bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data
Authors: Chen Guangyi , Liu Zhi-Ping 
Published: August 2022

AbstractMotivationSingle-cell RNA sequencing (scRNA-seq) data provides unprecedented opportunities to reconstruct gene regulatory networks (GRNs) at fine-grained resolution. Numerous unsupervised or self-supervised models have been proposed to infer GRN from bulk RNA-seq data, but few of them are appropriate for scRNA-seq data under the circumstance of low signal-to-noise ratio and dropout. Fortunately, the surging of TF-DNA binding data (e.g. ChIP-seq) makes supervised GRN inference possible. We regard supervised GRN inference as a graph-based link prediction problem that expects to learn gene low-dimensional vectorized representations to predict potential regulatory interactions.ResultsIn this paper, we present GENELink to infer latent interactions between transcription factors (TFs) and target genes in GRN using graph attention network. GENELink projects the single-cell gene expression with observed TF-gene pairs to a low-dimensional space. Then, the specific gene representations are learned to serve for downstream similarity measurement or causal inference of pairwise genes by optimizing the embedding space. Compared to eight existing GRN reconstruction methods, GENELink achieves comparable or better performance on seven scRNA-seq datasets with four types of ground-truth networks. We further apply GENELink on scRNA-seq of human breast cancer metastasis and reveal regulatory heterogeneity of Notch and Wnt signalling pathways between primary tumour and lung metastasis. Moreover, the ontology enrichment results of unique lung metastasis GRN indicate that mitochondrial oxidative phosphorylation (OXPHOS) is functionally important during the seeding step of the cancer metastatic cascade, which is validated by pharmacological assays.Availability and implementationThe code and data are available at https://github.com/zpliulab/GENELink.Supplementary informationSupplementary data are available at Bioinformatics online.
Self-modulation of motor cortex activity after stroke: a randomized controlled trial
Authors: Sanders Zeena-Britt , Fleming Melanie K , Smejka Tom , Marzolla Marilien C , Zich Catharina , Rieger Sebastian W , Lührs Michael , Goebel Rainer , Sampaio-Baptista Cassandra , Johansen-Berg Heidi 
Published: August 2022

AbstractReal-time functional MRI neurofeedback allows individuals to self-modulate their ongoing brain activity. This may be a useful tool in clinical disorders that are associated with altered brain activity patterns. Motor impairment after stroke has previously been associated with decreased laterality of motor cortex activity. Here we examined whether chronic stroke survivors were able to use real-time fMRI neurofeedback to increase laterality of motor cortex activity and assessed effects on motor performance and on brain structure and function.We carried out a randomized, double-blind, sham-controlled trial (ClinicalTrials.gov: NCT03775915) in which 24 chronic stroke survivors with mild to moderate upper limb impairment experienced three training days of either Real (n = 12) or Sham (n = 12) neurofeedback. Assessments of brain structure, brain function and measures of upper-limb function were carried out before and 1 week after neurofeedback training. Additionally, measures of upper-limb function were repeated 1 month after neurofeedback training. Primary outcome measures were (i) changes in lateralization of motor cortex activity during movements of the stroke-affected hand throughout neurofeedback training days; and (ii) changes in motor performance of the affected limb on the Jebsen Taylor Test (JTT).Stroke survivors were able to use Real neurofeedback to increase laterality of motor cortex activity within (P = 0.019), but not across, training days. There was no group effect on the primary behavioural outcome measure, which was average JTT performance across all subtasks (P = 0.116). Secondary analysis found improvements in the performance of the gross motor subtasks of the JTT in the Real neurofeedback group compared to Sham (P = 0.010). However, there were no improvements on the Action Research Arm Test or the Upper Extremity Fugl–Meyer score (both P &gt; 0.5). Additionally, decreased white-matter asymmetry of the corticospinal tracts was detected 1 week after neurofeedback training (P = 0.008), indicating that the tracts become more similar with Real neurofeedback. Changes in the affected corticospinal tract were positively correlated with participants neurofeedback performance (P = 0.002).Therefore, here we demonstrate that chronic stroke survivors are able to use functional MRI neurofeedback to self-modulate motor cortex activity in comparison to a Sham control, and that training is associated with improvements in gross hand motor performance and with white matter structural changes.
Faecal microbiota transplant ameliorates gut dysbiosis and cognitive deficits in Huntington’s disease mice
Authors: Gubert Carolina , Choo Jocelyn M , Love Chloe J , Kodikara Saritha , Masson Bethany A , Liew Jamie J M , Wang Yiwen , Kong Geraldine , Narayana Vinod K , Renoir Thibault , Lê Cao Kim Anh , Rogers Geraint B , Hannan Anthony J 
Published: August 2022

Abstract
Huntington’s disease is a neurodegenerative disorder involving psychiatric, cognitive and motor symptoms. Huntington’s disease is caused by a tandem-repeat expansion in the huntingtin gene, which is widely expressed throughout the brain and body, including the gastrointestinal system. There are currently no effective disease-modifying treatments available for this fatal disorder. Despite recent evidence of gut microbiome disruption in preclinical and clinical Huntington’s disease, its potential as a target for therapeutic interventions has not been explored. The microbiota–gut–brain axis provides a potential pathway through which changes in the gut could modulate brain function, including cognition. We now show that faecal microbiota transplant (FMT) from wild-type into Huntington’s disease mice positively modulates cognitive outcomes, particularly in females. In Huntington’s disease male mice, we revealed an inefficiency of FMT engraftment, which is potentially due to the more pronounced changes in the structure, composition and instability of the gut microbial community, and the imbalance in acetate and gut immune profiles found in these mice. This study demonstrates a role for gut microbiome modulation in ameliorating cognitive deficits modelling dementia in Huntington’s disease. Our findings pave the way for the development of future therapeutic approaches, including FMT and other forms of gut microbiome modulation, as potential clinical interventions for Huntington’s disease.
Detection of Influenza in Managed Quarantine in Australia and the Estimated Risk of Importation
Authors: Peck Heidi , Anbumurali Nithila , McMahon Kimberley , Freeman Kevin , Aziz Ammar , Gillespie Leah , Yang Bingyi , Moselen Jean , Deng Yi-Mo , Cowling Benjamin J , Barr Ian G , Subbarao Kanta , Sullivan Sheena G 
Published: August 2022

Abstract

Background
Influenza circulated at historically low levels during 2020/2021 due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic travel restrictions. In Australia, international arrivals were required to undergo a 14-day hotel quarantine to limit new introduction of SARS-CoV-2.

Methods
We usedtesting data for travelers arriving on repatriation flights to Darwin, Australia, from 3 January 2021 to 11 October 2021 to identify importations of influenza virus into Australia. We used this information to estimate the risk of a case exiting quarantine while still infectious. Influenza-positive samples were sequenced, and cases were followed up to identify transmission clusters. Data on the number of cases and total passengers were used to infer the risk of influenza cases exiting quarantine while infectious.

Results
Despite very low circulation of influenza globally, 42 cases were identified among 15 026 returned travelers, of which 30 were A(H3N2), 2 were A(H1N1)pdm09, and 10 were B/Victoria. Virus sequencing data identified potential in-flight transmission, as well as independent infections prior to travel. Under the quarantine strategy in place at the time, the probability that these cases could initiate influenza outbreaks in Australia neared 0. However, this probability rose as quarantine requirements relaxed.

Conclusions
Detection of influenza virus infections in repatriated travelers provided a source of influenza viruses otherwise unavailable and enabled development of the A(H3N2) vaccine seed viruses included in the 2022 Southern Hemisphere influenza vaccine. Failure to test quarantined returned travelers for influenza represents a missed opportunity for enhanced surveillance to better inform public health preparedness.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Testing and Detection During Peripartum Hospitalizations Among a Multicenter Cohort of Pregnant Persons: March 2020–February 2021
Authors: Delahoy Miranda J , Munoz Flor , Li De-Kun , Arriola Carmen Sofia , Bond Nanette Lee , Daugherty Michael , Ferber Jeannette , Ferguson Nickolas , Hadden Louise , Henderson Jillian T , Irving Stephanie A , Juergens Mary , Kancharla Venkatesh , Greenberg Mara , Odouli Roxana , Newes-Adeyi Gabriella , Nicholson Erin G , Reichle Lawrence , Sanyang Momodou , Snead Margaret , Dawood Fatimah S , Naleway Allison L 
Published: August 2022

Abstract

Background
Identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during peripartum hospitalizations is important to guide care, implement prevention measures, and understand infection burden.

Methods
This cross-sectional analysis used electronic health record data from hospitalizations during which pregnancies ended (peripartum hospitalizations) among a cohort of pregnant persons at 3 US integrated healthcare networks (sites 1–3). Maternal demographic, medical encounter, SARS-CoV-2 testing, and pregnancy and neonatal outcome information was extracted for persons with estimated delivery and pregnancy end dates during March 2020–February 2021 and ≥1 antenatal care record. Site-stratified multivariable logistic regression was used to identify factors associated with testing and compare pregnancy and neonatal outcomes among persons tested.

Results
Among 17 858 pregnant persons, 10 863 (60.8%) had peripartum SARS-CoV-2 testing; 222/10 683 (2.0%) had positive results. Testing prevalence varied by site and was lower during March–May 2020. Factors associated with higher peripartum SARS-CoV-2 testing odds were Asian race (adjusted odds ratio [aOR]: 1.36; 95% confidence interval [CI]: 1.03–1.79; referent: White) (site 1), Hispanic or Latino ethnicity (aOR: 1.33; 95% CI: 1.08–1.64) (site 2), peripartum Medicaid coverage (aOR: 1.33; 95% CI: 1.06–1.66) (site 1), and preterm hospitalization (aOR: 1.69; 95% CI: 1.19–2.39 [site 1]; aOR: 1.39; 95% CI: 1.03–1.88 [site 2]).

Conclusions
Findings highlight potential disparities in SARS-CoV-2 peripartum testing by demographic and pregnancy characteristics. Testing practice variations should be considered when interpreting studies relying on convenience samples of pregnant persons testing positive for SARS-CoV-2. Efforts to address testing differences between groups could improve equitable testing practices and care for pregnant persons with SARS-CoV-2 infections.
Successful treatment of recurrent cardiac sarcoidosis with the combination of corticosteroid and methotrexate monitored by 18F-fluoro-2-deoxyglucose positron emission tomography: case series
Authors: Ishizuka Masato , Uehara Masae , Katagiri Mikako , Ishida Junichi , Kojima Toshiya , Amiya Eisuke , Komuro Issei 
Published: August 2022

Abstract

Background
The standard treatment for cardiac sarcoidosis (CS) is corticosteroids, including prednisolone (PSL). Previous studies have shown that the addition of methotrexate (MTX) to PSL is effective for steroid-refractory and recurrent cases. 18F-fluoro-2-deoxyglucose positron emission tomography (FDG-PET) is an essential tool for the diagnosis of CS. However, it is unclear whether FDG-PET is useful for detecting recurrence of CS and monitoring the effectiveness of PSL and MTX combination therapy.

Case summary
We detected CS recurrence during PSL treatment using FDG-PET. Patient 1 was accompanied by increased FDG uptake in other organs, Patient 2 was complicated with a decrease in left ventricular ejection fraction, and Patient 3 showed enlargement of the late gadolinium enhancement area, which was compatible with the recurrence of CS. We successfully monitored the inflammation activity by FDG-PET and treated recurrent CS by increasing the PSL dose and adding MTX to suppress inflammation.

Discussion
FDG-PET is useful for detecting CS recurrence and monitoring the effectiveness of PSL and MTX combination therapy. Serial FDG-PET scans indicated that it might be more difficult to suppress inflammation in recurrent CS than in the initial treatment. The use of FDG-PET is necessary to monitor long-term disease activity.
Seasonal influenza vaccine uptake among patients with cardiovascular disease in Denmark, 2017–2019
Authors: Christensen Daniel Mølager , Jørgensen Sidsel Marie Bernt , El-Chouli Mohamad , Phelps Matthew , Schjerning Anne-Marie , Sehested Thomas S G , Gerds Thomas , Sindet-Pedersen Caroline , Biering-Sørensen Tor , Torp-Pedersen Christian , Schou Morten , Gislason Gunnar 
Published: August 2022

Abstract

Background
Influenza vaccination protects against morbidity and mortality in patients with cardiovascular disease (CVD). We aimed to describe influenza vaccine uptake in patients with CVD in a universal-access healthcare system.

Methods
Using nationwide Danish registries, we included all patients with prevalent CVD, defined as heart failure (HF), atrial fibrillation (AF), ischemic heart disease (IHD), or stroke during three consecutive influenza seasons (October–December 2017–2019). The outcome was relative frequency of influenza vaccination across strata of patient characteristics.

Results
There was an average of 397 346 patients with CVD yearly during 2017–2019. Vaccine uptake was 45.6% for the whole population and ranged from 55.0% in AF to 61.8% in HF among patients aged ≥65 years. Among patients aged &lt;65 years, uptake was 32.6% in HF, 19.0% in AF, 21.1% in IHD, and 18.3% in stroke. There was a lower uptake with decreasing age: 21.6% in HF, 5.5% in AF, 7.4% in IHD, and 6.3% in stroke among males aged &lt;45 years, as opposed to 25.5% in HF, 11.5% in AF, 13.8% in IHD, and 12.1% in stroke for males aged 45–54 years. In the further stratified analyses, uptake ranged from a low of 2.5% for males &lt;45 years with AF who were not vaccinated the previous season to a high of 87.0% for females ≥75 years with IHD who were vaccinated the previous season.

Conclusion
Seasonal influenza vaccine uptake is suboptimal among patients with CVD, even in a universal-access healthcare system with free-of-charge vaccinations. Vaccine uptake was particularly low among young patients.
Impact of Aging and Lifelong Exercise Training on Mitochondrial Function and Network Connectivity in Human Skeletal Muscle
Authors: Ringholm Stine , Gudiksen Anders , Frey Halling Jens , Qoqaj Albina , Meizner Rasmussen Philip , Prats Clara , Plomgaard Peter , Pilegaard Henriette 
Published: August 2022

AbstractAging is associated with metabolic decline in skeletal muscle, which can be delayed by physical activity. Moreover, both lifelong and short-term exercise training have been shown to prevent age-associated fragmentation of the mitochondrial network in mouse skeletal muscle. However, whether lifelong endurance exercise training exerts the same effects in human skeletal muscle is still not clear. Therefore, the aim of the present study was to examine the effect of volume-dependent lifelong endurance exercise training on mitochondrial function and network connectivity in older human skeletal muscle. Skeletal muscle complex I+II-linked mitochondrial respiration per tissue mass was higher, but intrinsic complex I+II-linked mitochondrial respiration was lower in highly trained older subjects than in young untrained, older untrained, and older moderately trained subjects. Mitochondrial volume and connectivity were higher in highly trained older subjects than in untrained and moderately trained older subjects. Furthermore, the protein content of the ADP/ATP exchangers ANT1 + 2 and VDAC was higher and of the mitophagic marker parkin lower in skeletal muscle from the highly trained older subjects than from untrained and moderately trained older subjects. In contrast, H2O2 emission in skeletal muscle was not affected by either age or exercise training, but SOD2 protein content was higher in highly trained older subjects than in untrained and moderately trained older subjects. This suggests that healthy aging does not induce oxidative stress or mitochondrial network fragmentation in human skeletal muscle, but high-volume exercise training increases mitochondrial volume and network connectivity, thereby increasing oxidative capacity in older human skeletal muscle.
Pretty Cool Beetles: Can Manipulation of Visible and Near-Infrared Sunlight Prevent Overheating?
Authors: Ospina-Rozo Laura , Subbiah Jegadesan , Seago Ainsley , Stuart-Fox Devi 
Published: August 2022

Synopsis
Passive thermoregulation is an important strategy to prevent overheating in thermally challenging environments. Can the diversity of optical properties found in Christmas beetles (Rutelinae) be an advantage to keep cool? We measured changes in temperature of the elytra of 26 species of Christmas beetles, exclusively due to direct radiation from a solar simulator in visible (VIS: 400–700 nm) and near infrared (NIR: 700–1700 nm) wavebands. Then, we evaluated if the optical properties of elytra could predict their steady state temperature and heating rates, while controlling for size. We found that higher absorptivity increases the heating rate and final steady state of the beetle elytra in a biologically significant range (3 to 5°C). There was substantial variation in the absorptivity of Christmas beetle elytra; and this variation was achieved by different combinations of reflectivity and transmissivity in both VIS and NIR. Size was an important factor predicting the change in temperature of the elytra after 5 min (steady state) but not maximum heating rate. Lastly, we show that the presence of the elytra covering the body of the beetle can reduce heating of the body itself. We propose that beetle elytra can act as a semi-insulating layer to enable passive thermoregulation through high reflectivity of elytra, resulting in low absorptivity of solar radiation. Alternatively, if beetle elytra absorb a high proportion of solar radiation, they may reduce heat transfer from the elytra to the body through behavioral or physiological mechanisms.
Assessment of spent hemp biomass as a potential ingredient in ruminant diet: nutritional quality and effect on performance, meat and carcass quality, and hematological parameters in finishing lambs
Authors: Parker Nathan B , Bionaz Massimo , Ford Hunter R , Irawan Agung , Trevisi Erminio , Ates Serkan 
Published: August 2022

Abstract
Spent hemp biomass (SHB), a byproduct of cannabinoid extraction from the production of industrial hemp has not been approved by FDA-CVM since its effects on animal health, performance, and product quality are unknown. Our objective was to investigate the effects of feeding two levels of SHB and a 4-wk withdrawal period on performance, carcass characteristic, meat quality, and hematological parameters in finishing lambs. A total of 35 weaned, Polypay male lambs kept in single pens were randomly assigned to five feeding treatments (n = 7) and fed diets containing either no SHB (CON) or SHB at 10% (LH1) or 20% (HH1) for 4 wk with 4 wk of clearing period from SHB, or SHB at 10% (LH2) or 20% (HH2) for 8 wk. Chemical analysis revealed SHB to have a nutritive quality similar to alfalfa with no mycotoxin, terpenes, or organic residuals as a result of the extraction process. Feed intake of lambs was negatively affected by 20% SHB in period 1 but not in period 2 where feed intake was the greatest in HH1 and LH2. In contrast, none of the performance data, including liveweight gains, were different across the groups and periods. In period 1, blood glucose, cholesterol, calcium, paraoxonase, and tocopherol were decreased by the level of SHB fed, while bilirubin and alkaline phosphatase (ALP) were increased. In period 2, the concentration in blood of urea, magnesium, bilirubin, ALP, and ferric reducing ability of the plasma (FRAP) were higher in LH2 and HH2 as compared with CON, while β-hydroxybutyrate was lower in HH2. Blood parameters related to liver health, kidney function, immune status, and inflammation were unaffected by feeding SHB. Most carcass and meat quality parameters did not differ across feeding groups either. Except carcass purge loss and meat cook loss were larger in lambs that were fed 20% SHB. Although lower feed intake of lambs that were fed 20% SHB initially in period 1 suggested SHB was not palatable to the lambs, increased feed intake at a lower level of inclusion at 10% in period 2 may point to a positive long-term effect of feeding SHB.
A New Test for Multiple Predictive Regression
Authors: Xu Ke-Li , Guo Junjie 
Published: August 2022

Abstract
We consider inference for predictive regressions with multiple predictors. Extant tests for predictability (especially for joint predictability) may perform unsatisfactorily and tend to discover spurious predictability as the number of predictors increases. We propose a battery of new instrumental variables-based tests which involve enforcement or partial enforcement of the null hypothesis in variance estimation. A test based on the few-predictors-at-a-time parsimonious system approach is recommended. Empirical Monte Carlos demonstrates the remarkable finite-sample performance regardless of numerosity of predictors and their persistence properties. Empirical application to equity premium predictability is provided.
Spatiotemporal Environmental Drivers of Eastern Equine Encephalitis Virus in Central Florida: Towards a Predictive Model for a Lethal Disease
Authors: Mundis Stephanie J , Harrison Steve , Pelley Dave , Durand Susan , Ryan Sadie J 
Published: August 2022

Abstract
Eastern equine encephalitis virus (EEEV) is a mosquito-borne virus that affects humans and horses, with a high case fatality rate in both species. The virus can be transmitted by several mosquito species and maintained in multiple reservoir hosts, making EEEV dynamics difficult to anticipate. In this study, we identified spatial and temporal factors that precede EEEV detection using sentinel chicken surveillance data from Orange County, Florida, from 2003 to 2017. We first examined the land cover and mosquito species composition associated with sentinel chicken sites. We then fit distributed lag nonlinear models of EEEV detection at the county scale, using monthly temperature, precipitation, and Southern Oscillation Index values, and at the sentinel flock-scale, using remotely sensed temperature and wetness indicators. We found positive associations between the percent wooded wetlands and the count of EEEV detections. We found Culiseta melanura (Diptera: Culicidae) were more abundant at positive sites in winter and summer, but Coquillettidia perturbans (Walker) were more abundant at positive sites in spring. In the county-wide model, precipitation, temperature, and Southern Oscillation Index values at lags of two, nine, and twelve months were significant, respectively, while temperature and wetness were significant at lags of eight and six months in the flock-specific models.