bluuebunny/crossref_metadata_2025_split huggingface dataset:
COATi: Statistical Pairwise Alignment of Protein-Coding Sequences
Authors: García Mesa Juan José , Zhu Ziqi , Cartwright Reed A 
Published: June 2024

Abstract
Sequence alignment is an essential method in bioinformatics and the basis of many analyses, including phylogenetic inference, ancestral sequence reconstruction, and gene annotation. Sequencing artifacts and errors made during genome assembly, such as abiological frameshifts and incorrect early stop codons, can impact downstream analyses leading to erroneous conclusions in comparative and functional genomic studies. More significantly, while indels can occur both within and between codons in natural sequences, most amino-acid- and codon-based aligners assume that indels only occur between codons. This mismatch between biology and alignment algorithms produces suboptimal alignments and errors in downstream analyses. To address these issues, we present COATi, a statistical, codon-aware pairwise aligner that supports complex insertion–deletion models and can handle artifacts present in genomic data. COATi allows users to reduce the amount of discarded data while generating more accurate sequence alignments. COATi can infer indels both within and between codons, leading to improved sequence alignments. We applied COATi to a dataset containing orthologous protein-coding sequences from humans and gorillas and conclude that 41% of indels occurred between codons, agreeing with previous work in other species. We also applied COATi to semiempirical benchmark alignments and find that it outperforms several popular alignment programs on several measures of alignment quality and accuracy.
Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity
Authors: Barrault Maxime , Chabelskaya Svetlana , Coronel-Tellez Rodrigo H , Toffano-Nioche Claire , Jacquet Eric , Bouloc Philippe 
Published: June 2024

Abstract
Pathogenic bacteria employ complex systems to cope with metal ion shortage conditions and propagate in the host. IsrR is a regulatory RNA (sRNA) whose activity is decisive for optimum Staphylococcus aureus fitness upon iron starvation and for full virulence. IsrR down-regulates several genes encoding iron-containing enzymes to spare iron for essential processes. Here, we report that IsrR regulates the tricarboxylic acid (TCA) cycle by controlling aconitase (CitB), an iron-sulfur cluster-containing enzyme, and its transcriptional regulator, CcpE. This IsrR-dependent dual-regulatory mechanism provides an RNA-driven feedforward loop, underscoring the tight control required to prevent aconitase expression. Beyond its canonical enzymatic role, aconitase becomes an RNA-binding protein with regulatory activity in iron-deprived conditions, a feature that is conserved in S. aureus. Aconitase not only negatively regulates its own expression, but also impacts the enzymes involved in both its substrate supply and product utilization. This moonlighting activity concurrently upregulates pyruvate carboxylase expression, allowing it to compensate for the TCA cycle deficiency associated with iron scarcity. These results highlight the cascade of complex posttranscriptional regulations controlling S. aureus central metabolism in response to iron deficiency.
Transcription factors BZR1 and PAP1 cooperate to promote anthocyanin biosynthesis in Arabidopsis shoots
Authors: Lee Se-Hwa , Kim So-Hee , Park Tae-Ki , Kim Young-Pil , Lee Jin-Won , Kim Tae-Wuk 
Published: June 2024

Abstract
Anthocyanins play critical roles in protecting plant tissues against diverse stresses. The complicated regulatory networks induced by various environmental factors modulate the homeostatic level of anthocyanins. Here, we show that anthocyanin accumulation is induced by brassinosteroids (BRs) in Arabidopsis (Arabidopsis thaliana) shoots and shed light on the underlying regulatory mechanism. We observed that anthocyanin levels are altered considerably in BR-related mutants, and BRs induce anthocyanin accumulation by upregulating the expression of anthocyanin biosynthetic genes. Our genetic analysis indicated that BRASSINAZOLE RESISTANT 1 (BZR1) and PRODUCTION OF ANTHOCYANIN PIGMENT 1 (PAP1) are essential for BR-induced anthocyanin accumulation. The BR-responsive transcription factor BZR1 directly binds to the PAP1 promoter, regulating its expression. In addition, we found that intense anthocyanin accumulation caused by the pap1-D-dominant mutation is significantly reduced in BR mutants, implying that BR activity is required for PAP1 function after PAP1 transcription. Moreover, we demonstrated that BZR1 physically interacts with PAP1 to cooperatively regulate the expression of PAP1-target genes, such as TRANSPARENT TESTA 8, DIHYDROFLAVONOL 4-REDUCTASE, and LEUKOANTHOCYANIDIN DIOXYGENASE. Our findings indicate that BZR1 functions as an integral component of the PAP1-containing transcription factor complex, contributing to increased anthocyanin biosynthesis. Notably, we also show that functional interaction of BZR1 with PAP1 is required for anthocyanin accumulation induced by low nitrogen stress. Taken together, our results demonstrate that BR-regulated BZR1 promotes anthocyanin biosynthesis through cooperative interaction with PAP1 of the MBW complex.
The emerging challenge of FLiRT variants: KP.1.1 and KP.2 in the global pandemic landscape
Authors: Kumar P , Jayan J , Sharma R K , Gaidhane A M , Zahiruddin Q S , Rustagi S , Satapathy P 
Published: June 2024

Abstract
The SARS-CoV-2 virus has undergone substantial evolution, leading to emergence of new FLiRT variants characterized by specific spike mutations—F to L at position 456 and R to T at position 346—enhancing their transmissibility and immune evasion capabilities. Particularly, KP.2 shows a significant increase in cases in the USA, indicating a potential shift in the pandemic landscape due to its greater ability to evade vaccine-induced immunity and its higher effective reproduction number compared to JN.1. This evolving scenario underscores the need for continuous monitoring and adaptive response strategies to address the challenges posed by these new variants. This abstract examines the emergence of FLiRT variants KP.2 and KP1.1, descendants of the Omicron JN.1 variant, as they draw global attention amidst the ongoing coronavirus disease-2019 pandemic.
Effect of using the Simple Erosion Narrowing Score or Sharp/van der Heijde score on the power of rheumatoid arthritis clinical trials to detect differences in radiographic progression
Authors: den Broeder Nathan , Bolhuis Thomas E , van Herwaarden Noortje , Bergstra Sytske Anne , Bouman Chantal A M , van den Hoogen Frank H J , Verhoef Lise M , den Broeder Alfons A , van der Maas Aatke 
Published: June 2024

Abstract

Objectives
The Simple Erosion Narrowing Score (SENS) is a simplification of the Sharp/van der Heijde score (SHS). Previous studies found SENS and SHS to have very similar measurement properties, but suggest that SENS has a lower discriminative ability that may result in reduced power. Therefore, we aimed to quantify the effect of using SENS rather than SHS on the power to show between-group differences in radiographic progression.

Methods
Using data from two clinical trials in RA (DRESS and BeSt), SENS was derived from the SHS. Criterion validity of the SENS in relation to the SHS was assessed by calculating the Spearman correlation. The power of both scores to show a difference between groups was compared using bootstrapping to generate 10 000 replications of each study. Then, the number of replications with a significant difference in progression (using analysis of covariance adjusted for baseline scores) were compared.

Results
Correlations between SENS and SHS were all &gt;0.9, indicating high criterion validity of SENS compared with SHS as a reference standard. There was one exception—the DRESS study showed a somewhat lower correlation for the change score at 18 months (0.787). The loss in power of SENS over SHS was limited to at most 19% (BeSt year 5). In addition, the difference in power between SENS and SHS is smaller at higher levels of power.

Conclusion
SENS appears to be a reasonable alternative to SHS, with only a limited loss of power to show between-group differences in radiographic progression.
Liechtenstein: Rights of beneficiaries of a Private Foundation—A legal comparison between Liechtenstein, the DIFC and Wyoming
Authors: Jandrasits David Karl 
Published: June 2024

Abstract
This article examines some of the most important similarities and differences between the foundation laws in Liechtenstein, the Dubai International Financial Center (DIFC) and Wyoming. The focus of this article lies on the rights of beneficiaries of private foundations and its aim is to provide the reader with an overview and comparison of the various categories of beneficiaries as well as of their legal positions and rights. Based on the principles developed by case law and doctrine in Liechtenstein, this article addresses possible issues related to beneficiary rights in the relatively new foundation laws of the DIFC and Wyoming.
Integrating Survey and Geospatial Data for Geographical Targeting of the Poor and Vulnerable: Evidence from Malawi
Authors: Gualavisi Melany , Newhouse David 
Published: June 2024

Abstract
To address the challenge of identifying the poorest villages in developing countries, this study introduces a cost-effective strategy that leverages a combination of household consumption surveys, geospatial data, and a partial registry. The study simulates a partial registry, containing data from 450 villages across 10 impoverished districts of Malawi, and contains proxy poverty indicators. These indicators are used to impute estimates of household per capita consumption, which in turn are used to train a prediction model using publicly available geospatial data. This method is evaluated against an imputed reference of village welfare, derived from the 2016 household survey. The partial registry approach is benchmarked against three alternatives: proxy means test scores, the Meta Relative Wealth Index, and predictions from household surveys with geospatial indicators. Results show the partial registry model's rank correlation with actual welfare measures at 0.75, outperforming the other methods significantly, which ranged from −0.02 to 0.2. These findings hold under various robustness checks, including the addition of Gaussian noise, indicating that collecting household-level proxy poverty data in low-income areas can significantly improve the performance of machine learning models that integrate survey and satellite imagery data for village-level geographic targeting.
Impact of lifestyle and dietary modifications for endometriosis development and symptom management
Authors: Lalla Amber Trujillo , Onyebuchi Christina , Jorgensen Elisa , Clark Nisse 
Published: June 2024

Purpose of review
Management of endometriosis is often complex and poorly studied. Patients with endometriosis have interest in how their lifestyle may affect their diagnosis. Self-management and lifestyle changes are often used as adjunct therapy, but best practices are not concrete in treatment guidelines.

Recent findings
Lifestyle impact on endometriosis and possible self-management treatment therapies are reviewed. Overall, there is a need for future studies in all topics. Data suggest a link between endocrine-disrupting chemicals (EDCs), particularly persistent EDCs, and endometriosis. More work is needed to isolate and quantify exposures and explore their connection to endometriosis in order to provide guidance for clinical practice recommendations. There is insufficient evidence to support a superior diet for management of endometriosis; however, the Mediterranean diet may have the most benefit without nutrition concerns. Exercise may be another tool to improve endometriosis symptoms, but once again data are limited and best type and frequency is not well studied. Best evidence supports body-mind practices such as yoga, although new evidence suggests benefit from a holistic combination of several types of exercises.

Summary
Overall, data on lifestyle effects and associated therapies are limited. Future high-quality studies are needed to guide practice.
Simultaneous Deep Anterior Lamellar Keratoplasty and Descemet Membrane Endothelial Keratoplasty for Corneal Endothelial Failure With Stromal Scarring
Authors: Kara Necip 
Published: June 2024

Abstract:
We present an alternative surgical procedure including simultaneous deep anterior lamellar keratoplasty (DALK) and Descemet membrane endothelial keratoplasty (DMEK) in a case with endothelial failure and stromal scarring. A 62-year-old woman presented with vision loss caused by pseudophakic bullous keratopathy. While waiting for a corneal transplant, the patient developed infectious keratitis, which was treated with medication. Although the keratitis healed, it left a scar. To improve the patient's vision, a corneal transplant surgery that included simultaneous DALK and DMEK was performed. Postoperatively, the corneal graft was clear, and the Descemet membrane was well attached. However, there was an interface haze because of residual stromal tissue. The patient's best-corrected visual acuity improved from hand motion to 0.2 (decimal). This combined procedure allows for lamellar keratoplasty in cases with coexistence of corneal endothelial and stromal involvement.
Developmental Monitoring in Special Supplemental Nutrition Programs for Women, Infants, and Children (WIC) Increases Referrals to Social Supports
Authors: Barlow Kate , Ghiringhelli Kara , Sullivan Kelsey , Daly Ava 
Published: June 2024

To examine the impact of developmental monitoring on child referrals, a retrospective data review, comparing seven pilot programs with seven matched controls in Special Supplemental Nutrition Programs for Women, Infants, and Children (WIC) was completed. Pilot programs were trained on developmental monitoring and how to refer families to their local Early Intervention (EI) program, Special Education, or Family TIES (Together in Enhancing Support), services when there is a developmental concern. The “Learn the Signs. Act Early” developmental monitoring program was implemented, and the outcomes included the number of referrals made over a 6-month period. The results indicated a statistically significant difference (p = <.001) in referrals made preimplementation compared to postimplementation with a large effect size (d = 0.96) for pilot programs. Additionally, when analyzing between-groups there were significantly more referrals (p = .001) made at the pilot programs compared to the control programs, again with a large effect size (d = 2.10). This study shows that the implementation of developmental monitoring within WIC programs was effective in increasing referrals to intervention services designed to support families with early identification of developmental delay.
Efficacy of Baclofen as Add-on Therapy for Refractory Gastroesophageal Reflux Disease
Authors: Dong Hongyi , Luo Ying , Liu Diangang , Du Xing , Du Haijun 
Published: June 2024

Objectives:
As a GABAB receptor agonist, baclofen has demonstrated efficacy in alleviating symptoms of refractory gastroesophageal reflux disease (r-GERD). This meta-analysis aims to evaluate the safety and effectiveness of baclofen as an add-on therapy for this condition.

Method:
We conducted a comprehensive search of the PubMed, Embase, and Web of Science databases for studies published up until October 2023. Subsequently, we performed a meta-analysis encompassing all eligible trials.

Results:
From 719 records, 10 studies were included, most of these studies were moderate risk. The findings demonstrated that the addition of baclofen as a supplementary treatment effectively improves symptoms (GERD Q score) in r-GERD (standardized mean difference=−0.78, 95% CI: −1.06 to −0.51, I
2=0%). The addition of this treatment also resulted in a decrease in the frequency of nonacidic reflux episodes (standardized mean difference=−0.93, 95% CI: −1.49 to −0.37, I
2=63%) and an improvement in DeMeester scores (standardized mean difference=−0.82, 95% CI: −1.61 to −0.04, I
2=81%) among patients with r-GERD when compared with the use of proton pump inhibitor (PPI) drugs alone. However, no significant disparity was observed in terms of reducing acid reflux episodes (standardized mean difference=−0.12, 95% CI: −0.49 to 0.19, I
2=0%) and proximal reflux (standardized mean difference=−0.47, 95% CI: −1.08 to 0.14, I
2=60%).

Conclusion:
Baclofen as an add-on treatment can effectively improve the symptoms of patients with r-GERD and reduce the incidence of nonacidic reflux and improve DeMeester score. However, long-term use of baclofen leads to an increased incidence of side effects and is not effective in reducing the occurrence of acid reflux.
The Genetic History of the South Caucasus from the Bronze to the Early Middle Ages: 5000 years of genetic continuity despite high mobility
Authors: Skourtanioti Eirini , Jia Xiaowen , Tavartkiladze Nino , Bitadze Liana , Shengelia Ramaz , Tushabramishvili Nikoloz , Neumann Gunnar U. , Bianco Raffaela Angelina , Mötsch Angela , Prüfer Kay , Lamnidis Thiseas C. , Traverso Luca , Sagona Claudia , Papac Luka , Haak Wolfgang , Reich David , Ellingvåg Sturla , Stockhammer Philipp W. , Krause Johannes , Ringbauer Harald 
Published: June 2024

AbstractArchaeological and archaeogenetic studies have highlighted the pivotal role of the Caucasus region throughout prehistory, serving as a central hub for cultural, technological, and linguistic innovations. However, despite its dynamic history, the critical area between the Greater and Lesser Caucasus mountain ranges, mainly corresponding to modern-day Georgia, has received limited attention. Here, we generated an ancient DNA time transect consisting of 219 individuals with genome-wide data from 47 sites in this region, supplemented by 97 new radiocarbon dates. Spanning from the Early Bronze Age 5000 years ago to the so-called ‘Migration Period’ that followed the fall of the Western Roman Empire, we document a largely persisting local gene pool that continuously assimilated migrants from Anatolia/Levant and the populations of the adjacent Eurasian steppe. More specifically, we observe these admixture events as early as the Middle Bronze Age. Starting with Late Antiquity (late first century AD), we also detect an increasing number of individuals with more southern ancestry, more frequently associated with urban centers – landmarks of the early Christianization in eastern Georgia. Finally, in the Early Medieval Period starting 400 AD, we observe genetic outlier individuals with ancestry from the Central Eurasian steppe, with artificial cranial deformations (ACD) in several cases. At the same time, we reveal that many individuals with ACD descended from native South Caucasus groups, indicating that the local population likely adopted this cultural practice.
Tailoring the self-blinking of sulfonamide rhodamine for long-term protein-localizing super-resolution imaging
Authors: Zhang Xue , Zheng Ying , Yang Lujia , Ye Zhiwei , Xiao Yi 
Published: June 2024

AbstractLife continually changes its protein arrangements, yet the molecular ultradetails are covered by the short-lived deficiency of fluorophore blinking for super-resolution imaging. Herein, we proposed a crowding strategy to conserve the self-blinking events for prolonging the imaging time. We engineered sulfonamide rhodamines through atom-radii expansion (O-C-Si), rationally reversing xanthene intersection and creating stacking to enhance ring-opening energetical barriers. Our stacked rhodamines demonstrated decreased recruiting rates and extended survival lifetimes at single-molecule level, validating the decreased self-blinking kinetics from stacking strategy. Accordingly, our silicon-substituted rhodamine enabled persistent molecular localization imaging of various sub-organelle proteins to state-of-art time (0.5 h) in living cells, with versatile capabilities for three-dimensional and dual-color imaging. We envision our crowding strategy sets a new stage for prolongating super-resolution imaging through structural engineering.
Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model
Authors: Masters Haley , Wang Shuxiong , Tu Christina , Nguyen Quy , Sha Yutong , Karikomi Matthew K. , Fung Pamela Shi Ru , Tran Benjamin , Martel Cristina , Kwang Nellie , Neel Michael , Jaime Olga G. , Espericueta Victoria , Johnson Brett A. , Kessenbrock Kai , Nie Qing , Monuki Edwin S. 
Published: June 2024

ABSTRACTDespite the major roles of choroid plexus epithelial cells (CPECs) in brain homeostasis and repair, their developmental lineage and diversity remain undefined. In simplified differentiations from human pluripotent stem cells, derived CPECs (dCPECs) displayed canonical properties and dynamic multiciliated phenotypes that interacted with Aβ uptake. Single dCPEC transcriptomes over time correlated well with human organoid and fetal CPECs, while pseudotemporal and cell cycle analyses highlighted the direct CPEC origin from neuroepithelial cells. In addition, time series analyses defined metabolic (type 1) and ciliogenic dCPECs (type 2) at early timepoints, followed by type 1 diversification into anabolic-secretory (type 1a) and catabolic-absorptive subtypes (type 1b) as type 2 cells contracted. These temporal patterns were then confirmed in independent derivations and mapped to prenatal stages using human tissues. In addition to defining the prenatal lineage of human CPECs, these findings suggest new dynamic models of ChP support for the developing human brain.
Online Epileptic Seizure Detection in Long-term iEEG Recordings Using Mixed-signal Neuromorphic Circuits
Authors: Gallou Olympia , Bartels Jim , Ghosh Saptarshi , Schindler Kaspar , Sarnthein Johannes , Indiveri Giacomo 
Published: June 2024

AbstractSeizure detection stands as a critical aspect of epilepsy management, which requires continuous monitoring to improve patient care. However, existing monitoring systems face challenges in providing reliable, long-term, portable solutions due to the computational expense and power demands of continuous processing and data transmission. Edge computing offers a viable solution by enabling efficient processing locally, close to the sensors and without having to transmit the sensory signals to remote computing platforms. In this work, we present a mixed-signal hardware implementation of a biologically realistic Spiking Neural Network (SNN) for always-on monitoring with on-line seizure detection. We validated the hardware system with wideband Electroencephalography (EEG) signal recordings with over 122 continuous hours of data, without pre-filtering. The network was tested with a cohort of 5 patients and a total number of 22 seizures including generalized and focal onsets. Our system effectively captures spatiotemporal features based on synchronized multichannel intracranial EEG activity, achieving 100% sensitivity across all patients and near zero false alarms. Remarkably, inference across patients required only calibrating the parameters of the network’s output layer on a single recorded seizure from the patient.
Lepton-neutron interaction and
S
-wave low-energy parameters
Authors: Carbonell Jaume , Frederico Tobias 
Published: June 2024

A lepton-neutron potential in configuration space is obtained. It is based on the Coulomb plus hyperfine interaction Hamiltonian integrated over the neutron charge and magnetic densities. Different parametrizations of the neutron electromagnetic form factors are compared. It is given in the operator form with central, spin-spin, tensor, and spin-orbit terms. The potentials for lowest partial wave states are presented. We compute the lepton-neutron low-energy parameters for the S waves, estimate the zero-energy cross sections for higher angular momentum states, and point out a possible divergence in the partial wave summation due to the spin-orbit potential.

Published by the American Physical Society
2024