bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycoproteomics of NOTCH1 EGF repeat fragments overexpressed with different glycosyltransferases in HEK293T cells reveals insights into O-GlcNAcylation of NOTCH1
Authors: Tsukamoto Yohei , Ogawa Mitsutaka , Yogi Kentarou , Tashima Yuko , Takeuchi Hideyuki , Okajima Tetsuya 
Published: March 2022

Abstract
O-GlcNAc modification of Notch receptors regulates Notch ligand interactions in a manner distinct from other forms of O-glycans on epidermal growth factor (EGF)-like repeats of Notch receptors. Although many proteins, besides Notch receptors, are expected to be O-GlcNAcylated by EGF domain-specific O-GlcNAc transferase (EOGT), only a small number of proteins have been reported to be modified in vivo, and elongated O-GlcNAc glycans have not been extensively explored. To extend our view of the specificity and variety of the glycan modification, we conducted a comprehensive analysis of O-GlcNAc glycans on NOTCH1 in mammals. Mass spectrometric analysis of NOTCH1 fragments expressed in HEK293T cells revealed that several EGF domains with putative O-GlcNAcylation sites were hardly modified with O-GlcNAc. Although amino acid residues before the modification site are preferentially occupied with aromatic residues, Phe and Tyr are preferable to Trp for the apparent modification with O-GlcNAc. Furthermore, a minor form of fucosylated O-GlcNAc glycans was detected in a subset of EGF domains. Fucosylation of O-GlcNAc glycans was enhanced by FUT1, FUT2, or FUT9 expression. The FUT9-dependent Lewis X epitope was confirmed by immunoblotting using an anti-Lewis X antibody. As expected from the similarity in the extended structures between O-Fuc and O-GlcNAc glycans, the Lexis X antigen was detected on NOTCH1 fragments co-expressed with L-Fringe, which mediates elongation of O-Fuc glycans. Our results refined the putative consensus sequence for the EOGT-dependent O-GlcNAc modification in mammals and revealed the structural diversity of functional Notch O-glycans.
Foregone healthcare during the COVID-19 pandemic: early survey estimates from 39 low- and middle-income countries
Authors: Kakietek Jakub Jan , Eberwein Julia Dayton , Stacey Nicholas , Newhouse David , Yoshida Nobuo 
Published: March 2022

Abstract
In addition to the direct health effects of the Coronavirus disease (COVID-19) pandemic, the pandemic has increased the risks of foregone non-COVID-19 healthcare. Likely, these risks are greatest in low- and middle-income countries (LMICs), where health systems are less resilient and economies more fragile. However, there are no published studies on the prevalence of foregone healthcare in LMICs during the pandemic. We used pooled data from phone surveys conducted between April and August 2020, covering 73 638 households in 39 LMICs. We estimated the prevalence of foregone care and the relative importance of various reported reasons for foregoing care, disaggregated by country income group and region. In the sample, 18.8% (95% CI 17.8–19.8%) of households reported not being able to access healthcare when needed. Financial barriers were the most-commonly self-reported reason for foregoing care, cited by 31.4% (28.6–34.3%) of households. More households in wealthier countries reported foregoing care for reasons related to COVID-19 [27.2% (22.5–31.8%) in upper-middle-income countries compared to 8.0% (4.7–11.3%) in low-income countries]; more households in poorer countries reported foregoing care due to financial reasons [65.6% (59.9–71.2%)] compared to 17.4% (13.1–21.6%) in upper-middle-income countries. A substantial proportion of households in LMICs had to forgo healthcare in the early months of the pandemic. While in richer countries this was largely due to fear of contracting COVID-19 or lockdowns, in poorer countries foregone care was due to financial constraints.
The Scaling of Olfaction: Moths have Relatively More Olfactory Surface Area than Mammals
Authors: Mohebbi Nina , Schulz Andrew , Spencer Thomas L , Pos Kelsie , Mandel Andrew , Casas Jérôme , Hu David L 
Published: March 2022

SynopsisBody size affects nearly every aspect of locomotion and sensing, but little is known of its influence on olfaction. One reason for this missing link is that olfaction differs fundamentally from vision and hearing in that molecules are advected by fluid before depositing on olfactory sensors. This critical role of fluid flow in olfaction leads to complexities and trade-offs. For example, a greater density of hairs and sensory neurons may lead to greater collection, but can also lead to reduced flow through hairs and additional weight and drag due to a larger olfactory organ. In this study, we report the surface area and sensory neuron density in olfactory organs of 95 species of moths and mammals. We find that approximately 12–14% of an olfactory system’s surface area is devoted to chemosensors. Furthermore, total olfactory surface area and olfactory sensing surface area scale with body mass to the 0.49 and 0.38 powers, respectively, indicating that moths have a higher proportion of olfactory surface area than mammals. The density of olfactory neurons appears to be near the limit, at 10,000 to 100,000 neurons per square mm across both insects and mammals. This study demonstrates the need for future work detailing how the scaling of olfaction and other senses vary across taxa.
High-risk landscapes of Japanese encephalitis virus outbreaks in India converge on wetlands, rain-fed agriculture, wild Ardeidae, and domestic pigs and chickens
Authors: Walsh Michael G , Pattanaik Amrita , Vyas Navya , Saxena Deepak , Webb Cameron , Sawleshwarkar Shailendra , Mukhopadhyay Chiranjay 
Published: March 2022

AbstractBackgroundJapanese encephalitis virus (JEV) is a zoonotic mosquito-borne virus that causes a significant burden of disease across Asia, particularly in India, with high mortality in children. JEV circulates in wild ardeid birds and domestic pig reservoirs, both of which generate sufficiently high viraemias to infect vector mosquitoes, which can then subsequently infect humans. The landscapes of these hosts, particularly in the context of anthropogenic ecotones and resulting wildlife–livestock interfaces, are poorly understood and thus significant knowledge gaps in the epidemiology of JEV persist. This study sought to investigate the landscape epidemiology of JEV outbreaks in India over the period 2010–2020 to determine the influence of shared wetland and rain-fed agricultural landscapes and animal hosts on outbreak risk.MethodsUsing surveillance data from India’s National Centre for Disease Control Integrated Disease Surveillance Programme, JEV outbreaks were modelled as an inhomogeneous Poisson point process and externally validated against independently sourced data.ResultsOutbreak risk was strongly associated with the habitat suitability of ardeid birds, both pig and chicken density, and the shared landscapes between fragmented rain-fed agriculture and both river and freshwater marsh wetlands.ConclusionThe results from this work provide the most complete understanding of the landscape epidemiology of JEV in India to date and suggest important One Health priorities for control and prevention across fragmented terrain comprising a wildlife–livestock interface that favours spillover to humans.
Estimation in tensor Ising models
Authors: Mukherjee Somabha , Son Jaesung , Bhattacharya Bhaswar B 
Published: March 2022

AbstractThe $p$-tensor Ising model is a one-parameter discrete exponential family for modeling dependent binary data, where the sufficient statistic is a multi-linear form of degree $p \geqslant 2$. This is a natural generalization of the matrix Ising model that provides a convenient mathematical framework for capturing, not just pairwise, but higher-order dependencies in complex relational data. In this paper, we consider the problem of estimating the natural parameter of the $p$-tensor Ising model given a single sample from the distribution on $N$ nodes. Our estimate is based on the maximum pseudolikelihood (MPL) method, which provides a computationally efficient algorithm for estimating the parameter that avoids computing the intractable partition function. We derive general conditions under which the MPL estimate is $\sqrt N$-consistent, that is, it converges to the true parameter at rate $1/\sqrt N$. Our conditions are robust enough to handle a variety of commonly used tensor Ising models, including spin glass models with random interactions and models where the rate of estimation undergoes a phase transition. In particular, this includes results on $\sqrt N$-consistency of the MPL estimate in the well-known $p$-spin Sherrington–Kirkpatrick model, spin systems on general $p$-uniform hypergraphs and Ising models on the hypergraph stochastic block model (HSBM). In fact, for the HSBM we pin down the exact location of the phase transition threshold, which is determined by the positivity of a certain mean-field variational problem, such that above this threshold the MPL estimate is $\sqrt N$-consistent, whereas below the threshold no estimator is consistent. Finally, we derive the precise fluctuations of the MPL estimate in the special case of the $p$-tensor Curie–Weiss model, which is the Ising model on the complete $p$-uniform hypergraph. An interesting consequence of our results is that the MPL estimate in the Curie–Weiss model saturates the Cramer–Rao lower bound at all points above the estimation threshold, that is, the MPL estimate incurs no loss in asymptotic statistical efficiency in the estimability regime, even though it is obtained by minimizing only an approximation of the true likelihood function for computational tractability.
The Singular Support of the Ising Model
Authors: Andrews George E , van Ekeren Jethro , Heluani Reimundo 
Published: March 2022

AbstractWe prove a new quasiparticle sum expression for the character of the Ising model vertex algebra, related to the Jackson–Slater $q$-series identity of Rogers–Ramanujan type and to Nahm sums for the matrix $\left (\begin {smallmatrix}8&3\\3&2 \end {smallmatrix}\right ) $. We find, as consequences, an explicit monomial basis for the Ising model and a description of its singular support. We find that the ideal sheaf of the latter, defining it as a subscheme of the arc space of its associated scheme, is finitely generated as a differential ideal. We prove three new $q$-series identities of the Rogers–Ramanujan–Slater type associated with the three irreducible modules of the Virasoro Lie algebra of central charge $1/2$. We give a combinatorial interpretation to the identity associated with the vacuum module.
Do Invasive and Naturalized Aphid Pest Populations Respond Differently to Climatic and Landscape Factors?
Authors: Adhikari Subodh , Seamon Erich , Wu Ying , Sadeghi Seyed E , Eigenbrode Sanford D 
Published: March 2022

AbstractOngoing environmental change affects pest populations, migration, and propensity to damage crops, but the responses to climatic drivers could vary among newly invasive and already naturalized closely related species. To compare these responses of a newly invasive aphid, Metopolophium festucae cerealium (Stroyan), with its naturalized congeneric [M. dirhodum (Walker)] and confamilial [Sitobian avenae (Fab.)], we conducted annual surveys over four years across a total of 141 winter wheat fields in the inland Pacific Northwest, USA. Key climatic factors (cumulative precipitation for each calendar year to sampling date, cumulative degree days), landscape factors (proportion of wheat and landscape diversity within the sample year), and Julian day were calculated for each sampling event, and aphid abundance by species, total aphid abundance, overall species richness, diversity, and aphid community composition were assessed. Metopolophium f. cerealium, the second most abundant species, was positively associated with precipitation, suggesting a projected increase in precipitation in winter and spring in the region could favor its establishment and expansion. Although M. dirhodum and S. avenae linearly (positively) associated with temperature, M. f. cerealium did not, indicating that continued warming may be detrimental to the species. Despite the weak impacts of landscape factors, our study indicated that more wheat generally facilitates cereal aphid abundance. Metopolophium f. cerealium abundance tended to be higher in earlier (May/early June vs. late June/July) samples when wheat crop could be vulnerable to aphid feeding. This study suggests that the new presence of M. f. cerealium has important pest management implications in the region.
Measuring PROMIS® Emotional Distress in Early Childhood
Authors: Sherlock Phillip , Blackwell Courtney K , Kallen Michael A , Lai Jin-Shei , Cella David , Krogh-Jespersen Sheila , Luby Joan L , Buss Kristin A , Burns James , Wakschlag Lauren S 
Published: March 2022

Abstract

Objective
Create and validate developmentally sensitive parent-report measures of emotional distress for children ages 1–5 years that conceptually align with the Patient-Reported Outcome Measurement Information System (PROMIS®) pediatric measures.

Methods
Initial items were generated based on expert and parent input regarding core components of emotional distress in early childhood and review of theoretical and empirical work in this domain. Items were psychometrically tested using data from two waves of panel surveys. Item response theory (IRT) was applied to develop item calibration parameters (Wave 1), and scores were centered on a general U.S. population sample (Wave 2). Final PROMIS early childhood (EC) instruments were compared with existing measures of related constructs to establish construct validity.

Results
Experts and parents confirmed the content validity of the existing PROMIS Pediatric emotional distress domains (i.e., anger, anxiety, and depressive symptoms) as developmentally salient for young children. Existing items were adapted and expanded for early childhood by employing best practices from developmental measurement science. Item banks as well as 4- and 8-item short forms, free from differential item functioning across sex and age, were constructed for the three domains based on rigorous IRT analyses. Correlations with subscales from previously validated measures provided further evidence of construct validity.

Conclusions
The PROMIS EC Anger/Irritability, Anxiety, and Depressive Symptoms measures demonstrated good reliability and initial evidence of validity for use in early childhood. This is an important contribution to advancing brief, efficient measurement of emotional distress in young children, closing a developmental gap in PROMIS pediatric emotional distress assessment.
A knotty problem: phytobezoar and small bowel occlusion as a complication of a gastro-jejunal catheter for continuous Duodopa infusion: a case report
Authors: Ivanov Todor , Perlot Ingrid , Stoca Laura Romero , Deleuze Catherine , Rasmont Celine , Lemaitre Jean 
Published: March 2022

Abstract
We report a case of small bowel occlusion due to the formation of a bezoar around a knot at the distal end a gastro-jejunal catheter used for continuous levodopa/carbidopa intestinal gel (LCIG) in a patient with advanced Parkinson’s disease. The patient presented with a history of abdominal pain and vomiting starting 24 h before admission and frequent failure of his LCIG device for the past week. Small bowel occlusion along with a knot formation on the distal catheter was confirmed by contrast enhanced CT scan. After failure of endoscopic extraction, the patient was taken to theater. The presence of a knot and a bezoar was confirmed and extraction proceeded via transverse enterotomy without the need for bowel resection. Despite inhalation pneumonia and prolonged ileus, the patient recovered fully. LCIG treatment was reinstated a month later through new gastro-jejunal catheter. This case highlights a severe and surprising complication of LCIG treatment.
Encoding, transmission, decoding, and specificity of calcium signals in plants
Authors: Allan Claudia , Morris Richard J , Meisrimler Claudia-Nicole 
Published: March 2022

Abstract
Calcium acts as a signal and transmits information in all eukaryotes. Encoding machinery consisting of calcium channels, stores, buffers, and pumps can generate a variety of calcium transients in response to external stimuli, thus shaping the calcium signature. Mechanisms for the transmission of calcium signals have been described, and a large repertoire of calcium binding proteins exist that can decode calcium signatures into specific responses. Whilst straightforward as a concept, mysteries remain as to exactly how such information processing is biochemically implemented. Novel developments in imaging technology and genetically encoded sensors (such as calcium indicators), in particular for multi-signal detection, are delivering exciting new insights into intra- and intercellular calcium signaling. Here, we review recent advances in characterizing the encoding, transmission, and decoding mechanisms, with a focus on long-distance calcium signaling. We present technological advances and computational frameworks for studying the specificity of calcium signaling, highlight current gaps in our understanding and propose techniques and approaches for unravelling the underlying mechanisms.
The evolution of the corona in MAXI J1535−571 through type-C quasi-periodic oscillations with Insight-HXMT
Authors: Zhang Yuexin , Méndez Mariano , García Federico , Zhang Shuang-Nan , Karpouzas Konstantinos , Altamirano Diego , Belloni Tomaso M , Qu Jinlu , Zhang Shu , Tao Lian , Zhang Liang , Huang Yue , Kong Lingda , Ma Ruican , Yu Wei , Rawat Divya , Bellavita Candela 
Published: March 2022

ABSTRACT
Type-C quasi-periodic oscillations (QPOs) in black hole X-ray transients can appear when the source is in the low-hard and hard-intermediate states. The spectral-timing evolution of the type-C QPO in MAXI J1535−571 has been recently studied with Insight-HXMT. Here, we fit simultaneously the time-averaged energy spectrum, using a relativistic reflection model, and the fractional rms and phase-lag spectra of the type-C QPOs, using a recently developed time-dependent Comptonization model when the source was in the intermediate state. For the first time, we show that the time-dependent Comptonization model can successfully explain the X-ray data up to 100 keV. We find that in the hard-intermediate state the frequency of the type-C QPO decreases from 2.6 to 2.1 Hz, then increases to 3.3 Hz, and finally increases to ∼9 Hz. Simultaneously with this, the evolution of corona size and the feedback fraction (the fraction of photons up-scattered in the corona that return to the disc) indicates the change of the morphology of the corona. Compared with contemporaneous radio observations, this evolution suggests a possible connection between the corona and the jet when the system is in the hard-intermediate state and about to transit into the soft-intermediate state.
Rec8 Cohesin-mediated Axis-loop chromatin architecture is required for meiotic recombination
Authors: Sakuno Takeshi , Tashiro Sanki , Tanizawa Hideki , Iwasaki Osamu , Ding Da-Qiao , Haraguchi Tokuko , Noma Ken-ichi , Hiraoka Yasushi 
Published: March 2022

Abstract
During meiotic prophase, cohesin-dependent axial structures are formed in the synaptonemal complex (SC). However, the functional correlation between these structures and cohesion remains elusive. Here, we examined the formation of cohesin-dependent axial structures in the fission yeast Schizosaccharomyces pombe. This organism forms atypical SCs composed of linear elements (LinEs) resembling the lateral elements of SC but lacking the transverse filaments. Hi-C analysis using a highly synchronous population of meiotic S. pombe cells revealed that the axis-loop chromatin structure formed in meiotic prophase was dependent on the Rec8 cohesin complex. In contrast, the Rec8-mediated formation of the axis-loop structure occurred in cells lacking components of LinEs. To dissect the functions of Rec8, we identified a rec8-F204S mutant that lost the ability to assemble the axis-loop structure without losing cohesion of sister chromatids. This mutant showed defects in the formation of the axis-loop structure and LinE assembly and thus exhibited reduced meiotic recombination. Collectively, our results demonstrate that the Rec8-dependent axis-loop structure provides a structural platform essential for LinE assembly, facilitating meiotic recombination of homologous chromosomes, independently of its role in sister chromatid cohesion.
Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information
Authors: Heather James M , Spindler Matthew J , Alonso Marta Herrero , Shui Yifang Ivana , Millar David G , Johnson David S , Cobbold Mark , Hata Aaron N 
Published: March 2022

AbstractThe study and manipulation of T cell receptors (TCRs) is central to multiple fields across basic and translational immunology research. Produced by V(D)J recombination, TCRs are often only recorded in the literature and data repositories as a combination of their V and J gene symbols, plus their hypervariable CDR3 amino acid sequence. However, numerous applications require full-length coding nucleotide sequences. Here we present Stitchr, a software tool developed to specifically address this limitation. Given minimal V/J/CDR3 information, Stitchr produces complete coding sequences representing a fully spliced TCR cDNA. Due to its modular design, Stitchr can be used for TCR engineering using either published germline or novel/modified variable and constant region sequences. Sequences produced by Stitchr were validated by synthesizing and transducing TCR sequences into Jurkat cells, recapitulating the expected antigen specificity of the parental TCR. Using a companion script, Thimble, we demonstrate that Stitchr can process a million TCRs in under ten minutes using a standard desktop personal computer. By systematizing the production and modification of TCR sequences, we propose that Stitchr will increase the speed, repeatability, and reproducibility of TCR research. Stitchr is available on GitHub.