bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three alginate lyases provide a new gut
Bacteroides ovatus
isolate with the ability to grow on alginate
Authors: Rønne Mette E. , Tandrup Tobias , Madsen Mikkel , Hunt Cameron J. , Myers Pernille N. , Moll Janne M. , Holck Jesper , Brix Susanne , Strube Mikael L. , Aachmann Finn L. , Wilkens Casper , Svensson Birte 
Published: October 2023

ABSTRACT

Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an
endo
-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new
Bacteroides ovatus
strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The
Bo
PL6 degraded polyG to oligosaccharides of DP 1–3, and
Bo
PL17 released 4,5-unsaturated monouronate from polyM.
Bo
PL38 degraded both alginates, polyM, polyG, and polyMG, in
endo
-mode; hence, it was assumed to deliver oligosaccharide substrates for
Bo
PL6 and
Bo
PL17, corresponding well with synergistic action on alginate.
Bo
PL17 and
Bo
PL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)
6
-barrel + anti-parallel β-sheet and (α/α)
7
-barrel folds, distinctive for these PL families.
Bo
PL17 had a more open active site than the two homologous structures.
Bo
PL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.

IMPORTANCE

Human ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new
Bacteroides ovatus
strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster.
Bo
PL6 and
Bo
PL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids.
Bo
PL38 produces oligosaccharides degraded by
Bo
PL6 and
Bo
PL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.
Tryptophan-based motifs in the LLP3 region of the HIV-1 envelope glycoprotein cytoplasmic tail direct trafficking to the endosomal recycling compartment and mediate particle incorporation
Authors: Lerner Grigoriy , Ding Lingmei , Spearman Paul 
Published: October 2023

ABSTRACT

The HIV-1 envelope glycoprotein complex (Env) is incorporated into developing particles at the plasma membrane (PM). The cytoplasmic tail (CT) of Env is known to play an essential role in particle incorporation, but the exact mechanisms underlying this function of the CT remain uncertain. Upon reaching the PM, trafficking signals in the CT interact with host cell endocytic machinery, directing Env into endosomal compartments within the cell. Prior studies have suggested that Env must travel through the endosomal recycling compartment (ERC) in order for it to return to the PM site of particle assembly. Expression of a truncated form of the ERC-resident trafficking adaptor Rab11 family interacting protein 1C resulted in CT-dependent sequestration of Env in the condensed ERC, preventing recycling of Env to the PM. In this work, the motifs within the CT responsible for ERC localization of Env were systematically mapped. A small deletion encompassing the N-terminal portion of lentiviral lytic peptide 3 (LLP3) eliminated ERC localization. Site-directed mutagenesis identified two tryptophan-based motifs (WE
790–791
and WW
796–797
) within the N-terminus of LLP3 that were essential for ERC localization of Env. Mutant viruses bearing substitutions in these motifs were deficient in Env incorporation, with a corresponding loss of particle infectivity and a significant defect in replication in a spreading infection assay. These results identify two tryptophan-based motifs at the N-terminal portion of LLP3 that mediate ERC localization and Env incorporation, providing additional supporting evidence for the importance of cellular recycling pathways in HIV-1 particle assembly.

IMPORTANCE
The HIV-1 envelope glycoprotein (Env) is an essential component of the virus and has an exceedingly long cytoplasmic tail (CT). Previous studies have suggested that trafficking signals in the CT interact with host factors to regulate the incorporation of Env into particles. One particular area of interest is termed lentiviral lytic peptide 3 (LLP3), as small deletions in this region have been shown to disrupt Env incorporation. In this study, we identify a small region within LLP3 that regulates how Env associates with cellular recycling compartments. Mutants that reduced or eliminated Env from the recycling compartment also reduced Env incorporation into particles. These findings emphasize the importance of two tryptophan motifs in LLP3 for the incorporation of Env into particles and provide additional support for the idea that the CT interacts with host recycling pathways to determine particle incorporation.
A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB
Authors: Bayer Avraham , Child Stephanie J. , Malik Harmit S. , Geballe Adam P. 
Published: October 2023

ABSTRACT
Myxovirus resistance proteins A and B (MxA and MxB) are interferon-induced proteins that exert antiviral activity against a diverse range of RNA and DNA viruses. In primates, MxA has been shown to inhibit myxoviruses, bunyaviruses, and the hepatitis B virus, whereas MxB restricts retroviruses and herpesviruses. As a result of their conflicts with viruses, both genes have been undergoing diversifying selection during primate evolution. Here, we investigate how MxB evolution in primates has affected its restriction of herpesviruses. In contrast to human MxB, we find that most primate orthologs, including the closely related chimpanzee MxB, do not inhibit herpes simplex virus (HSV-1) replication. However, all primate MxB orthologs tested restricted human cytomegalovirus. Through the generation of human and chimpanzee MxB chimeras, we show that a single residue, M83, is the key determinant of restriction of HSV-1 replication. Humans are the only primate species known to encode a methionine at this position, whereas most other primate species encode a lysine. Residue 83 is also the most polymorphic residue in MxB in human populations, with M83 being the most common variant. However, ~2.5% of human MxB alleles encode a threonine at this position, which does not restrict HSV-1. Thus, a single amino acid variant in MxB, which has recently risen to high frequency in humans, has endowed human MxB with HSV-1 antiviral activity.

IMPORTANCE
Herpesviruses present a major global disease burden. Understanding the host cell mechanisms that block viral infections, as well as how viruses can evolve to counteract these host defenses, is critically important for understanding viral disease pathogenesis. This study reveals that the major human variant of the antiviral protein myxovirus resistance protein B (MxB) inhibits the human pathogen herpes simplex virus (HSV-1), whereas a minor human variant and orthologous MxB genes from even closely related primates do not. Thus, in contrast to the many antagonistic virus-host interactions in which the virus is successful in thwarting the host’s defense systems, here the human gene appears to be at least temporarily winning at this interface of the primate-herpesvirus evolutionary arms race. Our findings further show that a polymorphism at amino acid 83 in a small fraction of the human population is sufficient to abrogate MxB’s ability to inhibit HSV-1, which could have important implications for human susceptibility to HSV-1 pathogenesis.
The T1-weighted/T2-weighted ratio as a biomarker of anti-NMDA receptor encephalitis
Authors: Hartung Tim Julian , Cooper Graham , Jünger Valentin , Komnenić Darko , Ryan Lara , Heine Josephine , Chien Claudia , Paul Friedemann , Prüss Harald , Finke Carsten 
Published: October 2023

BackgroundAnti-N-methyl-D-aspartate receptor (NMDAR) encephalitis rarely causes visible lesions in conventional MRI, yet advanced imaging detects extensive white matter damage. To improve prognostic capabilities, we evaluate the T1-weighted/T2-weighted (T1w/T2w) ratio, a measure of white matter integrity computable from clinical MRI sequences, in NMDAR encephalitis and examine its associations with cognitive impairment.MethodsT1-weighted and T2-weighted MRI were acquired cross-sectionally at 3 Tesla in 53 patients with NMDAR encephalitis (81% women, mean age 29 years) and 53 matched healthy controls. Quantitative and voxel-wise group differences in T1w/T2w ratios and associations with clinical and neuropsychological outcomes were assessed. P-values were false discovery rate (FDR) adjusted where multiple tests were conducted.ResultsPatients with NMDAR encephalitis had significantly lower T1w/T2w ratios across normal appearing white matter (p=0.009, Hedges’ g=−0.51), which was associated with worse verbal episodic memory performance (r=0.39, p=0.005, p(FDR)=0.026). White matter integrity loss was observed in the corticospinal tract, superior longitudinal fascicle, optic radiation and callosal body with medium to large effects (Cohen’s d=[0.42–1.17]). In addition, patients showed decreased T1w/T2w ratios in the hippocampus (p=0.002, p(FDR)=0.005, Hedges’ g=−0.62), amygdala (p=0.002, p(FDR)=0.005, Hedges’ g=−0.63) and thalamus (p=0.010, p(FDR)=0.019, Hedges’ g=−0.51).ConclusionsThe T1w/T2w ratio detects microstructural changes in grey and white matter of patients with NMDAR encephalitis that correlate with cognitive performance. Computable from conventional clinical MRI sequences, this measure shows promise in bridging the clinico-radiological dissociation in NMDAR encephalitis and could serve as an imaging outcome measure in clinical trials.
Interactions of $$\omega $$ mesons in nuclear matter and with nuclei
Authors: Lenske Horst 
Published: October 2023

AbstractIn-medium interactions of $$\omega $$
ω
-mesons in infinite nuclear matter and finite nuclei are investigated in a microscopic approach, focused on the particle-hole excitations of the medium involving nucleonic $$NN^{-1}$$

N

N

-
1

and $$N^*N^{-1}$$

N
∗

N

-
1

modes, where $$N^*$$

N
∗

denotes a nucleon resonance. The nuclear polarization tensors include relativistic mean-field dynamics by self–consistent scalar and vector fields. The resulting self-energies are transmitted to finite nuclei in local density approximation. Real and imaginary parts of longitudinal and transversal self-energies are discussed. The relation of the present approach to meson cloud models is addressed and an ambiguity is pointed out. Applications to recent data on the in–medium width of $$\omega $$
ω
mesons scattered on a Niobium target serve to determine unknown $$N^*N\omega $$

N
∗

N
ω

in-medium coupling constants. The data are well described by $$N^*N^{-1}$$

N
∗

N

-
1

self–energies containing S–wave and P-wave $$N^*$$

N
∗

resonances. Exploratory investigations, however, show that the spectroscopic composition of self-energies depends crucially on the near-threshold properties of the width which at present is known only within large error bars. The calculations predict the prevalence of transversal self–energies, implying that vector current conservation is still maintained in the nuclear medium by slightly more than 90%. Schrödinger-equivalent potentials are derived and scattering lengths and effective range parameters are extracted for the longitudinal and transversal channel. Longitudinal and transversal spectral distributions are discussed and the dependencies on momentum and nuclear density are investigated. Schrödinger-type $$\omega +{}^{93}$$

ω
+

93

Nb optical potentials are constructed. Low-energy parameters are determined, are used to study the pole structure of the S-matrix at threshold. The effective range expansion of the omega-nucleus K-matrix led to a $$\omega +{}^{93}$$

ω
+

93

Nb bound states with binding energy $$Re(\varepsilon _B)=-448$$

R
e
(

ε
B

)
=
-
448

keV but of width $$\Gamma _B=4445$$

Γ
B

=
4445

keV.
Bayesian analysis of systematic errors in the determination of the constant of gravitation
Authors: Rinaldi Stefano , Middleton Hannah , Del Pozzo Walter , Gair Jonathan 
Published: October 2023

AbstractMeasurements of the gravitational constant G are notoriously difficult. Individual state-of-the-art experiments have managed to determine the value of G with high precision: although, when considered collectively, the range in the measured values of G far exceeds individual uncertainties, suggesting the presence of unaccounted for systematic effects. Here, we propose a Bayesian framework to account for the presence of systematic errors in the various measurement of G while proposing a consensus value, following two paths: a parametric approach, based on the maximum entropy principle, and a non-parametric one, the latter being a very flexible approach not committed to any specific functional form. With both our methods, we find that the uncertainty on this fundamental constant, once systematics are included, is significantly larger than what quoted in CODATA 2018. Moreover, the morphology of the non-parametric distribution hints towards the presence of several sources of unaccounted for systematics. In light of this, we recommend a consensus value for the gravitational constant $$G = 6.6740^{+0.0015}_{-0.0015} \times 10^{-11}\ \textrm{m}^3\ \textrm{kg}^{-1}\ \textrm{s}^{-2}$$

G
=
6
.

6740

-
0.0015

+
0.0015

×

10

-
11

m
3

kg

-
1

s

-
2

.
Physiotherapy students’ rating on lecturers’ and supervisors’ clinical education attributes
Authors: Safo-Kantanka Nana Kwame , Quartey Jonathan , Kwakye Samuel Koranteng 
Published: October 2023

Background: Clinical education is considered a vital aspect of education of health science students. Attributes of clinical educators play a crucial role in determining the outcome of clinical teaching and learning. A good clinical educator ensures that students get maximum benefits of the clinical learning experience. Objective: To determine the ratings of physiotherapy students on clinical education attributes of lecturers and clinical supervisors. Methods: The study was conducted with 81 clinical physiotherapy students from two universities in Ghana. Two copies of McGill clinical teachers’ evaluation (CTE) tool were used to obtain students’ ratings on their clinical supervisors’ and lecturers’ clinical education attributes. Independent t-test was used to compare the means of students’ level of study and ratings regarding the clinical education attributes of clinical supervisors and lecturers. Results: Students had a high rating on their clinical education attributes of supervisors and lecturers with a mean score of ([Formula: see text]) and ([Formula: see text]), respectively. Rating on clinical education attributes of supervisors ([Formula: see text]) and lecturers ([Formula: see text]) did not differ significantly between the different levels of study. Conclusion: Clinical physiotherapy students rated the clinical education attributes of their lecturers and supervisors high.
Dysfunctional APPL1-Mediated Epigenetic Regulation in Diabetic Vascular Injury
Authors: Du Yunhui , Duan Yanru , Zhao Jianli , Liu Caihong , Zhang Zhen , Zhang John , Meng Zhijun , Wang Xiaoliang , Lau Wayne Bond , Xie Dina , Lopez Bernard L. , Christopher Theodore A. , Gao Erhe , Koch Walter J. , Liu Huirong , Liu Demin , Ma Xin-Liang , Gu Guoqiang , Wang Yajing 
Published: October 2023

BACKGROUND:
APN (adiponectin) and APPL1 (adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1) are potent vasculoprotective molecules, and their deficiency (eg, hypoadiponectinemia) contributes to diabetic vascular complications. However, the molecular mechanisms that govern their vasculoprotective genes as well as their alteration by diabetes remain unknown.

METHODS:
Diabetic medium-cultured rat aortic endothelial cells, mouse aortic endothelial cells from high-fat-diet animals, and diabetic human aortic endothelial cells were used for molecular/cellular investigations. The in vivo concept-prove demonstration was conducted using diabetic vascular injury and diabetic hindlimb ischemia models.

RESULTS:
In vivo animal experiments showed that APN replenishment caused APPL1 nuclear translocation, resulting in an interaction with HDAC (histone deacetylase) 2, which inhibited HDAC2 activity and increased H3Kac27 levels. Based on transcriptionome pathway-specific real-time polymerase chain reaction profiling and bioinformatics analysis, Angpt1 (angiopoietin 1), Ocln (occludin), and Cav1 (caveolin 1) were found to be the top 3 vasculoprotective genes suppressed by diabetes and rescued by APN in an APPL1-dependent manner. APN reverses diabetes-induced inhibition of Cav1 interaction with APPL1. APN-induced Cav1 expression was not affected by Angpt1 or Ocln deficiency, whereas APN-induced APPL1 nuclear translocation or upregulation of Angpt1/Ocln expression was abolished in the absence of Cav1 both in vivo and in vitro, suggesting Cav1 is upstream molecule of Angpt1/Ocln in response to APN administration. Chromatin immunoprecipitation–qPCR (quantitative polymerase chain reaction) demonstrated that APN caused significant enrichment of H3K27ac in Angpt1 and Ocln promoter region, an effect blocked by APPL1/Cav1 knockdown or HDAC2 overexpression. The protective effects of APN on the vascular system were attenuated by overexpression of HDAC2 and abolished by knocking out APPL1 or Cav1. The double knockdown of ANGPT1/OCLN blunted APN vascular protection both in vitro and in vivo. Furthermore, in diabetic human endothelial cells, HDAC2 activity is increased, H3 acetylation is decreased, and ANGPT1/OCLN expression is reduced, suggesting that the findings have important translational implications.

CONCLUSIONS:
Hypoadiponectinemia and dysregulation of APPL1-mediated epigenetic regulation are novel mechanisms leading to diabetes-induced suppression of vasculoprotective gene expression. Diabetes-induced pathological vascular remodeling may be prevented by interventions promoting APPL1 nuclear translocation and inhibiting HDAC2.
Expanding Pragmatism with Symbolic Interactionism: Recounting the Story of Two Frameworks
Authors: Koskinen Ilpo , Forlizzi Jodi , Battarbee Katja 
Published: October 2023

Abstract
This article describes the story of pragmatism and its transformation into symbolic interactionism at Carnegie Mellon University and Aalto University. In both universities, design researchers were interested in user experience in interactive systems. John Dewey's pragmatism taught them to study how experience sometimes transforms into an experience and occasionally into stories. Herbert Blumer's interactionism had its roots in Chicago School sociology, and it developed in association with pragmatism. His interactionism gave these researchers tools to study Dewey's concepts empirically. We show in the article how this theoretical connection came about after 2000 and how it has shaped research programs in these two communities since then. We also discuss the relevance of pragmatism and interactionism in our current technological landscape, dominated by social media and artificial intelligence.
The Value of Experience-Centered Design to Responsible Software Design and Engineering
Authors: McCarthy John , Wright Peter 
Published: October 2023

Abstract
In this conceptual article, we review experience-centered approaches to the design of personal digital interactive technologies, with a view to exploring how these approaches might be of value in understanding the experience-in-use and the responsible design of today's highly networked, data-rich, and ubiquitous software technologies. Experience-centered design research leans heavily on pragmatist philosophy for its conceptual underpinnings, particularly John Dewey's accounts of aesthetic experience and of inquiry. After reviewing this body of work, we argue that these foundations could be usefully extended to also include Dewey's approach to ethics as an empirical, situated act of moral imagination. In addition, we look to other researchers for perspectives that complement and extend Deweyan experiential pragmatics. In particular, we look to the ways in which Susan Leigh Star's account of socio-technical infrastructures and dialogical approaches to human relations together can provide important insights into the experience-in-use of today's digital infrastructure and can critically highlight issues of boundaries and privacy. We also offer pragmatic and methodological concepts that may be of value to the field of responsible software design and engineering.
Art-Kut! The Counter-Cultural and Feminist Spirituality of Shamanism in Postwar South Korean Art
Authors: Choi Sooran 
Published: October 2023

Abstract
On 17 January 1981, during a cold Winter Day at the height of an authoritarian military regime, a group of South Korean artists named “Baggat Misul [Outdoor Art]” gathered around a riverbank outside Seoul to interact with nature and called it “jayeon misul [nature art].” A young woman artist Yong-sin Suh performed an act the group called “a lark,” during which Suh alternated with two male artists in reading aloud sections of newspaper articles. These unhinged, free-spirited acts were inspired by the Korean folk theater tradition of pansori (traditional Korean musical opera), and kut (traditional Korean shamanistic exorcism). Korean shamanism by way of the mudang kut rituals has historically been a Korean indigenous belief intertwined with Buddhism and Taoism and stood as a counterforce to the mainstream nationalist neo-Confucian and imperial Christian conservative legacy that oppressed women and the nonconforming gender-neutral community in South Korea. The paper analyzes the Korean shamanistic elements that were utilized in performative, conceptual, and nature art practices by South Korean artists in the post-WWII period to the present, within the framework of the intersection of Korean feminism, art activism, and shamanistic spirituality.