bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Color Attributes on Trap Capture Rates ofChrysobothris femorata(Coleoptera: Buprestidae) and Related Species
Authors: Perkovich Cynthia L , Addesso Karla M , Basham Joshua P , Fare Donna C , Youssef Nadeer N , Oliver Jason B
Published: May 2022

Chrysobothris spp. (Coleoptera: Buprestidae) and other closely related buprestids are common pests of fruit, shade, and nut trees in the United States. Many Chrysobothris spp., including Chrysobothris femorata, are polyphagous herbivores. Their wide host range leads to the destruction of numerous tree species in nurseries and orchards. Although problems caused by Chrysobothris are well known, there are no reliable monitoring methods to estimate local populations before substantial damage occurs. Other buprestid populations have been effectively estimated using colored sticky traps to capture beetles. However, the attraction of Chrysobothris to specific color attributes has not been directly assessed. A multi-color trapping system was utilized to determine color attraction of Chrysobothris spp. Specific color attributes (lightness [L*], red to green [a*], blue to yellow [b*], chroma [C*], hue [h*], and peak reflectance [PR]) were then evaluated to determine beetle responses. In initial experiments with mostly primary colors, Chrysobothris were most attracted to traps with red coloration. Thus, additional experiments were performed using a range of trap colors with red reflectance values. Among these red reflectance colors, it was determined that the violet range of the electromagnetic spectrum had greater attractance to Chrysobothris. Additionally, Chrysobothris attraction correlated with hue and b*, suggesting a preference for traps with hues between red to blue. However, males and females of some Chrysobothris species showed differentiated responses. These findings provide information on visual stimulants that can be used in Chrysobothris trapping and management. Furthermore, this information can be used in conjunction with ecological theory to understand host-location methods of Chrysobothris.
Accounting for the Value of Unpaid Domestic Work: A Cross-National Study of Variation across Household Types
Authors: Ragnarsdóttir Berglind Hólm , Kostecki Sarah , Gornick Janet
Published: May 2022

This article estimates the value of extended earnings—market earnings plus the imputed value of unpaid work—and assesses how this alternative measure affects the level and distribution of economic wellbeing within households of differing compositions. Prior research finds that excluding the value of unpaid work distorts conclusions about women’s contributions to household income and inequality more generally. Variation across household types has been understudied. The authors use data from the Harmonized European and American Time Use Surveys, combined with income data from the Luxembourg Income Study Database, to assess outcomes in six European countries and the United States. The study compares market to extended earnings to assess inequality within and across household types: single adults with and without children, and cohabiting adults with and without children. Key findings include: (i) women's time in unpaid work exceeds men's in all study countries; (ii) shifting from market earnings to extended earnings narrows gender disparities in all countries; and (iii) moving to extended earnings reduces inequality among both women and men, but more so among women. On all outcomes, we find that household composition shapes women's outcomes more than men's, and, overall, parenting status plays a larger role than partnership status.
Familiarity Deficits for Words and Objects in Amnestic Mild Cognitive Impairment in a Context Minimizing the Role of Recollection
Authors: Sanger Brahm D , Anderson Nicole D
Published: May 2022

Objectives

Amnestic mild cognitive impairment (aMCI) is associated with cortical thinning in perirhinal and entorhinal cortices, key regions of the brain supporting familiarity. Individuals with aMCI demonstrate familiarity deficits in their behavior, often repeating questions in the same conversation. While familiarity deficits in healthy aging are minimal, past studies measuring familiarity in aMCI have mixed results, perhaps due to the influence of recollection. We therefore used a paradigm that minimized the influence of recollection, and hypothesized that familiarity would be impaired in aMCI relative to age-matched controls, but not in healthy older adults relative to younger adults. We also hypothesized that familiarity deficits in aMCI would be greater for objects than words because the perirhinal cortex plays a significant role in visual discrimination.

Methods

A sample of 36 younger adults, 38 cognitively intact older adults, and 30 older adults with aMCI made absolute frequency judgments for words and objects seen a variable number of times in an incidental encoding task. Estimates of familiarity were derived from correlating participants’ frequency judgments with the actual frequency of presentation.

Results

Familiarity was largely spared in healthy aging, with minor deficits in familiarity for words. Familiarity deficits were evident in aMCI comparably for words and objects.

Discussion

The present research underscores the need to study familiarity in contexts minimizing recollection, particularly when comparing groups with different levels of recollection, and adds to our understanding of the phenomenology of aMCI. Familiarity deficits may provide an early biomarker of dementia risk.
Dirac Series of GL(n, ℝ)
Authors: Dong Chao-Ping , Wong Kayue Daniel
Published: May 2022

The unitary dual of $GL(n, {\mathbb {R}})$ was classified by Vogan in the 1980s. In particular, the Speh representations and the special unipotent representations are the building blocks of the unitary dual with half-integral infinitesimal characters. In this paper, we classify all irreducible unitary $({\mathfrak {g}}, K)$-modules with non-zero Dirac cohomology for $GL(n, {\mathbb {R}})$, as well as a formula for (one of) their spin-lowest $K$-types. Moreover, analogous to the $GL(n,{\mathbb {C}})$ case given in [12], we count the number of the FS-scattered representations of $GL(n, {\mathbb {R}})$.
Evaluation of essential fatty acids in lactating sow diets on sow reproductive performance, colostrum and milk composition, and piglet survivability
Authors: Holen Julia P , Woodworth Jason C , Tokach Mike D , Goodband Robert D , DeRouchey Joel M , Gebhardt Jordan T , DeDecker Ashley E , Martinez Xochitl
Published: May 2022

Mixed parity sows (n = 3,451; PIC, Hendersonville, TN; parities 2 through 9) and their litters were used to evaluate the effects of essential fatty acid (EFA) intake on sow reproductive performance, piglet growth and survivability, and colostrum and milk composition. Our hypothesis, like observed in earlier research, was that increasing linoleic acid (LA) and α-linolenic acid (ALA) would improve sow and litter performance. At approximately day 112 of gestation, sows were randomly assigned within parity groups to 1 of 4 corn–soybean meal–wheat-based lactation diets that contained 0.5 (Control) or 3% choice white grease (CWG), 3% soybean oil (SO), or a combination of 3% soybean oil and 2% choice white grease (Combination). Thus, sows were provided diets with low LA and ALA in diets with CWG or high LA and ALA in diets that included soybean oil. Sows received their assigned EFA treatments until weaning and were then fed a common gestation and lactation diet in the subsequent reproductive cycle. Average daily feed intake during the lactation period increased (P < 0.05) for sows fed the Combination and CWG diets compared with sows fed the Control or SO diet. However, daily LA and ALA intakes of sows fed the Combination and SO diets were still greater (P < 0.05) than those of sows fed 0.5 or 3% CWG. Overall, sows consuming high EFA from the Combination or SO diets produced litters with heavier (P < 0.05) piglet weaning weights and greater (P < 0.05) litter ADG when compared with litters from sows fed diets with CWG that provided low EFA. Despite advantages in growth performance, there was no impact of sow EFA intake on piglet survivability (P > 0.10). Additionally, lactation diet EFA composition did not influence sow colostrum or milk dry matter, crude protein, or crude fat content (P > 0.10). However, LA and ALA content in colostrum and milk increased (P < 0.05) in response to elevated dietary EFA from SO. There was no evidence for differences (P > 0.10) in subsequent sow reproductive or litter performance due to previous lactation EFA intake. In conclusion, increased LA and ALA intake provided by soybean oil during lactation increased overall litter growth and pig weaning weights, reduced sow ADFI, but did not affect piglet survivability or subsequent performance of sows.
Oral histone deacetylase inhibitor HBI-8000 (tucidinostat) in Japanese patients with relapsed or refractory non-Hodgkin’s lymphoma: phase I safety and efficacy
Authors: Yoshimitsu Makoto , Ando Kiyoshi , Ishida Takashi , Yoshida Shinichiro , Choi Ilseung , Hidaka Michihiro , Takamatsu Yasushi , Gillings Mireille , Lee Gloria T , Onogi Hiroshi , Tobinai Kensei
Published: May 2022

Objective

HBI-8000 (tucidinostat) is a novel, oral histone deacetylase inhibitor that selectivity inhibits Class I (histone deacetylase 1, 2, 3) and Class II (histone deacetylase 10) with direct anti-tumor activity through various mechanisms of action, including epigenetic reprogramming and immunomodulation. It has been approved in China for the treatment of relapsed or refractory peripheral T-cell lymphoma.

Methods

This multicenter, prospective phase I dose-escalation trial evaluating the safety of twice weekly HBI-8000 was conducted in Japan. Eligible patients had non-Hodgkin’s lymphoma and no available standard therapy. The primary endpoint was maximum tolerated dose; secondary endpoints included anti-tumor activity, safety and pharmacokinetics.

Results

Fourteen patients were enrolled in the study. Twelve patients were assessed for dose-limiting toxicity: six patients in the 30 mg BIW cohort had no dose-limiting toxicitys; two of six patients in the 40 mg BIW cohort had asymptomatic dose-limiting toxicitys. Treatment was well tolerated; adverse events were predominantly mild to moderate hematologic toxicities and were managed with dose modification and supportive care. Thirteen patients were included in the efficacy analysis. Objective response was seen in five of seven patients in the 40 mg BIW cohort; three partial responders had adult T-cell leukemia-lymphoma. In the 30 mg BIW cohort, three of six patients had stable disease after the first cycle.

Conclusions

Treatment with HBI-8000 30 and 40 mg BIW were well-tolerated and safe, with hematological toxicities as expected from other studies of histone deacetylase inhibitor. The maximum tolerated dose and recommended dosage for phase II studies of HBI-8000 is 40 mg BIW. Preliminary efficacy results are encouraging.
Correlates and Patterns of COVID-19 Vaccination Intentions among Parents of Children with Type 1 Diabetes
Authors: Wang Christine H , Jones Jasmine , Hilliard Marisa E , Tully Carrie , Monaghan Maureen , Marks Brynn E , Hildebrandt Tom , Streisand Randi
Published: May 2022

Objective

To examine psychosocial, sociodemographic, medical, and coronavirus disease 2019 (COVID-19) experiences as correlates of COVID-19 vaccination intentions among parents of children with type 1 diabetes (T1D).

Methods

121 parents of children with T1D (Mchild age = 7.78 ± 1.70; MA1c = 8.3% ± 1.5%) in the mid-Atlantic and Southwest regions completed self-report measures in February to March 2021.

Results

Parents’ general vaccination behaviors and attitudes were associated with COVID-19 vaccination intentions. Child insurance type and social distancing adherence were associated with vaccination intention in the Southwest site. Higher A1c was associated with lower intention. Vaccine safety was the top reported concern.

Conclusions

COVID-19 vaccination intentions are important to address in parents of youth with health conditions.
Crop breeding for a changing climate in the Pannonian region: towards integration of modern phenotyping tools
Authors: Kondić-Špika Ankica , Mikić Sanja , Mirosavljević Milan , Trkulja Dragana , Marjanović Jeromela Ana , Rajković Dragana , Radanović Aleksandra , Cvejić Sandra , Glogovac Svetlana , Dodig Dejan , Božinović Sofija , Šatović Zlatko , Lazarević Boris , Šimić Domagoj , Novoselović Dario , Vass Imre , Pauk János , Miladinović Dragana
Published: May 2022

The Pannonian Plain, as the most productive region of Southeast Europe, has a long tradition of agronomic production as well as agronomic research and plant breeding. Many research institutions from the agri-food sector of this region have a significant impact on agriculture. Their well-developed and fruitful breeding programmes resulted in productive crop varieties highly adapted to the specific regional environmental conditions. Rapid climatic changes that occurred during the last decades led to even more investigations of complex interactions between plants and their environments and the creation of climate-smart and resilient crops. Plant phenotyping is an essential part of botanical, biological, agronomic, physiological, biochemical, genetic, and other omics approaches. Phenotyping tools and applied methods differ among these disciplines, but all of them are used to evaluate and measure complex traits related to growth, yield, quality, and adaptation to different environmental stresses (biotic and abiotic). During almost a century-long period of plant breeding in the Pannonian region, plant phenotyping methods have changed, from simple measurements in the field to modern plant phenotyping and high-throughput non-invasive and digital technologies. In this review, we present a short historical background and the most recent developments in the field of plant phenotyping, as well as the results accomplished so far in Croatia, Hungary, and Serbia. Current status and perspectives for further simultaneous regional development and modernization of plant phenotyping are also discussed.
Functional characterization and vacuolar localization of fructan exohydrolase derived from onion (Allium cepa)
Authors: Oku Satoshi , Ueno Keiji , Sawazaki Yukiko , Maeda Tomoo , Jitsuyama Yutaka , Suzuki Takashi , Onodera Shuichi , Fujino Kaien , Shimura Hanako
Published: May 2022

Fructans such as inulin and levan accumulate in certain taxonomic groups of plants and are a reserve carbohydrate alternative to starch. Onion (Allium cepa L.) is a typical plant species that accumulates fructans, and it synthesizes inulin-type and inulin neoseries-type fructans in the bulb. Although genes for fructan biosynthesis in onion have been identified so far, no genes for fructan degradation had been found. In this study, phylogenetic analysis predicted that we isolated a putative vacuolar invertase gene (AcpVI1), but our functional analyses demonstrated that it encoded a fructan 1-exohydrolase (1-FEH) instead. Assessments of recombinant proteins and purified native protein showed that the protein had 1-FEH activity, hydrolyzing the β-(2,1)-fructosyl linkage in inulin-type fructans. Interestingly, AcpVI1 had an amino acid sequence close to those of vacuolar invertases and fructosyltransferases, unlike all other FEHs previously found in plants. We showed that AcpVI1 was localized in the vacuole, as are onion fructosyltransferases Ac1-SST and Ac6G-FFT. These results indicate that fructan-synthesizing and -degrading enzymes are both localized in the vacuole. In contrast to previously reported FEHs, our data suggest that onion 1-FEH evolved from a vacuolar invertase and not from a cell wall invertase. This demonstrates that classic phylogenetic analysis on its own is insufficient to discriminate between invertases and FEHs, highlighting the importance of functional markers in the nearby active site residues.
The DIVING3D Survey – Deep IFS view of nuclei of galaxies – II. First results: nuclear emission-line properties of the mini-DIVING3D sample
Authors: Menezes R B , Steiner J E , Ricci T V , da Silva Patrícia
Published: May 2022

This work presents the first results of the Deep IFS View of Nuclei of Galaxies (DIVING3D) survey. We analysed the nuclear emission-line spectra of a sub-sample we call mini-DIVING3D, which includes all Southern galaxies with B < 11.2 and |b| > 15°. We verified that $23{{\ \rm per\ cent}} \pm 4{{\ \rm per\ cent}}$ of the galaxies show nuclear emission-line properties characteristic of Low Ionization Nuclear Emission-Line Regions (LINERs). Diagnostic diagram analysis reveals an apparent dichotomy, not detected in previous studies, between objects classified as H ii regions and as LINERs or Seyferts, with very few galaxies classified as transition objects. A possible explanation for this result is that at least part of the transition objects are composite systems, with a central LINER contaminated by the emission from circumnuclear H ii regions. The higher spatial resolution of the DIVING3D survey, in comparison with previous studies, allowed us to isolate the nuclear emission from circumnuclear contaminations, reducing the number of transition objects. We also propose an alternative scenario, in which the emission-line spectra of some transition objects are the result of shock heating by central outflows, together with photoionization by young stars. Clear evidence of active galactic nuclei, in the optical and X-ray spectral bands, were detected in 69 per cent of the LINERs in the mini-DIVING3D sample. Considering the entire mini-DIVING3D sample, evidence of AGNs were detected in 65 per cent of the objects.
Lensing cosmic drift
Authors: Covone Giovanni , Sereno Mauro
Published: May 2022

As the Universe expands, the redshift of distant sources changes with time. Here, we discuss gravitational lensing phenomena that are consequence of the redshift drift between lensed source, gravitational lens, and observer. When the source is located very close to the drifting caustics, a pair of images could occur (or disappear) because of the cosmological expansion. Furthermore, lensing systems act as signal converters of the redshift drift. The angular position, magnification, distortion, and time delay of already existing multiple images change. We estimate the expected frequency of these phenomena and the prospects to observe them in the era of deep and large surveys. The drift detection in image separation could be within reach of next-generation surveys with μarcsec angular resolution.
A subgrid turbulent mean field dynamo model for cosmological galaxy formation simulations
Authors: Liu Yuankang , Kretschmer Michael , Teyssier Romain
Published: May 2022

Magnetic fields have been included in cosmological simulations of galaxy formation only recently. In this paper, we develop a new subgrid model for the turbulent dynamo that takes place in the supersonic interstellar medium in star-forming galaxies. It is based on a mean-field approach that computes the turbulent kinetic energy at unresolved scales and modifies the induction equation to account for the corresponding α dynamo. Our subgrid model depends on one free parameter, the quenching parameter, that controls the saturation of the subgrid dynamo. Thanks to this mean-field approach, we can now model the fast amplification of the magnetic field inside turbulent star-forming galaxies without using prohibitively expensive high-resolution simulations. We show that the evolution of the magnetic field in our zoom-in Milky Way-like galaxy is consistent with a simple picture, in which the field is in equipartition with the turbulent kinetic energy inside the star-forming disc, with a field strength around 10 μG at low redshift, while at the same time strong galactic outflows fill the halo with a slightly weaker magnetic field, whose strength (10 nG) is consistent will the ideal MHD dilution factor. Our results are in good agreement with recent theoretical and numerical predictions. We also compare our simulation with Faraday depth observations at both low and high redshift, seeing overall good agreement with some caveats. Our model naturally predicts stronger magnetic fields at high redshift (around 100 μG in the galaxy and 1 μG in the halo), but also stronger depolarisation effects due to stronger turbulence at early time.
Detecting PAHs in high-z galaxies in proxy: modelling physical conditions in an extremely strong damped Lyman α absorber towards QSO SDSS J1143+1420 at z = 2.323
Authors: Shaw Gargi , Ranjan A
Published: May 2022

We explore indirect methods to detect polycyclic aromatic hydrocarbons (PAHs) in gas-rich, absorption-selected galaxies at high redshift. We look at the optical X-Shooter observations of an intervening, extremely strong damped Lyman α absorber (or ESDLA, with log [N(H i) ≳ 21.7)] towards QSO SDSS J1143+1420 at redshift, zESDLA  = 2.323. Literature studies have shown that this ESDLA contains signatures of dust and diffuse molecular hydrogen and it was specifically chosen for our study due to its close spatial proximity (impact parameter, $\rm \rho = 0.6\, \pm \, 0.3$kpc) with its associated galaxy. There is no direct detection of PAHs emission in the limited observations of infrared spectra along this sightline. Hence, we use cloudy numerical simulation modelling to indirectly probe the presence of PAHs in the ESDLA. We note that PAHs need to be included in the models to reproduce the observed column densities of warm H2 and C i. Thus, we infer the presence of PAHs indirectly in our ESDLA, with an abundance of PAH/H  = 10−7.046. We also measure a low 2175 Å  bump strength (E$\rm _{bump}\, \sim$0.03–0.19 mag) relative to star-forming galaxies by modelling extinction of quasar QSO spectra by dust at the absorber rest frame. This is consistent with the low PAH abundance obtained indirectly using cloudy modelling. Our study highlights the usage of cloudy modelling to indirectly detect PAH in high-redshift gas-rich absorption-selected galaxies.
The VVV open cluster project II. Near-infrared sequences of 37 open clusters on eight-dimensional parameter space
Authors: Ramírez K Peña , Smith L C , Alegría S Ramírez , Chené A-N , González-Fernández C , Lucas P W , Minniti D
Published: May 2022

Open clusters are key coeval structures that help us understand star formation stellar evolution and trace the physical properties of our Galaxy. In the past years, the isolation of open clusters from the field has been heavily alleviated by the access to accurate large-scale stellar parallaxes and proper motions along a determined line of sight. Still, there are limitations regarding their completeness since large-scale studies rely on optical wavelengths. Here we extend the open clusters sequences towards fainter magnitudes complementing the Gaia photometric and astrometric information with near-infrared data from the VVV survey. We performed a homogeneous analysis on 37 open clusters implementing two coarse-to-fine characterization methods: extreme deconvolution Gaussian mixture models coupled with an unsupervised machine learning method on 8-dimensional parameter space. The process allowed us to separate the clusters from the field at near-infrared wavelengths. We report an increase of ∼47 per cent new member candidates on average in our sample (considering only sources with high membership probability p≧0.9). This study is the second in a series intended to reveal open cluster near-infrared sequences homogeneously.
Observational bias and young massive cluster characterization – I. 2D perspective effects
Authors: Buckner Anne S M , Liow Kong You , Dobbs Clare L , Naylor Tim , Rieder Steven
Published: May 2022

Understanding the formation and evolution of high-mass star clusters requires comparisons between theoretical and observational data to be made. Unfortunately, while the full phase space of simulated regions is available, often only partial 2D spatial and kinematic data is available for observed regions. This raises the question as to whether cluster parameters determined from 2D data alone are reliable and representative of clusters real parameters and the impact of line-of-sight orientation. In this paper, we derive parameters for a simulated cluster formed from a cloud–cloud collision with the full 6D phase space, and compare them with those derived from three different 2D line-of-sight orientations for the cluster. We show the same qualitative conclusions can be reached when viewing clusters in 2D versus 3D, but that drawing quantitative conclusions when viewing in 2D is likely to be inaccurate. The greatest divergence occurs in the perceived kinematics of the cluster, which in some orientations appears to be expanding when the cluster is actually contracting. Increases in the cluster density compounds pre-existing perspective issues, reducing the relative accuracy and consistency of properties derived from different orientations. This is particularly problematic for determination of the number, and membership, of subclusters present in the cluster. We find the fraction of subclusters correctly identified in 2D decreases as the cluster evolves, reaching less than $3.4{{\ \rm percent}}$ at the evolutionary end point for our cluster.
Neutron-capture elements record the ordered chemical evolution of the disc over time
Authors: Horta Danny , Ness Melissa K , Rybizki Jan , Schiavon Ricardo P , Buder Sven
Published: May 2022

An ensemble of chemical abundances probing different nucleosynthetic channels can be leveraged to build a comprehensive understanding of the chemical and structural evolution of the Galaxy. Using GALAH DR3 data, we seek to trace the enrichment by the supernovae Ia, supernovae II, asymptotic giant branch stars, and neutron-star mergers and/or collapsars nucleosynthetic sources by studying the [Fe/H], [α/Fe], [Ba/Fe], and [Eu/Fe] chemical compositions of ∼50 000 red giant stars, respectively. Employing small [Fe/H]–[α/Fe] cells, which serve as an effective reference-frame of supernovae contributions, we characterize the abundance-age profiles for [Ba/Fe] and [Eu/Fe]. Our results disclose that these age–abundance relations vary across the [Fe/H]–[α/Fe] plane. Within cells, we find negative age–[Ba/Fe] relations and flat age–[Eu/Fe] relations. Across cells, we see the slope of the age–[Ba/Fe] relations evolve smoothly and the [Eu/Fe] relations vary in amplitude. We subsequently model our empirical findings in a theoretical setting using the flexible Chempy Galactic chemical evolution (GCE) code, using the mean [Fe/H], [Mg/Fe], [Ba/Fe], and age values for stellar populations binned in [Fe/H], [Mg/Fe], and age space. We find that within a one-zone framework, an ensemble of GCE model parameters vary to explain the data. Using present day orbits from Gaia EDR3 measurements we infer that the GCE model parameters, which set the observed chemical abundance distributions, vary systematically across mean orbital radii. Under our modelling assumptions, the observed chemical abundances are consistent with a small gradient in the high-mass end of the initial mass function (IMF) across the disc, where the IMF is more top heavy towards the inner disc and more bottom heavy in the outer disc.
Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution
Authors: Yang Meng , Huang Lichao , Huang Haiping , Tang Hui , Zhang Nan , Yang Huanming , Wu Jihong , Mu Feng
Published: May 2022

Interpretation of non-coding genome remains an unsolved challenge in human genetics due to impracticality of exhaustively annotating biochemically active elements in all conditions. Deep learning based computational approaches emerge recently to help interpret non-coding regions. Here, we present LOGO (Language of Genome), a self-attention based contextualized pre-trained language model containing only two self-attention layers with 1 million parameters as a substantially light architecture that applies self-supervision techniques to learn bidirectional representations of the unlabelled human reference genome. LOGO is then fine-tuned for sequence labelling task, and further extended to variant prioritization task via a special input encoding scheme of alternative alleles followed by adding a convolutional module. Experiments show that LOGO achieves 15% absolute improvement for promoter identification and up to 4.5% absolute improvement for enhancer-promoter interaction prediction. LOGO exhibits state-of-the-art multi-task predictive power on thousands of chromatin features with only 3% parameterization benchmarking against the fully supervised model, DeepSEA and 1% parameterization against a recent BERT-based DNA language model. For allelic-effect prediction, locality introduced by one dimensional convolution shows improved sensitivity and specificity for prioritizing non-coding variants associated with human diseases. In addition, we apply LOGO to interpret type 2 diabetes (T2D) GWAS signals and infer underlying regulatory mechanisms. We make a conceptual analogy between natural language and human genome and demonstrate LOGO is an accurate, fast, scalable, and robust framework to interpret non-coding regions for global sequence labeling as well as for variant prioritization at base-resolution.
The topoisomerase 3 zinc finger domain cooperates with the RMI1 scaffold to promote stable association of the BTR complex to recombination intermediates in the Caenorhabditis elegans germline
Authors: Dello Stritto Maria Rosaria , Vojtassakova Nina , Velkova Maria , Hamminger Patricia , Ulm Patricia , Jantsch Verena
Published: May 2022

Homologous recombination is the predominant DNA repair pathway used in the gonad. Of the excess DNA double-strand breaks formed in meiosis, only a subset matures into crossovers, with the remainder repaired as non-crossovers. The conserved BTR complex (comprising Bloom helicase, topoisomerase 3 and RMI1/2 scaffold proteins) acts at multiple steps during recombination to dismantle joint DNA molecules, thereby mediating the non-crossover outcome and chromosome integrity. Furthermore, the complex displays a role at the crossover site that is less well understood. Besides catalytic and TOPRIM domains, topoisomerase 3 enzymes contain a variable number of carboxy terminal zinc finger (ZnF) domains. Here, we studied the Caenorhabditis elegans mutant, in which the single ZnF domain is deleted. In contrast to the gene disruption allele, the top-3-ZnF mutant is viable, with no replication defects; the allele appears to be a hypomorph. The TOP-3-ZnF protein is recruited into foci but the mutant has increased numbers of crossovers along its chromosomes, with minor defects in repressing heterologous recombination, and a marked delay in the maturation/processing of recombination intermediates after loading of the RAD-51 recombinase. The ZnF domain cooperates with the RMI1 homolog RMH-2 to stabilize association of the BTR complex with recombination intermediates and to prevent recombination between heterologous DNA sequences.
Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats
Authors: D’Souza Michael H , Mrozowich Tyler , Badmalia Maulik D , Geeraert Mitchell , Frederickson Angela , Henrickson Amy , Demeler Borries , Wolfinger Michael T , Patel Trushar R
Published: May 2022

Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on the RNA tertiary structure. Previous studies have determined the two-dimensional secondary structures of the sense and antisense human LincRNA-p21 AluSx1 IRs using SHAPE. However, there were no insights into its three-dimensional structure. Therefore, we in vitro transcribed the sense and antisense regions of LincRNA-p21 AluSx1 Inverted Repeats (IRs) and performed analytical ultracentrifugation, size exclusion chromatography, light scattering, and small angle X-ray scattering (SAXS) studies. Based on these studies, we determined low-resolution, three-dimensional structures of sense and antisense LincRNA-p21. By adapting previously known two-dimensional information, we calculated their sense and antisense high-resolution models and determined that they agree with the low-resolution structures determined using SAXS. Thus, our integrated approach provides insights into the structure of LincRNA-p21 Alu IRs. Our study also offers a viable pipeline for combining the secondary structure information with biophysical and computational studies to obtain high-resolution atomistic models for long noncoding RNAs.
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets
Authors: Zheng Lei , Liu Dongyang , Li Yuan Alex , Yang Siqi , Liang Yuchao , Xing Yongqiang , Zuo Yongchun
Published: May 2022

Protein structure exhibits greater complexity and diversity than DNA structure, and usually affects the interpretation of the function, interactions and biological annotations. Reduced amino acid alphabets (Raaa) exhibit a powerful ability to decrease protein complexity and identify functional conserved regions, which motivated us to create RaacFold. The RaacFold provides 687 reduced amino acid clusters (Raac) based on 58 reduction methods and offers three analysis tools: Protein Analysis, Align Analysis, and Multi Analysis. The Protein Analysis and Align Analysis provide reduced representations of sequence-structure according to physicochemical similarities and computational biology strategies. With the simplified representations, the protein structure can be viewed more concise and clearer to capture biological insight than the unreduced structure. Thus, the design of artificial protein will be more convenient, and redundant interference is avoided. In addition, Multi Analysis allows users to explore biophysical variation and conservation in the evolution of protein structure and function. This supplies important information for the identification and exploration of the nonhomologous functions of paralogs. Simultaneously, RaacFold provides powerful 2D and 3D rendering performance with advanced parameters for sequences, structures, and related annotations. RaacFold is freely available at http://bioinfor.imu.edu.cn/raacfold.
Identification and characterization of a prokaryotic 6-4 photolyase from Synechococcus elongatus with a deazariboflavin antenna chromophore
Authors: Chen Simeng , Liu Chenxi , Zhou Chenchen , Wei Zhihui , Li Yuting , Xiong Lei , Yan Liang , Lv Jun , Shen Liang , Xu Lei
Published: May 2022

Synechococcus elongatus, formerly known as Anacystis nidulans, is a representative species of cyanobacteria. It is also a model organism for the study of photoreactivation, which can be fully photoreactivated even after receiving high UV doses. However, for a long time, only one photolyase was found in S. elongatus that is only able to photorepair UV induced cyclobutane pyrimidine dimers (CPDs) in DNA. Here, we characterize another photolyase in S. elongatus, which belongs to iron-sulfur bacterial cryptochromes and photolyases (FeS-BCP), a subtype of prokaryotic 6–4 photolyases. This photolyase was named SePhrB that could efficiently photorepair 6–4 photoproducts in DNA. Chemical analyses revealed that SePhrB contains a catalytic FAD cofactor and an iron-sulfur cluster. All of previously reported FeS-BCPs contain 6,7-dimethyl-8-ribityllumazine (DMRL) as their antenna chromophores. Here, we first demonstrated that SePhrB possesses 7,8-didemethyl-8-hydroxy-5-deazariboflavin (8-HDF) as an antenna chromophore. Nevertheless, SePhrB could be photoreduced without external electron donors. After being photoreduced, the reduced FAD cofactor in SePhrB was extremely stable against air oxidation. These results suggest that FeS-BCPs are more diverse than expected which deserve further investigation.
Metal-organic frameworks as effective sensors and scavengers for toxic environmental pollutants
Authors: Karmakar Avishek , Velasco Ever , Li Jing
Published: May 2022

Metal-organic frameworks (MOFs) constructed from a rich library of organic struts and metal ions/clusters represent promising candidates for a wide range of applications. The unique structure, porous nature, easy tunability and processability of these materials make them an outstanding class of materials for tackling serious global problems relating to energy and environment. Among them, environmental pollution is one aspect that has increased at an alarming rate in the past decade or so. With rapid urbanization and industrialization, toxic environmental pollutants are constantly released and accumulated leading to serious contamination in water bodies and thereby having adverse effects on human health. Recent studies have shown that many toxic pollutants, as listed by the World Health Organization and the US Environmental Protection Agency, can be selectively detected, captured, sequestered and removed by MOFs from air and aquatic systems. Most of these sensing/capture processes in MOFs are quantifiable and effective for even a trace amount of the targeted chemical species. The functional sites (ligands and metals) play a critical role in such recognition processes and offer an extensive scope of structural tunability for guest (pollutants, toxic entities) recognition. Whereas on the one hand, the underlying mechanisms governing such sensing and capture are important, it is also crucial to identify MOFs that are best suited for commercial applications for the future. In this review article, we provide an overview of the most recent progress in the sensing, capture and removal of various common toxic pollutants, including neutral and ionic, inorganic and organic species, with brief discussions on the mechanism and efficacy of selected MOFs.
A Fatal Fungal Infection: Cryptococcus gattii (VGI) Meningitis in Texas
Authors: Nielsen Marisa C , Peterson Joshua M , Shine Billie , Hornak J Patrik , Esechie Aimalohi , Bhatt Sandeep , Desai Kinjal , Dabi Alok , Felicella Michelle M , Ren Ping
Published: May 2022

Cryptococcus gattii is an underrecognized cause of meningitis, especially in nonendemic regions. This report details C gattii disease progression from admission to autopsy in an otherwise healthy 40-year-old male in Texas. It brings awareness to an often unsuspected organism that can cause severe infection requiring early recognition and treatment in immunocompetent individuals.
A Bundle of the Top 10 OPAT Publications in 2021
Authors: Rivera Christina G , Beieler Alison M , Childs-Kean Lindsey M , Cortés-Penfield Nicolás , Idusuyi Ann-Marie , Keller Sara C , Rajapakse Nipunie S , Ryan Keenan L , Yoke Leah H , Mahoney Monica V
Published: May 2022

As outpatient parenteral antimicrobial therapy (OPAT) becomes more common, it may be difficult to stay current with recent related publications. A group of multidisciplinary OPAT clinicians reviewed and ranked all OPAT publications published in 2021. This article provides a high-level summary of the OPAT manuscripts that were voted the “top 10” publications of 2021.
The Many Values of Night Soil in Wartime China
Authors: Barnes Nicole Elizabeth
Published: May 2022

In March 1940, leaders of the Chongqing night-soil trade union sent a petition to the governor of China’s Sichuan province to contest health officials’ attempts to seize the night-soil industry. Cleanliness in Chongqing, the national capital during the War of Resistance against Japan (1937–45), held profound significance for China’s hygienic modernity, but Nationalist authorities failed to ensure it. On their part, the petitioners failed to recognize the centrality of odour in health officials’ agenda. These joint failures left the wartime capital mired in muck. This article employs microhistorical analysis of the 1940 petition to highlight a significant shift in olfactory sensibility. Comparison with a similar instance in nearby Hankou eleven years later, when Communist cadres succeeded in breaking the local night-soil gang, elucidates key distinctions between the Nationalist and Communist states. The conclusion considers what might be possible if we imagine using night soil to fertilize soils not as an anti-modern practice but as a sustainable means of processing waste and caring for our planet. To regain a portion of night soil’s many values, we must conquer the obstacles of disease transmission and disgust. The former is a technical problem for which solutions already exist; the latter is a formidable social problem.
The ongoing need for rates: can physiology and omics come together to co-design the measurements needed to understand complex ocean biogeochemistry?
Authors: Strzepek Robert F , Nunn Brook L , Bach Lennart T , Berges John A , Young Erica B , Boyd Philip W
Published: May 2022

The necessity to understand the influence of global ocean change on biota has exposed wide-ranging gaps in our knowledge of the fundamental principles that underpin marine life. Concurrently, physiological research has stagnated, in part driven by the advent and rapid evolution of molecular biological techniques, such that they now influence all lines of enquiry in biological oceanography. This dominance has led to an implicit assumption that physiology is outmoded, and advocacy that ecological and biogeochemical models can be directly informed by omics. However, the main modeling currencies are biological rates and biogeochemical fluxes. Here, we ask: how do we translate the wealth of information on physiological potential from omics-based studies to quantifiable physiological rates and, ultimately, to biogeochemical fluxes? Based on the trajectory of the state-of-the-art in biomedical sciences, along with case-studies from ocean sciences, we conclude that it is unlikely that omics can provide such rates in the coming decade. Thus, while physiological rates will continue to be central to providing projections of global change biology, we must revisit the metrics we rely upon. We advocate for the co-design of a new generation of rate measurements that better link the benefits of omics and physiology.
ABERRANT PANICLE ORGANIZATION2 controls multiple steps in panicle formation through common direct-target genes
Authors: Miao Yiling , Xun Qian , Taji Teruaki , Tanaka Keisuke , Yasuno Naoko , Ding Chengqiang , Kyozuka Junko
Published: May 2022

At the transition from vegetative to reproductive growth in rice (Oryza sativa), a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. The IM generates branch meristems (BMs), indeterminate meristems that reiteratively generate next-order meristems. All meristems eventually acquire a determinate spikelet meristem identity and terminate after producing a floret. ABERRANT PANICLE ORGANIZATION2 (APO2) is the rice ortholog of Arabidopsis (Arabidopsis thaliana) LEAFY (LFY), a plant-specific transcription factor (TF). APO2 is a positive regulator of panicle branch formation. Here, we show that APO2 is also required to increase the meristem size of the IM and suppress bract outgrowth. We identified genes directly and indirectly regulated by APO2 and identified APO2-binding sites. These analyses showed that APO2 directly controls known regulators of panicle development, including SQUAMOSA PROMOTER BINDING PROTEIN LIKE14 and NECK LEAF1. Furthermore, we revealed that a set of genes act as downstream regulators of APO2 in controlling meristem cell proliferation during reproductive transition, bract suppression, and panicle branch formation. Our findings indicate that APO2 acts as a master regulator of rice panicle development by regulating multiple steps in the reproductive transition through directly controlling a set of genes.
SAfety and Feasibility of EArly Resistance Training After Median Sternotomy: The SAFE-ARMS Study
Authors: Pengelly Jacqueline , Boggett Stuart , Bryant Adam , Royse Colin , Royse Alistair , Williams Gavin , El-Ansary Doa
Published: May 2022

Objective

The purpose of this study was to determine the safety and feasibility of subacute upper limb resistance exercise on sternal micromotion and pain and the reliability of sternal ultrasound assessment following cardiac surgery via median sternotomy.

Methods

This experimental study used a pretest–posttest design to investigate the effects of upper limb resistance exercise on the sternum in patients following their first cardiac surgery via median sternotomy. Six bilateral upper limb machine-based exercises were commenced at a base resistance of 20 lb (9 kg) and progressed for each participant. Sternal micromotion was assessed using ultrasound at the mid and lower sternum at 2, 8, and 14 weeks postsurgery. Intrarater and interrater reliability was calculated using intraclass correlation coefficients (ICCs). Participant-reported pain was recorded at rest and with each exercise using a visual analogue scale.

Results

Sixteen adults (n = 15 males; 71.3 [SD = 6.2] years of age) consented to participate. Twelve participants completed the study, 2 withdrew prior to the 8-week assessment, and 2 assessments were not completed at 14 weeks due to assessor unavailability. The highest median micromotion at the sternal edges was observed during the bicep curl (median = 1.33 mm; range = −0.8 to 2.0 mm) in the lateral direction and the shoulder pulldown (median = 0.65 mm; range = −0.8 to 1.6 mm) in the anterior–posterior direction. Furthermore, participants reported no increase in pain when performing any of the 6 upper limb exercises. Interrater reliability was moderate to good for both lateral–posterior (ICC = 0.73; 95% CI = 0.58 to 0.83) and anterior–posterior micromotion (ICC = 0.83; 95% CI = 0.73 to 0.89) of the sternal edges.

Conclusion

Bilateral upper limb resistance exercises performed on cam-based machines do not result in sternal micromotion exceeding 2.0 mm or an increase in participant-reported pain.

Impact

Upper limb resistance training commenced as early as 2 weeks following cardiac surgery via median sternotomy and performed within the safe limits of pain and sternal micromotion appears to be safe and may accelerate postoperative recovery rather than muscular deconditioning.