bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inflammatory Bowel Disease Associated with Primary Sclerosing Cholangitis is Associated with an Altered Gut Microbiome and Bile Acid Profile
Authors: Leibovitzh Haim , Nayeri Shadi , Borowski Krzysztof , Hernandez-Rocha Cristian , Lee Sun-Ho , Turpin Williams , Stempak Joanne M , Sandhu Iqbaljit , Milgrom Raquel , Smith Michelle I , Croitoru Kenneth , Hirschfield Gideon M , Gulamhusein Aliya , Silverberg Mark S 
Published: July 2024

Abstract

Background
Primary sclerosing cholangitis associated with inflammatory bowel disease [IBD-PSC] carries significant morbidity compared to IBD without PSC. Alterations in microbial composition and bile acid [BA] profiles have been shown to modulate chronic inflammation in IBD, but data in IBD-PSC are scarce. We aimed to assess the differences in gut microbiome composition as well as in the BAs profile and BA-related microbial functions between IBD-PSC and IBD-only.

Methods
In total, 54 IBD-PSC and 62 IBD-only subjects were enrolled from 2012 to 2021. Baseline samples were collected for faecal DNA shotgun metagenomic sequencing, faecal and serum BA quantification using mass spectrometry, and faecal calprotectin. Liver fibrosis measured by transient elastography was assessed in the IBD-PSC group. Data were analysed using general linear regression models and Spearman rank correlation tests.

Results
Patients with IBD-PSC had reduced microbial gene richness [p = 0.004] and significant compositional shifts [PERMANOVA: R2 = 0.01, p = 0.03] compared to IBD-only. IBD-PSC was associated with altered microbial composition and function, including decreased abundance of Blautia obeum, increased abundance of Veillonella atypica, Veillonella dispar, and Clostridium scindens [q &lt; 0.05 for all], and increased abundance of microbial genes involved in secondary BA metabolism. Decreased serum sulphated and increased serum conjugated secondary BAs were associated with IBD-PSC and increased liver fibrosis.

Conclusion
We identified differences in microbial species, functional capacity, and serum BA profiles in IBD-PSC compared with IBD-only. Our findings provide insight into the pathophysiology of IBD associated with PSC and suggest possible targets for modulating the risk and course of IBD in subjects with PSC.
Prognostic Impact of Anemia in Patients Undergoing Aortic Valve Replacement: A Nationwide Study
Authors: Brems Daniel Alexander , Petersen Jeppe Kofoed , Begun Xenia , Smerup Morten , Butt Jawad Haider , Køber Lars , Fosbøl Emil 
Published: July 2024

Abstract

Background
Patients undergoing aortic valve replacement (AVR) have high readmission rates. Several risk factors have been proposed as potential modifiable targets, including anemia. We examined the association between anemia at discharge and subsequent outcomes in these patients.

Methods
Using Danish nationwide registries, we identified all patients who underwent AVR between 2015-2021, were alive at discharge (index date), and had an available hemoglobin (Hb) measurement taken between procedure and discharge. Patients were categorized as having i) moderate/severe anemia (Hb&lt;6.2 mmol/L) or ii) no/mild anemia (Hb≥6.2 mmol). The one-year rates of all-cause mortality, all-cause hospital admission, heart failure (HF) admission, and atrial fibrillation (AF) admission were compared using multivariable Cox regression models.

Results
8,614 patients were identified; 2,847 (33.1%) had moderate/severe anemia (60.2% male, median age 74) and 5,767 (66.9%) had no/mild anemia (68.0% male, median age 76). For these two groups, respectively, the cumulative one-year incidences of the outcomes were: i) all-cause mortality: 5.1% vs. 4.3%; ii) all-cause admission: 53.8% vs. 47.5%; iii) AF admission: 14.0% vs. 11.6%); iv) HF admission: 6.8% vs. 6.2%. In adjusted analysis, moderate/severe anemia, compared with no/mild anemia, was associated with higher rates of all-cause mortality (hazard ratio (HR) 1.27 [95%CI 1.02-1.58]), all-cause admission (HR 1.22 [95%CI 1.14-1.30]), and AF admission (HR 1.23 [95%CI 1.08-1.40]), but not HF admission (HR 1.09 [95%CI 0.91-1.31]).

Conclusion
In patients undergoing AVR, moderate/severe anemia at discharge, compared with no/mild anemia, was associated with increased all-cause mortality, all-cause hospital admission, and AF admission, but not HF admission, at one-year post-discharge.
Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum
Authors: Korth Nate , Yang Qinnan , Van Haute Mallory J , Tross Michael C , Peng Bo , Shrestha Nikee , Zwiener-Malcom Mackenzie , Mural Ravi V , Schnable James C , Benson Andrew K 
Published: July 2024

Abstract
Substantial functional metabolic diversity exists within species of cultivated grain crops that directly or indirectly provide more than half of all calories consumed by humans around the globe. While such diversity is the molecular currency used for improving agronomic traits, diversity is poorly characterized for its effects on human nutrition and utilization by gut microbes. Moreover, we know little about agronomic traits’ potential tradeoffs and pleiotropic effects on human nutritional traits. Here, we applied a quantitative genetics approach using a meta-analysis and parallel genome-wide association studies of Sorghum bicolor traits describing changes in the composition and function of human gut microbe communities, and any of 200 sorghum seed and agronomic traits across a diverse sorghum population to identify associated genetic variants. A total of 15 multiple-effect loci (MEL) were initially found where different alleles in the sorghum genome produced changes in seed that affected the abundance of multiple bacterial taxa across 2 human microbiomes in automated in vitro fermentations. Next, parallel genome-wide studies conducted for seed, biochemical, and agronomic traits in the same population identified significant associations within the boundaries of 13/15 MEL for microbiome traits. In several instances, the colocalization of variation affecting gut microbiome and agronomic traits provided hypotheses for causal mechanisms through which variation could affect both agronomic traits and human gut microbes. This work demonstrates that genetic factors affecting agronomic traits in sorghum seed can also drive significant effects on human gut microbes, particularly bacterial taxa considered beneficial. Understanding these pleiotropic relationships will inform future strategies for crop improvement toward yield, sustainability, and human health.
Global patterns in the epidemiology, cancer risk, and surgical implications of inflammatory bowel disease
Authors: Zhang Yiming , Chu Xiaotian , Wang Li , Yang Hong 
Published: July 2024

Abstract
Inflammatory bowel disease (IBD), mainly including ulcerative colitis and Crohn’s disease, imposes a huge medical and economic burden worldwide. Recently, the diagnosis, treatment, and surveillance of IBD have advanced rapidly, which has changed the epidemiology, cancer risk, and surgery risk of IBD. Here, we reviewed the recent literature on the epidemiology, IBD-related cancer, and IBD-related surgery. We created a choropleth map to show the worldwide incidence trend for Crohn’s disease and ulcerative colitis. We also found that the cancer risk and surgery risk of IBD are declining and discussed some risk factors associated with them. Based on the recent trend, we proposed several suggestions and hoped to reduce the global burden of IBD as far as possible.
Sharps injuries among healthcare workers in Liberia and Ghana: a cross-sectional survey
Authors: Ridge Laura Jean , Arko-Mensah John , Lambert Josh , Aziato Lydia , Zeantoe G Clinton , Duah Henry , McCullagh Marjorie 
Published: July 2024

Abstract
There are little data on sharps injuries among healthcare workers in West Africa despite the region’s high rate of hepatitis B and human immunodeficiency virus. The purpose of this study is to investigate healthcare workers’ history of sharps injuries in Liberia and Ghana. An electronic cross-sectional survey was conducted among healthcare workers in Liberia and Ghana from February to June 2022. A link to the survey was texted to participants through professional association membership lists, including nursing, midwifery, and physician assistant organizations in both Liberia and Ghana and a physician organization in Ghana only. Five hundred and nine participants reported an average of 1.8 injuries per year in Liberia and 1.1 in Ghana (P ≤ .01); 15.1% of healthcare workers reported three or more injuries in the past year. Liberia had a higher proportion of frequently injured workers (P = .01). Frequently injured workers were evenly distributed across worker types. Workers in this region are vulnerable to sharps injuries. A frequently injured subset of workers likely has distinctive risk factors and would benefit from further investigation and intervention.
Morphological and Mechanical Tube Feet Plasticity among Populations of Sea Urchin (Strongylocentrotus purpuratus)
Authors: Narvaez C A , Stark A Y , Russell M P 
Published: July 2024

Synopsis
Sea urchins rely on an adhesive secreted by their tube feet to cope with the hydrodynamic forces of dislodgement common in nearshore, high wave-energy environments. Tube feet adhere strongly to the substrate and detach voluntarily for locomotion. In the purple sea urchin, Strongylocentrotus purpuratus, adhesive performance depends on both the type of substrate and the population of origin, where some substrates and populations are more adhesive than others. To explore the source of this variation, we evaluated tube foot morphology (disc surface area) and mechanical properties (maximum disc tenacity and stem breaking force) of populations native to substrates with different lithologies: sandstone, mudstone, and granite. We found differences among populations, where sea urchins native to mudstone substrates had higher disc surface area and maximum disc tenacity than sea urchins native to sandstone substrates. In a lab-based reciprocal transplant experiment, we attempted to induce a plastic response in tube foot morphology. We placed sea urchins on nonnative substrates (i.e., mudstone sea urchins were placed on sandstone and vice versa), while keeping a subgroup of both populations on their original substrates as a control. Instead of a reciprocal morphological response, we found that all treatments, including the control, reduced their disc area in laboratory conditions. The results of this study show differences in morphology and mechanical properties among populations, which explains population differences in adhesive performance. Additionally, this work highlights the importance of considering the impact of phenotypic plasticity in response to captivity when interpreting the results of laboratory studies.
Analysis of mcr family of colistin resistance genes in Gram-negative isolates from a tertiary care hospital in India
Authors: Irusan Dhinakaran , Akshay Sadanand Dangari , Shetty Varsha Prakash , Karunasagar Iddya , Deekshit Vijaya Kumar , Rohit Anusha 
Published: July 2024

Abstract

Aim
Colistin serves as the drug of last resort for combating numerous multidrug-resistant (MDR) Gram-negative infections. Its efficacy is hampered by the prevalent issue of colistin resistance, which severely limits treatment options for critically ill patients. Identifying resistance genes is crucial for controlling resistance spread, with horizontal gene transfer being the primary mechanism among bacteria. This study aimed to assess the prevalence of plasmid-mediated mcr genes associated with colistin resistance in Gram-negative bacteria, utilizing both genotypic and phenotypic tests.

Methods and results
The clinical isolates (n = 913) were obtained from a tertiary care center in Chennai, India. Colistin resistance was seen among Gram-negative isolates. These strains underwent screening for mcr-1, mcr-3, mcr-4, and mcr-5 genes via conventional PCR. Additionally, mcr-positive isolates were confirmed through Sanger sequencing and phenotypic testing. The bacterial isolates predominantly comprised Klebsiella pneumoniae (62.43%), Escherichia coli (19.71%), Pseudomonas aeruginosa (10.73%), and Acinetobacter baumannii (4.81%), along with other species. All isolates exhibited multidrug resistance to three or more antibiotic classes. Colistin resistance, determined via broth microdilution (BMD) using CLSI guidelines, was observed in 13.08% of the isolates studied. Notably, mcr-5 was detected in K. pneumoniae in PCR, despite its absence in Sanger sequencing and phenotypic tests (including the combined-disk test, colistin MIC in the presence of EDTA, and Zeta potential assays). This finding underscores the importance of employing multiple diagnostic approaches to accurately identify colistin resistance mechanisms.
Inducible defense phytohormones in annual bluegrass (Poa annua) and creeping bentgrass (Agrostis stolonifera) in response to annual bluegrass weevil (Listronotus maculicollis) infestation
Authors: Simard Audrey , Gendjar Megan , Merewitz Emily , McGraw Benjamin A 
Published: July 2024

Abstract
The annual bluegrass weevil (Listronotus maculicollis) is the most damaging insect pest of short-mown turfgrass on golf courses in eastern North America. Listronotus maculicollis larvae cause limited visible damage as stem-borers (L1-3), compared to the crown-feeding (L4-5) developmental instars. Prolonged larval feeding results in discoloration and formation of irregular patches of dead turf, exposing soil on high-value playing surfaces (fairways, collars, tee boxes, and putting greens). Annual bluegrass (Poa annua) is highly susceptible to L. maculicollis compared to a tolerant alternate host plant, creeping bentgrass (Agrostis stolonifera). This study explored whether defense signaling phytohormones contribute to A. stolonifera tolerance in response to L. maculicollis. Concentrations (ng/g) of salicylic acid (SA), jasmonic acid (JA), jasmonic-isoleucine (JA-Ile), 12-oxophytodienoic acid (OPDA), and abscisic acid (ABA) were extracted from turfgrass (leaf, stem, and root) tissue samples as mean larval age reached 2nd (L2), 3rd (L3), and 4th (L4) instar. Poa annua infested with L. maculicollis larvae (L2-4) possessed significantly greater SA in above-ground tissues than A. stolonifera. Levels of constitutive JA, JA-Ile, OPDA, and ABA were significantly higher within non-infested A. stolonifera aboveground tissues compared to P. annua. Inducible defense phytohormones may play a role in P. annua susceptibility to L. maculicollis but are unlikely to provide tolerance in A. stolonifera. Additional studies in turfgrass breeding, particularly focusing on cultivar selection for increased constitutive JA content, could provide a non-chemical alternative management strategy for L. maculicollis for turfgrass managers.
Integrative Review of Music and Music Therapy Interventions on Functional Outcomes in Children with Acquired Brain Injury
Authors: Burns James , Healy Hannah , O’Connor Rebecca , Moss Hilary 
Published: July 2024

Abstract
Acquired brain injury (ABI) can result in a multitude of impairments to physical, cognitive, communicative, psychological, and psychosocial functioning. Music interventions are emerging as a valuable form of intervention in the rehabilitation of children with ABI, stimulating brain functions involved in movement, cognition, speech, emotions, and sensory perceptions. To date, the literature detailing the impact of music and music therapy interventions on functional outcomes in children with ABI has not been reviewed systematically. To address this, Whittemore and Knafl’s five-stage integrative review framework was employed, which includes (a) problem identification, (b) literature search, (c) data evaluation, (d) data analysis and synthesis, and (e) presentation of the findings. A total of 388 articles were retrieved, and 8 studies met the inclusion criteria. Analysis and synthesis resulted in 3 overarching themes: outcomes of using music therapy in pediatric ABI, music therapy as a motivator in pediatric ABI rehabilitation, and collaboration. The review highlights the pivotal role of music as a motivational catalyst that promotes adherence to rehabilitative intervention. Nevertheless, it underscores a significant gap in empirical research within the field, emphasizing the necessity for larger, more rigorous studies.
Polycyclic aromatic hydrocarbon emission in galaxies as seen with JWST
Authors: Rigopoulou D , Donnan F R , García-Bernete I , Pereira-Santaella M , Alonso-Herrero A , Davies R , Hunt L K , Roche P F , Shimizu T 
Published: July 2024

ABSTRACT
We present a systematic study of mid-infrared spectra of galaxies including star-forming galaxies and active galactic nuclei observed with JWST MIRI-MRS and NIRSpec-IFU. We focus on the relative variations of the 3.3, 6.2, 7.7, 11.3, 12.7, and 17 $\mu$m polycyclic aromatic hydrocarbon (PAH) features within spatially resolved regions of galaxies including NGC 3256, NGC 7469, VV 114, II Zw96, and NGC 5728. Using theoretical PAH models and extending our earlier work, we introduce a new PAH diagnostic involving the 17 $\mu$m PAH feature. To determine the drivers of PAH band variations in galaxies, we compare observed PAH spectral bands to predictions from theoretical PAH models. We consider extinction, dehydrogenation, and PAH size and charge as possible drivers of PAH band variations. We find a surprising uniformity in PAH size distribution among the spatially resolved regions of the galaxies studied here, with no evidence for preferential destruction of the smallest grains, contrary to earlier findings. Neither extinction nor dehydrogenation play a crucial role in setting the observed PAH bands. Instead, we find that PAH charge plays a significant role in PAH inter-band variations. We find a tight relation between PAH charge and the intensity of the radiation field as traced by the [Ne iii]$/$[Ne ii] maps. In agreement with recent JWST results, we find a predominance of neutral PAH molecules in the nuclei of active galaxies and their outflows. Ionized PAHs are the dominant population in star-forming galaxies. We discuss the implications of our findings for the use of PAHs as ISM tracers in high redshift galaxies.
The afterglow of GW170817 from every angle: prospects for detecting the afterglows of binary neutron star mergers
Authors: Morsony Brian J , De Los Santos Ryan , Hernandez Rubin , Bustamante Joshua , Yassuiae Brandon , Astorga German , Parra Juan , Workman Jared C 
Published: July 2024

ABSTRACT
To date GW170817, produced by a binary neutron star (BNS) merger, is the only gravitational wave (GW) event with an electromagnetic counterpart. It was associated with a prompt short gamma-ray burst (GRB), an optical kilonova, and the afterglow of a structured off-axis relativistic jet. We model the prospects for future mergers discovered in gravitational waves to produce detectable afterglows. Using a model fit to GW170817, we assume all BNS mergers produce jets with the same parameters, and model the afterglow luminosity for a full distribution of observer angles, ISM densities, and distances. We find that in the LIGO/Virgo/KAGRA O4 run, 30 per cent–45 per cent of BNS mergers with a well-localized counterpart will have an afterglow detectable with current instrumentation in the X-ray, radio and optical. Without a previously detected counterpart, 10 per cent–15 per cent will have an afterglow detectable by wide-area radio and optical surveys, compared to only about 5 per cent–12 per cent of events expected to have bright (on-axis) gamma-ray emission. Most afterglows that are detected will be from off-axis jets. Further in the future, in the A + era (O5), 40 per cent–50 per cent of mergers will have afterglows detectable with next-generation X-ray and radio instruments. Future wide-area radio survey instruments, particularly DSA-2000, could detect 40 per cent of afterglows, even without a kilonova counterpart. Finding and monitoring these afterglows will provide valuable insight into the structure and diversity of relativistic jets, the rate at which mergers produce jets, and constrain the angle of the mergers relative to our line of sight.
Probing cold gas with Mg ii and Ly α radiative transfer
Authors: Chang Seok-Jun , Gronke Max 
Published: July 2024

ABSTRACT
The Mg ii resonance doublet at 2796 Å and 2803 Å is an increasingly important tool to study cold, $T \sim 10^{4}\,$ K, gas – an observational-driven development requiring theoretical support. We develop a new Monte Carlo radiative transfer code to systematically study the joined Mg ii and Ly α escape through homogeneous and ‘clumpy’ multiphase gas with dust in arbitrary three-dimensional geometries. Our main findings are (i) the Mg ii spectrum differs from Ly α due to the large difference in column densities, even though the atomic physics of the two lines are similar. (ii) The Mg ii escape fraction is generally higher than that of Ly α because of lower dust optical depths and path lengths – but large variations due to differences in dust models and the clumpiness of the cold medium exist. (iii) Clumpy media possess a ‘critical covering factor’ above which Mg ii radiative transfer matches a homogeneous medium. The critical covering factors for Mg ii and Ly α differ, allowing constraints on the cold gas structure. (iv) The Mg ii doublet ratio $R_{\rm MgII}$ varies for strong outflows/inflows ($\gtrsim 700 \,\mathrm{km\, s}^{-1}$), in particular, $R_{\rm MgII}\lt 1$ being an unambiguous tracer for powerful galactic winds. (v) Scattering of stellar continuum photons can decrease $R_{\rm MgII}$ from two to one, allowing constraints on the scattering medium. Notably, we introduce a novel probe of the cold gas column density – the halo doublet ratio – which we show to be a powerful indicator of ionizing photon escape. We discuss our results in the context of interpreting and modelling observations as well as their implications for other resonant doublets.
Multi-epoch X-ray spectral analysis of Centaurus A: Revealing new constraints on iron emission line origins
Authors: Iwata Toshiya , Tanimoto Atsushi , Odaka Hirokazu , Bamba Aya , Inoue Yoshiyuki , Hagino Kouichi 
Published: July 2024

Abstract
We conduct X-ray reverberation mapping and spectral analysis of the radio galaxy Centaurus A to uncover its central structure. We compare the light curve of the hard X-ray continuum from Swift Burst Alert Telescope observations with that of the Fe K$\alpha$ fluorescence line, derived from the Nuclear Spectroscopic Telescope Array (NuSTAR), Suzaku, XMM–Newton, and Swift X-ray Telescope observations. The analysis of the light curves suggests that a top-hat transfer function, commonly employed in reverberation mapping studies, is improbable. Instead, the relation between these light curves can be described by a transfer function featuring two components: one with a lag of $0.19_{- 0.02}^{+ 0.10} \,\, \mathrm{pc}/c$, and another originating at $r \\gt 1.7 \,\, \mathrm{pc}$ that produces an almost constant light curve. Further, we analyze the four-epoch NuSTAR and six-epoch Suzaku spectra, considering the time lag of the reflection component relative to the primary continuum. This spectral analysis supports that the reflecting material is Compton-thin, with $N_{\mathrm{H}} = 3.14_{-0.74}^{+0.44} \times 10^{23} \,\, \mathrm{cm}^{-2}$. These results suggest that the Fe K$\alpha$ emission may originate from Compton-thin circumnuclear material located at a sub-parsec scale, likely a dust torus, and materials at a greater distance.