/C) is provided as a new cathode material for ACIBs. Due to the robust structure of polyanion material and the wide electrochemical window of water‐in‐salt electrolyte, KVP/C delivers a high working voltage of 3.74 V versus Ca2+/Ca with a specific capacity of 102.4 mAh g−1 and a long‐life of 6000 cycles at 500 mA g−1. Furthermore, the calcium storage mechanism of KVP/C is shown to be the coexistence of solid solution and two‐phase reaction by in situ X‐ray diffraction, ex situ transmission electron microscope, and X‐ray photoelectron spectroscopy. Finally, an aqueous calcium‐ion full cell, based on an organic compound as anode and KVP/C as cathode, is constructed and it shows good stability for 200 cycles and a specific capacity of 80.2 mAh g−1. This work demonstrates that vanadium‐based phosphate materials are promising high‐voltage cathode materials for ACIBs and renew the prospects for ACIBs.
The Late Miocene mammals from the Humahuaca Basin (northwestern Argentina) provide new evidence on the initial stages of the Great American Biotic Interchange
Authors: Candela Adriana M. , Abello María A. , Reguero Marcelo A. , García Esponda César M. , Pardiñas Ulyses F.J. , Zurita Alfredo A. , Pujos Francois , Miño‐Boilini Ángel , Quiñones Sofía , Galli Claudia I. , Luna Carlos , Voglino Damián , De Los Reyes Martín , Cuaranta Pedro 
Published: October 2023

AbstractWe describe new Late Miocene mammalian specimens from the Maimará Formation (Late Miocene to Early Pliocene) exposed at Humahuaca Basin (23°–24°S), northwestern Argentina (NWA), and analyse their taxonomy and relevance for our understanding of the initial stages of the Great American Biotic Interchange (GABI). The stratigraphical and geochronological control of the studied specimens indicates a time window ofc. 6.6–5.8 Ma. These data are crucial for establishing the oldest records of the Holarctic immigrants of the GABI. The first record of cricetid rodents from the Maimará Formation is reported. Moreover, with an age ofc. 6 Ma it is the first appearance datum (FAD) of these rodents in South America. The age of the procyonidCyonasuarecorded in this unit is estimated betweenc. 6.6 andc. 6.4 Ma. The record of procyonids and cricetids in the same continuous sedimentary sequence suggests that the time interval between the dispersion of both groups into the continent during GABI wasc.1 myr. Of the autochthonous mammals from the Maimará Formation, the first records of litopterns, chlamyphorid and mylodontine xenarthrans, and caviomorph rodents (including new speciesPithanotomys?solisaeandPalaeocavia humahuaquense) are described. FADs of immigrant and autochthonous mammals in NWA suggest a major faunal turnover during GABI at the Messinian, probably linked to global climatic changes and the tectonic activity that affected the Humahuaca Basin at that time. Hypsodonty, a dominant feature among Maimaran mammals, may be related to a landscape strongly influenced by the Andean uplift.
A new method to determine composition of sphalerite without secondary pollution based on CIELAB color space
Authors: Liu Yong , Duan Ning , Jiang Linhua , He Hongping , Cheng Han , Liao Jiaqi , Xu Yanli , Cheng Wen , Chen Ying , Zhu Guangbin , Xu Fuyuan 
Published: October 2023

AbstractCurrently, most of the methods for mineral materials analysis generate secondary pollution, which is detrimental to human health. For instance, traditional methods for sphalerite analysis in the zinc (Zn) smelting industry including chemical titration, atomic absorption spectrometry, and inductively coupled atomic emission spectroscopy. Colored indicators and toxic heavy metals are used in the analytical processes, causing severe pollution. For some methods, liquid is transformed into gaseous plasma, which is more dangerous to human health. Due to large quantities of sphalerite being used, secondary pollution cannot be ignored. This study proposes a green analysis method for the detection of sphalerite based on colorimetry, which does not generate secondary pollution. The results show that the strong substitution ability of iron (Fe) for Zn contributes to their inverse correlation in contents. The lattice parameters decrease with the increasing Fe content, resulting in a darker coloration. Here, key colorimetry parameters of L*, a*, and b* show clear linear correlations with the Zn and Fe contents. Compared with traditional approaches, this new method is environmental friendly with high sensitivity and accuracy. The relative error and relative standard deviation were less than 10% and 5%, respectively. This study provides a significant reference for nonpollution determination of other mineral materials.
Geochemical modeling and hydrochemical analysis for water quality determination around mine drainage areas
Authors: Sikakwe Gregory Udie , Eyong Godswill Abam , Ojo Samuel Adebayo 
Published: October 2023

AbstractWater sources in mining areas do not retain their natural quality due to the influence of mine drainage. Water quality test was through hydrochemical analysis, speciation modeling, and saturation indices. Water samples were analyzed for pH, conductivity, nitrate, phosphate, sulfate, chlorite, sodium, magnesium, calcium, turbidity, total hardness, lead, zinc, iron, copper, cadmium, manganese, nickel, and chromium. Mean values of turbidity (0.13 mg/L), lead (0.01 mg/L), and cadmium (6.40 mg/L) exceeded their permissible values for potable water. Multivariate statistical analysis shows geogenic and anthropogenic sources of chemical species. Chemical speciation shows that the cations exist mostly in their soluble and mobile forms as free ions. Water quality index of 35–45.5 shows good water for drinking, irrigation, and industrial uses. The values of 63.8–68.8 and 103–121 reflect suitable water for industrial and irrigation uses. The research is integrated and credible in predicting groundwater pollutants to solve water pollution problems.Practitioner Points
The mean value of turbidity, Pb, and Cd exceeded the WHO/NSDWQ standards for potable water.
Correlation and principal component analyses show that the chemical species are from both geogenic and anthropogenic sources.
Chemical speciation shows that the cations exist in their soluble and mobile forms as free ions except Cr.
Saturation indices show that the minerals anhydrite, anglesite, vivianite, langite, larnakite, melanterite, and mirabilite are undersaturated in the water sources.
Water quality index shows that the water is more suitable for irrigation than drinking and industrial uses.
Refining Temporal Visualizations Using the Directional Coherence Loss
Authors: Poličar Pavlin G. , Zupan Blaž 
Published: October 2023

AbstractMany real-world data sets contain a temporal component or include transitions from state to state. For exploratory data analysis, we can present these high-dimensional data sets in two-dimensional maps, using embeddings of data objects under exploration and representing their temporal relations with directed edges. Most existing dimensionality reduction techniques, such as t-SNE and UMAP, disregard the temporal or relational nature of the data during embedding construction, leading to cluttered visualizations obscuring potentially interesting temporal patterns. To address this issue, we introduce Directional Coherence Loss (DCL), a differentiable loss function that we can incorporate into existing dimensionality reduction techniques. We have designed DCL to highlight the temporal aspects of the data, revealing temporal patterns that might otherwise remain unnoticed. By encouraging local directional coherence of the directed edges, the DCL produces more temporally-meaningful and less-cluttered visualizations. We demonstrate the effectiveness of our approach on a real-world multivariate time-series data set tracking the progression of the COVID-19 pandemic in Slovenia. We show that incorporating the DCL into the t-SNE algorithm elucidates the time progression of the pandemic in the embedding and reveals interesting cyclical patterns otherwise hidden in standard embeddings.
Gene Interactions in Survival Data Analysis: A Data-Driven Approach Using Restricted Mean Survival Time and Literature Mining
Authors: Kokošar Jaka , Špendl Martin , Zupan Blaž 
Published: October 2023

AbstractUnveiling gene interactions is crucial for comprehending biological processes, particularly their combined impact on phenotypes. Computational methodologies for gene interaction discovery have been extensively studied, but their application to censored data has yet to be thoroughly explored. Our work introduces a data-driven approach to identifying gene interactions that profoundly influence survival rates through the use of survival analysis. Our approach calculates the restricted mean survival time (RMST) for gene pairs and compares it against their individual expressions. If the interaction’s RMST exceeds that of the individual gene expressions, it suggests a potential functional association. We focused on L1000 landmark genes using TCGA na METABRIC data sets. Our findings demonstrate numerous additive and competing interactions and a scarcity of XOR-type interactions. We substantiated our results by cross-referencing with existing interactions in STRING and BioGRID databases and using large language models to summarize complex biological data. Although many potential gene interactions were hypothesized, only a fraction have been experimentally explored. This novel approach enables biologists to initiate a further investigation based on our ranked gene pairs and the generated literature summaries, thus offering a comprehensive, data-driven approach to understanding gene interactions affecting survival rates.
EXPHLOT: EXplainable Privacy Assessment for Human LOcation Trajectories
Authors: Naretto Francesca , Pellungrini Roberto , Rinzivillo Salvatore , Fadda Daniele 
Published: October 2023

AbstractHuman mobility data play a crucial role in understanding mobility patterns and developing analytical services across various domains such as urban planning, transportation, and public health. However, due to the sensitive nature of this data, accurately identifying privacy risks is essential before deciding to release it to the public. Recent work has proposed the use of machine learning models for predicting privacy risk on raw mobility trajectories and the use of shap for risk explanation. However, applying shap to mobility data results in explanations that are of limited use both for privacy experts and end-users. In this work, we present a novel version of the Expert privacy risk prediction and explanation framework specifically tailored for human mobility data. We leverage state-of-the-art algorithms in time series classification, as Rocket and InceptionTime, to improve risk prediction while reducing computation time. Additionally, we address two key issues with shap explanation on mobility data: first, we devise an entropy-based mask to efficiently compute shap values for privacy risk in mobility data; second, we develop a module for interactive analysis and visualization of shap values over a map, empowering users with an intuitive understanding of shap values and privacy risk.
RIMBO - An Ontology for Model Revision Databases
Authors: Kronström Filip , Gower Alexander H. , Tiukova Ievgeniia A. , King Ross D. 
Published: October 2023

AbstractThe use of computational models is growing throughout most scientific domains. The increased complexity of such models, as well as the increased automation of scientific research, imply that model revisions need to be systematically recorded. We present RIMBO (Revisions for Improvements of Models in Biology Ontology), which describes the changes made to computational biology models.The ontology is intended as the foundation of a database containing and describing iterative improvements to models. By recording high level information, such as modelled phenomena, and model type, using controlled vocabularies from widely used ontologies, the same database can be used for different model types. The database aims to describe the evolution of models by recording chains of changes to them. To make this evolution transparent, emphasise has been put on recording the reasons, and descriptions, of the changes.We demonstrate the usefulness of a database based on this ontology by modelling the update from version 8.4.1 to 8.4.2 of the genome-scale metabolic model Yeast8, a modification proposed by an abduction algorithm, as well as thousands of simulated revisions. This results in a database demonstrating that revisions can successfully be modelled in a semantically meaningful and storage efficient way. We believe such a database is necessary for performing automated model improvement at scale in systems biology, as well as being a useful tool to increase the openness and traceability for model development. With minor modifications the ontology can also be used in other scientific domains.The ontology is made available at https://github.com/filipkro/rimbo and will be continually updated.
LGEM+: A First-Order Logic Framework for Automated Improvement of Metabolic Network Models Through Abduction
Authors: Gower Alexander H. , Korovin Konstantin , Brunnsåker Daniel , Tiukova Ievgeniia A. , King Ross D. 
Published: October 2023

AbstractScientific discovery in biology is difficult due to the complexity of the systems involved and the expense of obtaining high quality experimental data. Automated techniques are a promising way to make scientific discoveries at the scale and pace required to model large biological systems. A key problem for 21st century biology is to build a computational model of the eukaryotic cell. The yeast Saccharomyces cerevisiae is the best understood eukaryote, and genome-scale metabolic models (GEMs) are rich sources of background knowledge that we can use as a basis for automated inference and investigation.We present LGEM+, a system for automated abductive improvement of GEMs consisting of: a compartmentalised first-order logic framework for describing biochemical pathways (using curated GEMs as the expert knowledge source); and a two-stage hypothesis abduction procedure.We demonstrate that deductive inference on logical theories created using LGEM+, using the automated theorem prover iProver, can predict growth/no-growth of S. cerevisiae strains in minimal media. LGEM+ proposed 2094 unique candidate hypotheses for model improvement. We assess the value of the generated hypotheses using two criteria: (a) genome-wide single-gene essentiality prediction, and (b) constraint of flux-balance analysis (FBA) simulations. For (b) we developed an algorithm to integrate FBA with the logic model. We rank and filter the hypotheses using these assessments. We intend to test these hypotheses using the robot scientist Genesis, which is based around chemostat cultivation and high-throughput metabolomics.
Die soziologische Partitur gemeinsamen Musizierens
Authors: Vollmer Theresa 
Published: October 2023

Zusammenfassung„Gemeinsam Musizieren“ ist nicht nur Titel der vorliegenden Promotionsschrift, sondern vielmehr eines bekannten Aufsatzes von Alfred Schütz (2016 b [1951]). In ihm verspricht sich der Autor, von der Untersuchung gemeinsamen Musizierens die Grundlagen des Sozialen näher bestimmen zu können.
Instanton contributions to the ABJM free energy from quantum M2 branes
Authors: Beccaria M. , Giombi S. , Tseytlin A. A. 
Published: October 2023

Abstract
We present a quantum M2 brane computation of the instanton prefactor in the leading non-perturbative contribution to the ABJM 3-sphere free energy at large N and fixed level k. Using supersymmetric localization, such instanton contribution was found earlier to take the form $$ {F}^{inst}\left(N,k\right)=-{\left({\sin}^2\frac{2\pi }{k}\right)}^{-1}\exp \left(-2\pi \sqrt{\frac{2N}{k}}\right)+.\dots $$

F
inst

N
k

=
−

sin
2

2
π

k

−
1

exp

−
2
π

2
N

k

+
.
…
The exponent comes from the action of an M2 brane instanton wrapped on S3/ℤk, which represents the M-theory uplift of the ℂP1 instanton in type IIA string theory on AdS4 × ℂP3. The IIA string computation of the leading large k term in the instanton prefactor was recently performed in arXiv:2304.12340. Here we find that the exact value of the prefactor $$ {\left({\sin}^2\frac{2\pi }{k}\right)}^{-1} $$

sin
2

2
π

k

−
1

is reproduced by the 1-loop term in the M2 brane partition function expanded near the S3/ℤk instanton configuration. As in the Wilson loop example in arXiv:2303.15207, the quantum M2 brane computation is well defined and produces a finite result in exact agreement with localization.
Changes in river ice cover in the context of climate change and dam impacts: a review
Authors: Fukś Maksymilian 
Published: October 2023

AbstractThis article presents a review of previous studies on the impacts of climate change and the operation of dam reservoirs on the characteristics of river ice cover. Based on a review of the existing literature, the spatial and temporal variability of trends in individual river ice cover conditions and their relationship to both climate change and the operation of dam reservoirs is explored. From this analysis, climate change is identified as the main determinant of the river ice cover disturbances observed since the start of the twentieth century. The study found that in the twentieth century, climate change contributed to a decrease in the duration of ice cover on rivers. The shortening of ice cover duration occurs primarily through earlier breakup rather than later formation. The trends in ice cover freeze-up and breakup are less spatially variable across Eurasia than in North America. The analysis indicates that dam reservoirs can exert a significant control on the spatiotemporal distribution of ice cover occurrence on rivers, even on a global scale. The first quantitative estimate of the number of dam reservoirs in river ice cover areas was also presented based on climatological and reservoir location data. The obtained results highlight the need to research river ice cover changes based on remote sensing data; such studies will make it possible to recognize the temporal–spatial distribution of trends in river ice cover parameters and the strength and extent of the influence of dam reservoirs.
Impact of empty flowers on foraging choice and movement within floral patches by the honey bee, Apis mellifera
Authors: Forster C. Y. , Middleton E. J. T. , Gloag R. , Hochuli D. F. , White T. E. , Latty T. 
Published: October 2023

AbstractFloral displays often signal the presence of nectar, but nectar may not always be present due to previous visits by nectarivores or temporal changes in nectar availability. But how does the presence of empty flowers impact the preferences of foraging honey bees for the available flowers? We aimed to test if previously rewarding flowers changed the preference relationship between neighboring flowers, and if empty flowers impacted overall visitation, in the honey bee Apis mellifera. Using artificial flowers, we showed that although empty flowers did not influence foraging choices in A. mellifera workers, empty flowers did increase movement between flowers in the patch. The presence of empty flowers also resulted in increased rates of patch abandonment. Our results suggest that while empty flowers may not directly impact foraging preferences in bees, they can have an impact on visitation within patches and in the surrounding area, with possible knock-on effects for the pollination of both the emptied flower and neighboring plants.
Prediction of postoperative speech comprehension with the transcutaneous partially implantable bone conduction hearing system Osia®
Authors: Arndt Susan , Wesarg Thomas , Aschendorff Antje , Speck Iva , Hocke Thomas , Jakob Till Fabian , Rauch Ann-Kathrin 
Published: October 2023

Abstract
Background
The active transcutaneous, partially implantable osseointegrated bone conduction system Cochlear™ Osia® (Cochlear, Sydney, Australia) has been approved for use in German-speaking countries since April 2021. The Osia is indicated for patients either having conductive (CHL) or mixed hearing loss (MHL) with an average bone conduction (BC) hearing loss of 55 dB HL or less, or having single-sided deafness (SSD).

Objectives
The aim of this retrospective study was to investigate the prediction of postoperative speech recognition with Osia® and to evaluate the speech recognition of patients with MHL and in particular an aided dynamic range of less than 30 dB with Osia®.

Materials and methods
Between 2017 and 2022, 29 adult patients were fitted with the Osia®, 10 patients (11 ears) with CHL and 19 patients (25 ears) with MHL. MHL was subdivided into two groups: MHL‑I with four-frequency pure-tone average in BC (BC-4PTA) ≥ 20 dB HL and < 40 dB HL (n = 15 patients; 20 ears) vs. MHL-II with BC-4PTA ≥ 40 dB HL (n = 4 patients; 5 ears). All patients tested a bone conduction hearing device on a softband preoperatively. Speech intelligibility in quiet was assessed preoperatively using the Freiburg monosyllabic test in unaided condition, with the trial BCHD preoperatively and with Osia® postoperatively with Osia®. The maximum word recognition score (mWRS) unaided and the word recognition score (WRS) with the test system at 65 dB SPL were correlated with the postoperative WRS with Osia® at 65 dB SPL.

Results
Preoperative prediction of postoperative outcome with Osia® was better using the mWRS than by the WRS at 65 dB SPL with the test device on the softband. Postoperative WRS was most predictive for patients with CHL and less predictable for patients with mixed hearing loss with BC-4PTA ≥ 40 dB HL. For the test device on a softband, the achievable outcome tended to a minimum, with the mWRS tending to predict the realistically achievable outcome.

Conclusion
Osia® can be used for the treatment of CHL and MHL within the indication limits. The average preoperative bone conduction hearing threshold also provides an approximate estimate of the postoperative WRS with Osia®, for which the most accurate prediction is obtained using the preoperative mWRS. Prediction accuracy decreases from a BC-4PTA of ≥ 40 dB HL.