bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant
Authors: Pegg Cassandra L , Modhiran Naphak , Parry Rhys H , Liang Benjamin , Amarilla Alberto A , Khromykh Alexander A , Burr Lucy , Young Paul R , Chappell Keith , Schulz Benjamin L , Watterson Daniel 
Published: December 2023

Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity towards the viral spike protein, whether acquired from infection or vaccination. Mutations that impact N-glycosylation of spike may be particularly important in influencing antigenicity, but their consequences are difficult to predict. Here, we compare the glycosylation profiles and antigenicity of recombinant viral spike of ancestral Wu-1 and the Gamma strain, which has two additional N-glycosylation sites due to amino acid substitutions in the N-terminal domain (NTD). We found that a mutation at residue 20 from threonine to asparagine within the NTD caused the loss of NTD-specific antibody COVA2-17 binding. Glycan site-occupancy analyses revealed that the mutation resulted in N-glycosylation switching to the new sequon at N20 from the native N17 site. Site-specific glycosylation profiles demonstrated distinct glycoform differences between Wu-1, Gamma, and selected NTD variant spike proteins, but these did not affect antibody binding. Finally, we evaluated the specificity of spike proteins against convalescent COVID-19 sera and found reduced cross-reactivity against some mutants, but not Gamma spike compared to Wuhan spike. Our results illustrate the impact of viral divergence on spike glycosylation and SARS-CoV-2 antibody binding profiles.
Uncovering the Nature of ECHR Rights: An Analytical and Methodological Framework
Authors: Tripkovic Bosko , Zysset Alain 
Published: December 2023

Abstract
How does the European Court of Human Rights (ECtHR) understand the nature of human rights? The article develops a framework for the analysis of this question and shows how it can be applied. The first part identifies a gap at the intersection of doctrinal and philosophical approaches to human rights practice that leaves the ECtHR’s understanding of the nature of rights unaccounted for. The second part develops an analytic and methodological framework based on the idea of grounds, content and scope of human rights to bridge this disciplinary divide and facilitate a more perspicuous analysis of the Court’s conception of the nature of human rights. The third part tests this framework by examining the Court’s doctrines in relation to freedom of thought, conscience and religion and the right to free elections.
Peaceful settlement of inter-state energy disputes: applicable law, defence arguments, and remedies in the ICC arbitration between Iraq and Turkey
Authors: Demirkol Berk 
Published: December 2023

Abstract
At this critical juncture in the energy transition dominated by debates over armed conflicts, advisory opinions on climate changes, and investor-State arbitration, it is critical to also consider developments in the peaceful settlement of inter-State energy disputes. One central dispute between the Republic of Iraq and the Republic of Turkey arose out of the Crude Oil Pipeline Agreement for the supply and purchase of crude oil. Iraq filed a request for arbitration in May 2014 under the International Chamber of Commerce Rules of Arbitration. The Tribunal awarded Iraq nearly United States Dollars (USD) 1.5 billion. The Tribunal’s unanimous final award in 2023 discusses fascinating aspects of international energy transactions, including the choice of domestic law in a treaty dispute, defences under the law of treaties, a putative norm of jus cogens to prevent genocide, and possible remedies in an inter-State pipeline arbitration.
Frequency of serological markers of rheumatoid arthritis in patients with Hashimoto’s thyroiditis
Authors: Ghozzi Mariam , Mankai Amani , Melayah Sarra , Mechi Fatma , Chedly Zeineb , Trabelsi Abdelhalim , Ghedira Ibtissem 
Published: December 2023

Abstract

Background
Hashimoto’s thyroiditis (HT) is an autoimmune disease that is frequently associated with other autoimmune conditions.

Objective
To perform serological screening for rheumatoid arthritis (RA) in patients with HT.

Methods
Our study included 88 consecutive serum specimens of patients with confirmed HT and 88 sex- and age-matched healthy subjects. All study participants were tested for anti-cyclic citrullinated peptides antibodies (CCP-Ab) and rheumatoid factor (RF). CCP-Ab and RF were performed using ELISA commercial kits. Statistical analysis was conducted using Epi Info, version 3.

Results
Out of 88 patients with HT, 15 (17.0%) had CCP-Ab or RF. The frequency of serological markers of RA was significantly higher in patients than in control individuals (17.0% vs 4.5%; P = .007). RF was more frequent in patients than in the control group, and the difference was statistically significant (13.6% vs 3.4%; P = .01). Isolated RF-IgM was absent in all controls and present in 6 patients with HT (6.8% vs 0%; P = .02). Out of 14 male patients, 3 (21.4%) had antibodies of RA. There was no significant difference in age between patients with CCP-Ab or RF and those without.

Conclusion
A high frequency of serological markers of RA was highlighted in patients with HT.
Observational chemical signatures of the past FU Ori outbursts
Authors: Zwicky Lis , Molyarova Tamara , Akimkin Vitaly , Smirnov-Pinchukov Grigorii V , Semenov Dmitry , Kóspál Ágnes , Ábrahám Péter 
Published: December 2023

ABSTRACT
FU Ori-type stars (FUors) are young stellar objects (YSOs) experiencing luminosity outbursts by a few orders of magnitude, which last for ∼102 yr. A dozen of FUors are known up to date, but many more currently quiescent YSOs could have experienced such outbursts in the last ∼103 yr. To find observational signatures of possible past outbursts, we utilize andes, radmc-3d code as well as casa ALMA simulator to model the impact of the outburst on the physical and chemical structure of typical FU Ori systems and how it translates to the molecular lines’ fluxes. We identify several combinations of molecular lines that may trace past FU Ori objects both with and without envelopes. The most promising outburst tracers from an observational perspective are the molecular flux combinations of the N2H+J = 3–2, C18O J = 2–1, H2CO $(J_{\rm K_a, K_c}) = 4_{04}-3_{03}$, and HCN J = 3–2 lines. We analyse the processes leading to molecular flux changes and show that they are linked with either thermal desorption or enhanced chemical reactions in the molecular layer. Using observed CO, HCN, N2H+, and H2CO line fluxes from the literature, we identify ten nearby disc systems that might have undergone FU Ori outbursts in the past ∼103 yr: [MGM2012] 556, [MGM2012] 371, and [MGM2012] 907 YSOs in L1641, Class II protoplanetary discs around CI Tau, AS 209, and IM Lup and transitional discs DM Tau, GM Aur, LkCa 15, and J1640-2130.
Could the TeV emission of starburst galaxies originate from pulsar wind nebulae?
Authors: Chen Xiao-Bin , Liu Ruo-Yu , Wang Xiang-Yu , Chang Xiao-Chuan 
Published: December 2023

ABSTRACT
While the GeV γ-ray emission of starburst galaxies (SBGs) is commonly thought to arise from hadronic interactions between accelerated cosmic rays and interstellar gas, the origin of the TeV γ-ray emission is more uncertain. One possibility is that a population of pulsar wind nebulae (PWNe) in these galaxies could be responsible for the TeV γ-ray emission. In this work, we first synthesize a PWNe population in the Milky Way and assess their contribution to the γ-ray emission of the Galaxy, using a time-dependent model to calculate the evolution of the PWN population. Such a synthetic PWN population can reproduce the flux distribution of PWNe identified in the Milky Way given a distribution of the initial state of the pulsar population. We then apply it to starburst galaxies and quantitatively calculate the spectral energy distribution of all PWNe in the SBGs NGC 253 and M82. We propose that TeV γ-ray emission in starburst galaxies can be dominated by PWNe for a wide range of parameter space. The energetic argument requires that ηe × vSN &gt; 0.01 yr−1, where ηe is the fraction of spin-down energy going to electrons and vSN is the supernova rate. By requiring the synchrotron emission flux of all PWNe in the galaxy not to exceed the hard X-ray measurement of NGC 253, we constrain the initial magnetic field strength of PWNe to be $\lesssim 400\,\mu{\rm G}$. Future observations at higher energies with the Large High Altitude Air Shower Observatory (LHAASO) or the next-generation neutrino observatory IceCube-Gen2 will help us to understand the origin of the TeV γ-ray emission in SBGs better.
Aggregated chromosomes/chromatin transfer: a novel approach for mitochondrial replacement with minimal mitochondrial carryover: the implications of mouse experiments for human aggregated chromosome transfer
Authors: Okamoto Ryota , Xiao Wei , Fukasawa Hiroko , Hirata Shuji , Sankai Tadashi , Masuyama Hisashi , Otsuki Junko 
Published: December 2023

Abstract
Nuclear transfer techniques, including spindle chromosome complex (SC) transfer and pronuclear transfer, have been employed to mitigate mitochondrial diseases. Nevertheless, the challenge of mitochondrial DNA (mtDNA) carryover remains unresolved. Previously, we introduced a method for aggregated chromosome (AC) transfer in human subjects, offering a potential solution. However, the subsequent rates of embryonic development have remained unexplored owing to legal limitations in Japan, and animal studies have been hindered by a lack of AC formation in other species. Building upon our success in generating ACs within mouse oocytes via utilization of the phosphodiesterase inhibitor 3-isobutyl 1-methylxanthine (IBMX), this study has established a mouse model for AC transfer. Subsequently, a comparative analysis of embryo development rates and mtDNA carryover between AC transfer and SC transfer was conducted. Additionally, the mitochondrial distribution around SC and AC structures was investigated, revealing that in oocytes at the metaphase II stage, the mitochondria exhibited a relatively concentrated arrangement around the spindle apparatus, while the distribution of mitochondria in AC-formed oocytes appeared to be independent of the AC position. The AC transfer approach produced a marked augmentation in rates of fertilization, embryo cleavage, and blastocyst formation, especially as compared to scenarios without AC transfer in IBMX-treated AC-formed oocytes. No significant disparities in fertilization and embryo development rates were observed between AC and SC transfers. However, relative real-time PCR analyses revealed that the mtDNA carryover for AC transfers was one-tenth and therefore significantly lower than that of SC transfers. This study successfully accomplished nuclear transfers with ACs in mouse oocytes, offering an insight into the potential of AC transfers as a solution to heteroplasmy-related challenges. These findings are promising in terms of future investigation with human oocytes, thus advancing AC transfer as an innovative approach in the field of human nuclear transfer methodology.
MutSβ protects common fragile sites by facilitating homology-directed repair at DNA double-strand breaks with secondary structures
Authors: Li Youhang , Zhang Yunkun , Shah Sameer Bikram , Chang Chia-Yu , Wang Hailong , Wu Xiaohua 
Published: December 2023

Abstract
Common fragile sites (CFSs) are regions prone to chromosomal rearrangements, thereby contributing to tumorigenesis. Under replication stress (RS), CFSs often harbor under-replicated DNA regions at the onset of mitosis, triggering homology-directed repair known as mitotic DNA synthesis (MiDAS) to complete DNA replication. In this study, we identified an important role of DNA mismatch repair protein MutSβ (MSH2/MSH3) in facilitating MiDAS and maintaining CFS stability. Specifically, we demonstrated that MutSβ is required for the increased mitotic recombination induced by RS or FANCM loss at CFS-derived AT-rich and structure-prone sequences (CFS-ATs). We also found that MSH3 exhibits synthetic lethality with FANCM. Mechanistically, MutSβ is required for homologous recombination (HR) especially when DNA double-strand break (DSB) ends contain secondary structures. We also showed that upon RS, MutSβ is recruited to Flex1, a specific CFS-AT, in a PCNA-dependent but MUS81-independent manner. Furthermore, MutSβ interacts with RAD52 and promotes RAD52 recruitment to Flex1 following MUS81-dependent fork cleavage. RAD52, in turn, recruits XPF/ERCC1 to remove DNA secondary structures at DSB ends, enabling HR/break-induced replication (BIR) at CFS-ATs. We propose that the specific requirement of MutSβ in processing DNA secondary structures at CFS-ATs underlies its crucial role in promoting MiDAS and maintaining CFS integrity.
Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes
Authors: Hernández Greco , García Alejandra , Weingarten-Gabbay Shira , Mishra Rishi Kumar , Hussain Tanweer , Amiri Mehdi , Moreno-Hagelsieb Gabriel , Montiel-Dávalos Angélica , Lasko Paul , Sonenberg Nahum 
Published: December 2023

Abstract
mRNA translation is a fundamental process for life. Selection of the translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for mRNA decoding. Studies in vertebrate mRNAs discovered that a purine at −3 and a G at +4 (where A of the AUG initiator codon is numbered + 1), promote TIS recognition. However, the TIS context in other eukaryotes has been poorly experimentally analyzed. We analyzed in vitro the influence of the −3, −2, −1 and + 4 positions of the TIS context in rabbit, Drosophila, wheat, and yeast. We observed that −3A conferred the best translational efficiency across these species. However, we found variability at the + 4 position for optimal translation. In addition, the Kozak motif that was defined from mammalian cells was only weakly predictive for wheat and essentially non-predictive for yeast. We discovered eight conserved sequences that significantly disfavored translation. Due to the big differences in translational efficiency observed among weak TIS context sequences, we define a novel category that we termed ‘barren AUG context sequences (BACS)’, which represent sequences disfavoring translation. Analysis of mRNA-ribosomal complexes structures provided insights into the function of BACS. The gene ontology of the BACS-containing mRNAs is presented.
Phosphorus balance calculator: an individualized tool for treatment of hyperphosphatemia in hemodialysis patients
Authors: Wang Mengjing , Xiao Jing , Du Qiuna , Zhang Weichen , Zhang Jiaying , Yan Zhenwen , Luo Jianfeng , Yu Chen , Ye Zhibin , Chen Jing 
Published: December 2023

ABSTRACT

Background
Lack of evaluations of the dietary phosphorus and dialysis phosphorus removal in daily clinical practice are common obstacles to assessing phosphorus balance and controlling phosphorus in hemodialysis patients. We aimed to investigate whether individualized therapy using a phosphorus balance calculator improves phosphorus control.

Methods
A randomized, open-label, multicenter, 4-week clinical trial was conducted. A total of 119 maintenance hemodialysis patients aged 18–85 years old and with serum phosphorus level &gt;1.45 mmol/L from three university teaching hospitals in Shanghai were enrolled. Patients were randomized in a 1:1 ratio to individualized therapy (n = 60) or conventional therapy (n = 59). The primary outcome was the serum phosphorus concentration after 4-week treatment. Secondary outcomes included the serum calcium and parathyroid hormone (PTH) concentrations, changes in serum phosphorus, calcium and PTH concentrations, and the proportion of patients achieving target ranges of serum phosphorus, calcium and PTH after 4-week treatment.

Results
Among 119 randomized participants [mean age 62 years; 68 male (57%)], 116 completed the trial. Using the phosphorus balance calculator, the individualized group achieved a better phosphorus balance state and significantly reduced serum phosphorus (1.62 ± 0.45 mmol/L versus 1.85 ± 0.45 mmol/L, P = .006), increased the proportions of patients achieving target serum phosphorus range (41% versus 18%, P = .006) and had greater adjusted mean difference in change in serum phosphorus over the 4 weeks (−0.47 versus −0.23 mmol/L, P = .010) when compared with conventional therapy. No significant changes were observed in serum calcium and PTH levels, the proportion of patients achieving target serum calcium or PTH levels, or the adjusted mean difference of serum calcium and PTH levels over the treatment period.

Conclusion
Phosphorus balance calculator was proved to improve serum phosphorus control in patients undergoing maintenance hemodialysis, offering a new tool for managing hyperphosphatemia.
Long-term dynamics, population structure and connectivity of the helmet jellyfish Periphylla periphylla in a Norwegian fjord and adjacent waters
Authors: Aberle Nicole , Volpe Charlotte , Østensen Mari-Ann , Majaneva Sanna 
Published: December 2023

Abstract
Mass occurrences of Periphylla periphylla in Norwegian fjords cause major concerns related to potential regime shifts that could affect ecosystem stability. 15 years of trawl data (2006–2015), complemented with comprehensive sampling in different areas and seasons (2018–2021) allowed new insights on the dynamics, structure and connectivity of P. periphylla populations within and beyond Trondheimsfjorden. Despite assumed population bursts, no clear trend on P. periphylla population size in Trondheimsfjorden were identified. Sampling frequency and population size suggest a local reproduction of P. periphylla, especially in the inner part of the fjord where young-of-the-year (YOY) individuals occur. Size variations occurred in relation to sampling month, thus pointing at seasonal patterns in growth and reproduction. No distinct population structure of P. periphylla populations within Trondheimsfjorden and over larger spatial scales (&gt; 100 km) along the Norwegian coast was observed. Such poor geographic population structure provides evidence for a strong dispersal of P. periphylla, potentially triggered by frequent deep-water renewals of the fjords’ basins that enable a high gene flow. Data on P. periphylla long-term dynamics, population structure and connectivity provide valuable information for ecosystem state assessments and enable the advancement of ecosystem management approaches, thus accounting for both stakeholder and ecosystem demands.
Mastering Our Own Magic in the Evolution Toward Precision Practice
Authors: Field-Fote Edelle Carmen 
Published: December 2023

Abstract
Edelle (Edee) Field-Fote, PT, PhD, FASIA, FAPTA, the 54th Mary McMillan lecturer, is director of the Shepherd Center Spinal Cord Injury Research Program & Hulse Laboratory; professor in the division of physical therapy at Emory University School of Medicine; and professor of the practice in the school of biological sciences at the Georgia Institute of Technology. In her role as the director of spinal cord injury (SCI) research at Shepherd Center, Field-Fote leads a team dedicated to improving motor function in people with SCI through the development of neuromodulation and neurorehabilitation approaches informed by the latest neuroscience research and guided by outcomes that have meaning for people with SCI. With a clinical background as a physical therapist, PhD training in a preclinical model of SCI, and postdoctoral training in motor control physiology, her 25-plus years of SCI research have spanned the breadth of basic and clinical/translational research related to SCI. Dr Field-Fote has conducted randomized clinical trials with funding from the National Institutes of Health since 1997; other clinical trials in her lab have been funded by the Department of Defense, the National Institute on Disability Independent Living and Rehabilitation Research, and numerous foundations. Field-Fote is the recipient of multiple honors from the American Physical Therapy Association (APTA) and its components. She is a Fellow of APTA and a Fellow of the American Spinal Injury Association. She has also served in numerous APTA and APTA component appointed or elected positions and as a member and president of the Foundation for Physical Therapy Research Board of Trustees.
Pain assessment and management among adult patients in a gynecology ward: a best practice implementation project
Authors: Bernués-Caudillo Leticia , Albornos-Muñoz Laura , Rodrigo M. Paz Fernández , García Marta Álvarez , Benito Marta De Rioja , Serrano María Jesús Ruano , Navarro Paloma García , Pérez Patricia Ledesma , Sotelo Sonia González , Moreno-Casbas M. Teresa , Vrbová Tereza , Klugar Miloslav , Klugarová Jitka , Gonzalez-María Esther 
Published: December 2023

ABSTRACT

Objectives:
This project aimed to improve compliance with evidence-based practice in pain assessment and management in a gynecology ward.

Introduction:
Effective pain control is important to prevent the negative consequences of pain that is poorly managed. However, it remains undervalued and inadequately treated. Applying evidence-based practices to correctly evaluate and manage pain is essential to improve pain relief.

Methods:
This project followed the JBI Evidence Implementation Framework. A baseline audit of 41 women admitted to the gynecology ward was conducted and measured against 5 best practice criteria, along with a patient satisfaction questionnaire. Targeted strategies were then implemented and a follow-up audit was conducted using the same criteria, methods, and sample size as the baseline audit.

Results:
The baseline audit revealed gaps between current and best practice. Barriers to implementation were identified and strategies to resolve the barriers were designed and implemented (nurse education, informative materials, electronic patient records system improvements). Comprehensive pain assessment, including dynamic and static pain assessment, use of a validated tool, and education provided to patients and carers, improved in the follow-up audit. There was no change in patient satisfaction levels; however, the discrepancy between pain measured by nurses and pain measured by patients was reduced.

Conclusions:
The JBI methodology was useful in improving compliance with evidence-based practice criteria. It also facilitated adaptation to new barriers, such as the COVID-19 pandemic. Improving nurses’ knowledge of pain assessment can lead to more accurate assessment. Inadequate records systems also made it difficult to record the care that was provided. Subsequent audits will assess sustainability and the project will be escalated to other wards.
Pharmacogenomics in Tailoring First-Line Therapy for Breast Cancer: PharmGKB Database Insights
Authors: Porfírio de Aguiar Murilo 
Published: December 2023

ABSTRACTThis study delves into the role of pharmacogenomics in optimizing first-line breast cancer treatments, leveraging insights from the PharmGKB database. It emphasizes the importance of understanding genetic variations and their influence on the efficacy and side effects of key drugs like Letrozole, Anastrozole, Tamoxifen, Trastuzumab, and Pertuzumab. By analyzing these drugs in the context of genetic profiles, the research highlights the necessity of incorporating genetic testing into treatment planning. The findings underscore the potential of pharmacogenetics to personalize therapy, aiming to improve outcomes and reduce adverse reactions in breast cancer patients. This approach marks a significant stride towards tailored cancer treatments, underscoring the need for continued research in this field.