bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying vulnerable brain networks associated with Alzheimer’s disease risk
Authors: Mahzarnia Ali , Stout Jacques A , Anderson Robert J , Moon Hae Sol , Yar Han Zay , Beck Kate , Browndyke Jeffrey N , Dunson David B , Johnson Kim G , O’Brien Richard J , Badea Alexandra 
Published: November 2022

AbstractThe selective vulnerability of brain networks in individuals at risk for Alzheimer’s disease (AD) may help differentiate pathological from normal aging at asymptomatic stages, allowing the implementation of more effective interventions. We used a sample of 72 people across the age span, enriched for the APOE4 genotype to reveal vulnerable networks associated with a composite AD risk factor including age, genotype, and sex. Sparse canonical correlation analysis (CCA) revealed a high weight associated with genotype, and subgraphs involving the cuneus, temporal, cingulate cortices, and cerebellum. Adding cognitive metrics to the risk factor revealed the highest cumulative degree of connectivity for the pericalcarine cortex, insula, banks of the superior sulcus, and the cerebellum. To enable scaling up our approach, we extended tensor network principal component analysis, introducing CCA components. We developed sparse regression predictive models with errors of 17% for genotype, 24% for family risk factor for AD, and 5 years for age. Age prediction in groups including cognitively impaired subjects revealed regions not found using only normal subjects, i.e. middle and transverse temporal, paracentral and superior banks of temporal sulcus, as well as the amygdala and parahippocampal gyrus. These modeling approaches represent stepping stones towards single subject prediction.
Comparison of Single Molecule, Real-Time Sequencing and Nanopore Sequencing for Analysis of the Size, End-Motif, and Tissue-of-Origin of Long Cell-Free DNA in Plasma
Authors: Yu Stephanie C Y , Deng Jiaen , Qiao Rong , Cheng Suk Hang , Peng Wenlei , Lau So Ling , Choy L Y Lois , Leung Tak Y , Wong John , Wong Vincent Wai-Sun , Wong Grace L H , Jiang Peiyong , Chiu Rossa W K , Chan K C Allen , Lo Y M Dennis 
Published: November 2022

Abstract

Background
Recent studies using single molecule, real-time (SMRT) sequencing revealed a substantial population of analyzable long cell-free DNA (cfDNA) in plasma. Potential clinical utilities of such long cfDNA in pregnancy and cancer have been demonstrated. However, the performance of different long-read sequencing platforms for the analysis of long cfDNA remains unknown.

Methods
Size biases of SMRT sequencing by Pacific Biosciences (PacBio) and nanopore sequencing by Oxford Nanopore Technologies (ONT) were evaluated using artificial mixtures of sonicated human and mouse DNA of different sizes. cfDNA from plasma samples of pregnant women at different trimesters, hepatitis B carriers, and patients with hepatocellular carcinoma were sequenced with the 2 platforms.

Results
Both platforms showed biases to sequence longer (1500 bp vs 200 bp) DNA fragments, with PacBio showing a stronger bias (5-fold overrepresentation of long fragments vs 2-fold in ONT). Percentages of cfDNA fragments 500 bp were around 6-fold higher in PacBio compared with ONT. End motif profiles of cfDNA from PacBio and ONT were similar, yet exhibited platform-dependent patterns. Tissue-of-origin analysis based on single-molecule methylation patterns showed comparable performance on both platforms.

Conclusions
SMRT sequencing generated data with higher percentages of long cfDNA compared with nanopore sequencing. Yet, a higher number of long cfDNA fragments eligible for the tissue-of-origin analysis could be obtained from nanopore sequencing due to its much higher throughput. When analyzing the size and end motif of cfDNA, one should be aware of the analytical characteristics and possible biases of the sequencing platforms being used.
Increased Primary Bile Acids with Ileocolonic Resection Impact Ileal Inflammation and Gut Microbiota in Inflammatory Bowel Disease
Authors: Battat Robert , Scherl Ellen J , Lukin Dana , Charilaou Paris , Mahtani Prerna , Gerber Juliette , Gandara Jorge A ,   JRI IBD Live Cell Bank Consortium, Longman Randy , Sonnenberg Gregory , Scherl Ellen , Sockolow Robbyn , Lukin Dana , Battat Robert , Ciecierega Thomas , Solomon Aliza , Barfield Elaine , Chien Kimberley , Ferreira Johanna , Williams Jasmin , Khan Shaira , Chong Peik Sean , Mozumder Samah , Chou Lance , Zhou Wenqing , Ahmed Anees , Zhong Connie , Joseph Ann , Gladstone Joseph , Jensen Samantha , Dündar Friederike , Zumbo Paul , Betel Doron , Guo Chun-Jun , Longman Randy S 
Published: November 2022

Abstract

Background
Most Crohn’s disease [CD] patients require surgery. Ileitis recurs after most ileocolectomies and is a critical determinant for outcomes. The impacts of ileocolectomy-induced bile acid [BA] perturbations on intestinal microbiota and inflammation are unknown. We characterized the relationships between ileocolectomy, stool BAs, microbiota and intestinal inflammation in inflammatory bowel disease [IBD].

Methods
Validated IBD clinical and endoscopic assessments were prospectively collected. Stool primary and secondary BA concentrations were compared based on ileocolectomy and ileitis status. Primary BA thresholds for ileitis were evaluated. Metagenomic sequencing was use to profile microbial composition and function. Relationships between ileocolectomy, BAs and microbiota were assessed.

Results
In 166 patients, elevated primary and secondary BAs existed with ileocolectomy. With ileitis, only primary BAs [795 vs 398 nmol/g, p = 0.009] were higher compared to without ileitis. The optimal primary BA threshold [≥228 nmol/g] identified ileitis on multivariable analysis [odds ratio = 2.3, p = 0.04]. Microbial diversity, Faecalibacterium prausnitzii and O-acetylhomoserine aminocarboxypropyltransferase [MetY] were decreased with elevated primary BAs. Amongst ileocolectomy patients, only those with elevated primary BAs had diversity, F. prausnitzii and MetY reductions. Those with both ileocolectomy and intermediate [p = 0.002] or high [≥228 nmol/g, p = 9.1e-11]] primary BA concentrations had reduced F. prausnitzii compared to without ileocolectomy. Those with ileocolectomy and low [&lt;29.2 nmol/g] primary BA concentrations had similar F. prausnitzii to those without ileocolectomy [p = 0.13]. MetY was reduced with ileitis [p = 0.02].

Conclusions
Elevated primary BAs were associated with ileitis, and reduced microbial diversity, F. prausnitzii abundance and enzymatic abundance of MetY [acetate and l-methionine-producing enzyme expressed by F. prausnitzii], and were the only factors associated with these findings after ileocolectomy.
Foot, ankle, and leg problems in Australian primary care: consultation patterns, management practices, and costs
Authors: Menz Hylton B , Williams Cylie M , Lazzarini Peter A , Gordon Julie , Harrison Christopher 
Published: November 2022

Abstract

Objective
To explore consultation patterns, management practices, and costs of foot, ankle, and leg problems in Australian primary care.

Study design
We analyzed data from the Bettering the Evaluation and Care of Health program, April 2000 to March 2016. Foot, ankle, and leg problems were identified using the International Classification of Primary Care, Version 2 PLUS terminology. Data were summarized using descriptive statistics examining general practitioner (GP) and patient characteristics associated with a foot, ankle, or leg problem being managed. Cost to government was estimated by extracting fees for GP consultations, diagnostic imaging, and pathology services from the Medicare Benefits Schedule (MBS) database. Costs for prescription-only medicines were extracted from the Pharmaceutical Benefits Schedule and for nonprescribed medications, large banner discount pharmacy prices were used.

Results
GPs recorded 1,568,100 patient encounters, at which 50,877 foot, ankle, or leg problems were managed at a rate of 3.24 (95% confidence intervals [CIs] 3.21–3.28) per 100 encounters. The management rate of foot, ankle, or leg problems was higher for certain patient characteristics (older, having a health care card, socioeconomically disadvantaged, non-Indigenous, and being English speaking) and GP characteristics (male sex, older age, and Australian graduate). The most frequently used management practice was the use of medications. The average cost (Australian dollars) per encounter was A$52, with the total annual cost estimated at A$256m.

Conclusions
Foot, ankle, and leg problems are frequently managed by GPs, and the costs associated with their management represent a substantial economic impact in Australian primary care.
The impact of conformational sampling on first-principles calculations of vicinal COCH J-couplings in carbohydrates
Authors: Reeves Hannah L , Wang Lee-Ping 
Published: November 2022

Abstract
Dihedral angles in organic molecules and biomolecules are vital structural parameters that can be indirectly probed by nuclear magnetic resonance (NMR) measurements of vicinal J-couplings. The empirical relations that map the measured couplings to dihedral angles are typically determined by fitting using static structural models, but this neglects the effects of thermal fluctuations at the finite temperature conditions under which NMR measurements are often taken. In this study, we calculate ensemble-averaged J-couplings for several structurally rigid carbohydrate derivatives using first-principles molecular dynamics simulations to sample the thermally accessible conformations around the minimum energy structure. Our results show that including thermal fluctuation effects significantly shifts the predicted couplings relative to single-point calculations at the energy minima, leading to improved agreement with experiments. This provides evidence that accounting for conformational sampling in first-principles calculations can improve the accuracy of NMR-based structure determination for structurally complex carbohydrates.
Virtual sovereignty? Private internet capital, digital platforms and infrastructural power in the United States
Authors: Kelton Maryanne , Sullivan Michael , Rogers Zac , Bienvenue Emily , Troath Sian 
Published: November 2022

Abstract
Infrastructural power in the United States, which is the capacity to extract and deploy social resources and initiate and harness technological innovation, is increasingly generated by private internet capital and exercised by digital platforms. In this article we argue that while these private actors do not possess legitimacy, this is a form of ‘virtual sovereignty’ which complicates the capacity of the US state to exercise infrastructural power. Though internet software was designed largely by US corporations, commercial users operate increasingly in deterritorialized global spaces, where citizen consent and the interests of the US state are not business priorities. Moreover, much of the internet's hardware is financed by private internet capital within global wealth chains and digital spaces populated by US and non-US corporations. We argue that digital platforms acquire infrastructural power through the accumulation and commercialization of big data, from which they curate individual thinking and behaviour. We point to the targeting of US liberal democratic resilience by hostile, domestic and foreign actors weaponizing social media, and the potential ramifications of the exercise of virtual sovereignty for the return of great power rivalry in international relations. The article concludes that private internet capital's command of vast socio-economic resources reinforces the digital platforms' leadership in technological innovation and challenges the sovereign state's monopoly over national security.
Russia, Ukraine and state survival through neutrality
Authors: Allison Roy 
Published: November 2022

Abstract
During the Cold War neutrality and a ‘non-bloc’ status were used by certain European states to escape great power rivalries. But these foreign and security policy strategies declined in significance and have received little scholarly attention since the early 1990s. This article argues that in a period of renewed confrontation between Russia and western powers, significant insights may be derived from a critical review of the past experiences of neutral and non-bloc states. These help scholars and practitioners assess the contemporary options of states in vulnerable locations which choose or are compelled to survive outside alliances. This article probes the critical case of Ukraine as a sovereign but potentially neutral state. Relevant criteria for neutrality are drawn from short interpretive case-studies of Austria and Finland during the Cold War, as well as Moldova and Finland in post-Cold War years. Soviet and Russian policy prioritized the strategic denial of these states to NATO, while forms of armed neutrality helped sustain conventional deterrence against Russian coercion. If Moscow reigns in its ambitions for the political subjugation of Ukraine and accepts its statehood, such thinking may form part of an eventual security policy settlement beyond the current war.
Impact of Biologic Agents on the Immune Response Induced by the Additional Dose of SARS-CoV-2 Vaccine in Inflammatory Bowel Disease Patients
Authors: Ramos Laura , Hernández-Porto Miriam , Carrillo-Palau Marta , Alonso-Abreu Inmaculada , Reygosa Cristina , Hernandez-Guerra Manuel 
Published: November 2022

Lay Summary
The immusne response to the vaccine against SARS-CoV-2 is altered in patients with inflammatory bowel disease using biological agents, and so we should ensure effective immunization in these patients by prioritizing those receiving anti-tumor necrosis factor agents in the indication of new doses or booster doses of the vaccine.
Revisiting due diligence in cyberspace: crafting international law’s arsenal against transboundary Botnets
Authors: Shrivastava Abhijeet , Lakra Rudraksh 
Published: November 2022

Abstract
The emergence of cyberspace has been followed by increasingly unpredictable threats to cybersecurity, including Botnets, which have been frequently exploited in cyber-criminal activities affecting dozens or hundreds of States at once. In existing scholarship, many reasons have informed growing support for the promise of ‘due diligence’ obligations in regulating transboundary cyber operations. We affirm this position through a study of the specific context of Botnets, although bringing much-needed caution and complexity to the discourse. We offer a comprehensive account of the standard of conduct expected of States in detecting, mitigating and preventing Botnet-linked harms under due diligence; as well as to pursue cyber capacity building toward discharging these obligations. In so doing, we problematize and elaborate on the nature of due diligence as an obligation of conduct, therefore accounting for differential State capacities against Botnet-linked harms. The paper involves attempts to unpack a coherent conception of due diligence, appreciating the spectrum of obligations that it demands, and demonstrating these nuances through an appraisal of good practices adopted by States and private actors against Botnets. Consequently, we provide a unique holistic account of how States and their law enforcement could practically understand the conduct expected of them when faced with transboundary Botnets on a case-to-case basis. In the end, while underscoring potential dilemmas within this legal regime that may be faced by target States, as also its unresolved questions, we submit that due diligence is indeed the most appropriate candidate to act as a legal arsenal against transboundary Botnets.
Isoparametric Polynomials and Sums of Squares
Authors: Ge Jianquan , Tang Zizhou 
Published: November 2022

Abstract
Hilbert’s 17th problem asks whether every nonnegative polynomial can be a sum of squares of rational functions. It has been answered affirmatively by Artin. However, the question as to whether a given nonnegative polynomial is a sum of squares of polynomials is still a central question in real algebraic geometry. In this paper, we solve this question completely for the nonnegative polynomials associated with isoparametric polynomials, initiated by E. Cartan, which define the focal submanifolds of the corresponding isoparametric hypersurfaces.
Dedicated to Professor Chia-Kuei Peng on his 80th birthday
Genome-Wide Association Studies Identify an Association of Transferrin Binding Protein B Variation and Invasive Serogroup Y Meningococcal Disease in Older Adults
Authors: Maynard-Smith Laura , Derrick Jeremy P , Borrow Ray , Lucidarme Jay , Maiden Martin C J , Heyderman Robert S , Harrison Odile B 
Published: November 2022

Abstract

Background
Neisseria meningitidis serogroup Y, especially ST-23 clonal complex (Y:cc23), represents a larger proportion of invasive meningococcal disease (IMD) in older adults compared to younger individuals. This study explored the meningococcal genetic variation underlying this association.

Methods
Maximum-likelihood phylogenies and the pangenome were analyzed using whole-genome sequence (WGS) data from 200 Y:cc23 isolates in the Neisseria PubMLST database. Genome-wide association studies (GWAS) were performed on WGS data from 250 Y:cc23 isolates from individuals with IMD aged ≥65 years versus &lt; 65 years.

Results
Y:cc23 meningococcal variants did not cluster by age group or disease phenotype in phylogenetic analyses. Pangenome comparisons found no differences in presence or absence of genes in IMD isolates from the different age groups. GWAS identified differences in nucleotide polymorphisms within the transferrin-binding protein B (tbpB) gene in isolates from individuals ≥65 years of age. TbpB structure modelling suggests these may impact binding of human transferrin.

Conclusions
These data suggest differential iron scavenging capacity amongst Y:cc23 meningococci isolated from older compared to younger patients. Iron acquisition is essential for many bacterial pathogens including the meningococcus. These polymorphisms may facilitate colonization, thereby increasing the risk of disease in vulnerable older people with altered nasopharyngeal microbiomes and nutritional status.
Serologic Response to Human Papillomavirus Genotypes Among Unvaccinated Women: Findings From the HITCH Cohort Study
Authors: Morais Samantha , Wissing Michel D , Khosrow-Khavar Farzin , Burchell Ann N , Tellier Pierre-Paul , Coutlée François , Waterboer Tim , El-Zein Mariam , Franco Eduardo L 
Published: November 2022

Abstract

Background
Humoral immune responses may be critical for preventing, controlling, and/or eliminating human papillomavirus (HPV) infection. We analyzed humoral response to natural HPV infection considering phylogenetic relatedness among unvaccinated women.

Methods
We included 399 young women attending university/college in Montreal, Canada who were participants of the HITCH cohort. Participants provided blood samples at baseline and 5 follow-up visits. Antibody response to bacterially expressed L1 and E6 glutathione S-transferase (GST) fusion proteins, and virus-like particles (VLP-L1) of Alphapapillomavirus types were measured using multiplex serology. We assessed correlations and associations between HPV types at baseline using Pearson correlation coefficients (r) and univariable linear regressions.

Results
At baseline, &gt; 40% were seropositive for GST-L1 antibodies of at least 1 HPV type. Strong correlations between GST-L1 were observed for α9 HPV types: 58–52 (r = 0.86), 58–33 (r = 0.75), 33–52 (r = 0.72), and between GST-E6: 52–11 (r = 0.84), 52–18 (r = 0.79), 58–33 (r = 0.78), 35–11 (r = 0.76). HPV16 VLP-L1 moderately explained variability in HPV16 GST-L1 (regression coefficient [b] = 0.38, R2 = 43.1%), and HPV45 GST-L1 in HPV18 GST-L1 (b = 0.68, R2 = 42.8%). GST-E6 antibodies accounted for a low to moderate proportion of variability in HPV16 and HPV18 GST-E6 (R2 = 6.4%–62.2%).

Conclusions
Associations between naturally induced HPV-specific antibodies depend on phylogenetic relatedness.
A Quantitative Assessment of Staphylococcus aureus Community Carriage in Yuma, Arizona
Authors: Russakoff Benjamin , Wood Colin , Lininger Monica R , Barger Steven D , Trotter Robert T , Maltinsky Sara , Mbegbu Mimi , Coyne Briana , Panisello Yagüe David , Kyman Shari , Tucker-Morgan Kara , Ceniceros Kathya , Padilla Cristina , Hurtado Kevin , Menard Ashley , Villa Francisco , Wayment Heidi A , Hepp Crystal , Furstenau Tara , Fofanov Viacheslav , Liu Cindy M , Pearson Talima R 
Published: November 2022

Abstract

Background
Disease control relies on pathogen identification and understanding reservoirs. Staphylococcus aureus infection prevention is based upon decades of research on colonization and infection, but diminishing returns from mitigation efforts suggest significant knowledge gaps. Existing knowledge and mitigation protocols are founded upon culture-based detection, with almost no information about pathogen quantities.

Methods
We used culture and a quantitative polymerase chain reaction assay on samples from 3 body sites to characterize colonization more comprehensively than previous studies by describing both prevalence and pathogen quantity.

Results
We show a much higher overall prevalence (65.9%) than previously documented, with higher quantities and prevalence associated with the nares, non-Hispanic males (86.9%), and correlating with colonization in other body sites. These results suggest that research and clinical practices likely misclassify over half of colonized persons, limiting mitigation measures and their impact.

Conclusions
This work begins the process of rebuilding foundational knowledge of S aureus carriage with more accurate and wholistic approaches.
I had not time to make it shorter: an exploratory analysis of how physicians reduce note length and time in notes
Authors: Apathy Nate C , Hare Allison J , Fendrich Sarah , Cross Dori A 
Published: November 2022

Abstract

Objective
We analyze observed reductions in physician note length and documentation time, 2 contributors to electronic health record (EHR) burden and burnout.

Materials and Methods
We used EHR metadata from January to May, 2021 for 130 079 ambulatory physician Epic users. We identified cohorts of physicians who decreased note length and/or documentation time and analyzed changes in their note composition.

Results
37 857 physicians decreased either note length (n = 15 647), time in notes (n = 15 417), or both (n = 6793). Note length decreases were primarily attributable to reductions in copy/paste text (average relative change of –18.9%) and templated text (–17.2%). Note time decreases were primarily attributable to reductions in manual text (–27.3%) and increases in note content from other care team members (+21.1%).

Discussion
Organizations must consider priorities and tradeoffs in the distinct approaches needed to address different contributors to EHR burden.

Conclusion
Future research should explore scalable burden-reduction initiatives responsive to both note bloat and documentation time.
A probabilistic temporal epistemic logic: Strong completeness
Authors: Ognjanović Zoran , Ilić Stepić Angelina , Perović Aleksandar 
Published: November 2022

AbstractThe paper offers a formalization of reasoning about distributed multi-agent systems. The presented propositional probabilistic temporal epistemic logic $\textbf {PTEL}$ is developed in full detail: syntax, semantics, soundness and strong completeness theorems. As an example, we prove consistency of the blockchain protocol with respect to the given set of axioms expressed in the formal language of the logic. We explain how to extend $\textbf {PTEL}$ to axiomatize the corresponding first-order logic.