bluuebunny/crossref_metadata_2025_split huggingface dataset:
R2-DDI: relation-aware feature refinement for drug–drug interaction prediction
Authors: Lin Jiacheng , Wu Lijun , Zhu Jinhua , Liang Xiaobo , Xia Yingce , Xie Shufang , Qin Tao , Liu Tie-Yan 
Published: November 2022

Abstract
Precisely predicting the drug–drug interaction (DDI) is an important application and host research topic in drug discovery, especially for avoiding the adverse effect when using drug combination treatment for patients. Nowadays, machine learning and deep learning methods have achieved great success in DDI prediction. However, we notice that most of the works ignore the importance of the relation type when building the DDI prediction models. In this work, we propose a novel R$^2$-DDI framework, which introduces a relation-aware feature refinement module for drug representation learning. The relation feature is integrated into drug representation and refined in the framework. With the refinement features, we also incorporate the consistency training method to regularize the multi-branch predictions for better generalization. Through extensive experiments and studies, we demonstrate our R$^2$-DDI approach can significantly improve the DDI prediction performance over multiple real-world datasets and settings, and our method shows better generalization ability with the help of the feature refinement design.
AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting
Authors: Su Changqing , Gao Yuhan , Zhou You , Sun Yaoqi , Yan Chenggang , Yin Haibing , Xiong Bo 
Published: November 2022

Abstract

Motivation
Light-field microscopy (LFM) is a compact solution to high-speed 3D fluorescence imaging. Usually, we need to do 3D deconvolution to the captured raw data. Although there are deep neural network methods that can accelerate the reconstruction process, the model is not universally applicable for all system parameters. Here, we develop AutoDeconJ, a GPU-accelerated ImageJ plugin for 4.4× faster and more accurate deconvolution of LFM data. We further propose an image quality metric for the deconvolution process, aiding in automatically determining the optimal number of iterations with higher reconstruction accuracy and fewer artifacts.

Results
Our proposed method outperforms state-of-the-art light-field deconvolution methods in reconstruction time and optimal iteration numbers prediction capability. It shows better universality of different light-field point spread function (PSF) parameters than the deep learning method. The fast, accurate and general reconstruction performance for different PSF parameters suggests its potential for mass 3D reconstruction of LFM data.

Availability and implementation
The codes, the documentation and example data are available on an open source at: https://github.com/Onetism/AutoDeconJ.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
dnadna: a deep learning framework for population genetics inference
Authors: Sanchez Théophile , Bray Erik Madison , Jobic Pierre , Guez Jérémy , Letournel Anne-Catherine , Charpiat Guillaume , Cury Jean , Jay Flora 
Published: November 2022

Abstract

Motivation
We present dnadna, a flexible python-based software for deep learning inference in population genetics. It is task-agnostic and aims at facilitating the development, reproducibility, dissemination and re-usability of neural networks designed for population genetic data.

Results
dnadna defines multiple user-friendly workflows. First, users can implement new architectures and tasks, while benefiting from dnadna utility functions, training procedure and test environment, which saves time and decreases the likelihood of bugs. Second, the implemented networks can be re-optimized based on user-specified training sets and/or tasks. Newly implemented architectures and pre-trained networks are easily shareable with the community for further benchmarking or other applications. Finally, users can apply pre-trained networks in order to predict evolutionary history from alternative real or simulated genetic datasets, without requiring extensive knowledge in deep learning or coding in general. dnadna comes with a peer-reviewed, exchangeable neural network, allowing demographic inference from SNP data, that can be used directly or retrained to solve other tasks. Toy networks are also available to ease the exploration of the software, and we expect that the range of available architectures will keep expanding thanks to community contributions.

Availability and implementation
dnadna is a Python (≥3.7) package, its repository is available at gitlab.com/mlgenetics/dnadna and its associated documentation at mlgenetics.gitlab.io/dnadna/.
Border Region Attachment: An Empirical Study on Regional Social Capital in the French–German Border Area
Authors: Wiens Marcus , Klein Miriam , Schultmann Frank 
Published: November 2022

Abstract
In today’s globalized and interconnected world, international relationships are becoming ever more important. This applies not only to political relations but also to transnational attachment, a positive and solidary mutual attitude between the citizens of two countries, which is mainly based on social capital and trust. In particular border areas can benefit enormously when people have a bond with their neighboring country and its inhabitants. Due to their geographic proximity and historically shaped identity, border regions have a high potential for increased economic and social exchange. While empirical work on these characteristics of specific border areas is scarce, this article presents a novel approach which applies the concept of transnational social capital taking the French–German border area as an example. The representative study is based on telephone interviews, which were conducted in the border area and in regions within the two countries as a control for country-level effects. We find strong evidence for border region attachment in form of higher levels of social capital and trust in the border area. Our findings have important implications for borderland economies in general and in particular for cross-border resilience with regard to prevailing risks like upcoming nationalism and disasters such as the Covid-19 pandemic.
PNCTS: A Prediction and Network Coding-Based Transmission Scheme for Efficient Screen Updates Delivery in DaaS
Authors: Luo Qin , Cao Xin 
Published: November 2022

Abstract
Desktop as a Service (DaaS) provides users with flexible, customizable and highly secure cloud based virtual desktop access. As the major carrier of execution results in DaaS, screen updates play an important role in users’ quality of experience. In order to bring users the same feelings like manipulating a local device, timeliness and reliability should be balanced. However, a timely but unreliable transmission scheme (i.e. UDP) or a completely reliable transmission scheme (i.e. TCP) is inappropriate for such a transmission scenario, especially under a high-loss network. In this paper, we propose a Prediction and Network Coding based Transmission Scheme (PNCTS) for efficient screen updates delivery in DaaS. As an end-to-end partially reliable transmission scheme, it prioritizes different data obtained by partitioning screen updates and employs network coding and TFRC (TCP Friendly Rate Control) to compensate for data loss and adjust the sending rate of screen updates, respectively. To reduce the overhead of network coding, PNCTS uses a Hidden Markov Model to predict the reliability level of network and makes different encoding strategies for the data with different priorities. Simulation results show that PNCTS can improve display quality and instantaneous goodput effectively while maintaining end-to-end delay and jitter at a relatively low level under the static and time-varying network conditions.
Assessing the Suitability of Chinese Cabbage as an Alternative Host forSpodoptera frugiperda(Lepidoptera: Noctuidae)
Authors: Wu Meng-Ling , Zhao Hao-Yang , Liu Tong-Xian , Pan Ming-Zhen 
Published: November 2022

AbstractWhen the favored host of an herbivorous insect pest is absent, the availability of alternative host plants can maintain insect pest populations. Spodoptera frugiperda (Lepidoptera: Noctuidae) is a major invasive, polyphagous insect pest in China. To investigate the suitability of Chinese cabbage as an alternative host for S. frugiperda, oviposition preferences and life history traits were determined for S. frugiperda on Chinese cabbage, corn, and winter wheat over three generations. Results showed that S. frugiperda females preferred to lay their eggs on corn compared to winter wheat and Chinese cabbage. The survival rate of S. frugiperda decreased after switching from corn to Chinese cabbage, only 6% of individuals successfully pupated in the third generation. In addition, S. frugiperda reared on Chinese cabbage had lower pupal weight and fecundity. Winter wheat was a good host for S. frugiperda; although the survival rate decreased when S. frugiperda switched from corn to winter wheat in the parental generation, the survival rate increased over the next two generations to be as high as those reared on corn. Chinese cabbage is not a good long-term host for S. frugiperda, but it could maintain the pest population for at least two generations when more suitable host plants are unavailable. These results will inform management strategies for S. frugiperda.
Plasma Leptin Is Associated With Amyloid CSF Biomarkers and Alzheimer’s Disease Diagnosis in Cognitively Impaired Patients
Authors: Lilamand Matthieu , Bouaziz-Amar Elodie , Dumurgier Julien , Cognat Emmanuel , Hourregue Claire , Mouton-Liger François , Sanchez Manuel , Troussière Anne-Cécile , Martinet Matthieu , Hugon Jacques , Paquet Claire 
Published: November 2022

AbstractBackgroundMetabolic dysfunction and dysregulation of leptin signaling have been linked to Alzheimer’s disease (AD)’s pathophysiology. The objectives of this study were to examine the associations between plasma leptin, cerebrospinal fluid (CSF), beta-amyloid (Aβ), and tau biomarkers (AT[N] status) and with the stage of cognitive impairment.MethodsCross-sectional analysis of data from cognitively impaired patients from a tertiary memory clinic. Plasma leptin levels were compared according to the stage of cognitive impairment and biomarker profiles, using the AT(N) classification. Linear regression models were performed to examine the relationship between leptin and CSF biomarkers. Results were adjusted for age, gender, body mass index (BMI), and APOE ε4. In a subgroup of A+T+ individuals, we compared the 2-year evolution of Mini-Mental State Examination scores, according to the participants’ tertile of plasma leptin levels.ResultsWe included 1 036 participants (age 68.7 ± 9.1, females = 54.1%). A+T+ and A+T− patients had significantly lower plasma leptin levels than amyloid negative participants (p &lt; .01). CSF Aβ concentration was significantly associated with lower plasma leptin β = −4.3 (1.5), p = .005 unadjusted; and β = −3.4 (1.6), p = .03 after adjustment for age, female gender, BMI, and APOE ε4. Patients with major neurocognitive disorder due to AD had a difference of leptin of −7.3 ng/mL 95% confidence interval (CI; −11.8; −2.8), p = .0002, compared to individuals with other causes of cognitive impairment. Leptin was not associated with the slope of cognitive decline.ConclusionPlasma leptin levels were associated with CSF Aβ and with the diagnosis of AD confirmed by CSF biomarkers, suggesting a molecular interplay between leptin metabolism and brain amyloid deposition.
Effects of bamboo leaf extract on energy metabolism, antioxidant capacity, and biogenesis of small intestine mitochondria in broilers
Authors: Xie Zechen , Yu Ge , Yun Yang , Zhang Xin , Shen Mingming , Jia Minghui , Li Anqi , Zhang Hao , Wang Tian , Zhang Jingfei , Zhang Lili 
Published: November 2022

Abstract
The present study was carried out to investigate the effects of bamboo leaf extract (BLE) on energy metabolism, antioxidant capacity, and biogenesis of broilers’ small intestine mitochondria. A total of 384 one-day-old male Arbor Acres broiler chicks were randomly divided into four groups with six replicates each for 42 d. The control group was fed a basal diet, whereas the BLE1, BLE2, and BLE3 groups consumed basal diets with 1.0, 2.0, and 4.0 g/kg of BLE, respectively. Some markers of mitochondrial energy metabolism including isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and malate dehydrogenase and some markers of redox system including total superoxide dismutase, malondialdehyde, and glutathione were measured by commercial colorimetric kits. Mitochondrial and cellular antioxidant genes, mitochondrial biogenesis-related genes, and mitochondrial DNA copy number were measured by quantitative real-time-polymerase chain reaction (qRT-PCR). Data were analyzed using the SPSS 19.0, and differences were considered as significant at P &lt; 0.05. BLE supplementation linearly increased jejunal mitochondrial isocitrate dehydrogenase (P &lt; 0.05) and total superoxide dismutase (P &lt; 0.05) activity. The ileal manganese superoxide dismutase mRNA expression was linearly affected by increased dietary BLE supplementation (P &lt; 0.05). Increasing BLE supplementation linearly increased jejunal sirtuin 1 (P &lt; 0.05) and nuclear respiratory factor 1 (P &lt; 0.05) mRNA expression. Linear (P &lt; 0.05) and quadratic (P &lt; 0.05) responses of the ileal nuclear respiratory factor 2 mRNA expression occurred with increased dietary BLE levels. In conclusion, BLE supplementation was beneficial to the energy metabolism, antioxidant capacity, and biogenesis of small intestine mitochondria in broilers. The dose of 4.0 g/kg BLE demonstrated the best effects.
Should we treatBlastocystissp.? A double-blind placebo-controlled randomized pilot trial
Authors: Cobuccio Ludovico Gennaro , Laurent Marie , Gardiol Celine , Wampfler Rahel , Poppert Sven , Senn Nicolas , Eperon Gilles , Genton Blaise , Locatelli Isabella , de Vallière Serge 
Published: November 2022

AbstractBackgroundBlastocystis sp. is a worldwide-distributed protist colonizing the guts of humans and a great variety of animals. It is unclear whether it is just a commensal or an infectious parasite that prompts eradication.The main objective of this study was to evaluate the usefulness of metronidazole in patients with gastrointestinal symptoms harbouring only Blastocystis sp. In addition, we explored whether Blastocystis subtype or concomitant parasitic infection detected by polymerase chain reaction (PCR) may influence treatment outcome.MethodsWe included adults with persistent gastrointestinal symptoms (&gt;14 days) visiting a primary care physician and in whom stool microscopy revealed only Blastocystis sp. Eligible patients were randomized to receive 10 days of metronidazole or placebo, followed by a crossover if still symptomatic. The primary outcome was normal stool consistency. Secondary outcomes were the changes in other abdominal symptoms (bloating, flatulence, abdominal pain, number of daily bowel movements) and general wellbeing. After the clinical phase of the study, Blastocystis subtypes were determined by PCR sequencing and stool samples were tested for 11 other protozoa with an in-house PCR.ResultsWe screened 581 outpatients for inclusion, of which 50 met the eligibility criteria. There was no difference in the primary outcome, nor any of the secondary outcomes between the subjects treated with metronidazole and placebo.The most frequent Blastocystis subtypes were ST4 (11/36) and ST2 (10/36). The in-house PCR was positive for other protozoa in 25% (10/40) of the patients. We identified Dientamoeba fragilis in 5, Entamoeba dispar in 3 and Cyclospora cayetanensis in 2 patients. Stratified analysis according to Blastocystis subtype or the presence of other protozoa showed no significant difference in treatment outcome with metronidazole or placebo.ConclusionsAmong patients infected with Blastocystis sp., metronidazole, compared with placebo, was not better in improving gastrointestinal symptoms, irrespective of subtype or microscopically undetected coinfection with other protozoa.
Long-Term Follow-up of Human Immunodeficiency Virus-Associated Pulmonary Hypertension: Clinical Features and Survival Outcomes of the Pan Africa Pulmonary Hypertension Cohort (PAPUCO)
Authors: Thienemann Friedrich , Katoto Patrick D M C , Azibani Feriel , Kodogo Vitaris , Mukasa Sandra L , Sani Mahmoud U , Karaye Kamilu M , Mbanze Irina , Mocumbi Ana O , Dzudie Anastase , Sliwa Karen 
Published: November 2022

Abstract

Background
Data characterizing risk factors and long-term outcome studies on human immunodeficiency virus (HIV)-associated pulmonary hypertension (PH) in Africa are lacking.

Methods
The Pan African Pulmonary Hypertension Cohort, a multinational registry of 254 consecutive patients diagnosed with PH (97% of African descent) from 9 centers in 4 African countries was implemented. We compared baseline characteristics and 3-year survival of an HIV-infected cohort newly diagnosed with PH (PH/HIV+) to an HIV-uninfected cohort with PH (PH/HIV−).

Results
One hundred thirty-four participants with PH completed follow up (47 PH/HIV+ and 87 PH/HIV−; age median, 36 versus 44 years; P = .0004). Cardiovascular risk factors and comorbidities were similar except for previous tuberculosis (62% versus 18%, P &lt; .0001). Six-minute walk distance (6MWD) &lt;300 meters was common in PH/HIV− (P = .0030), but PH/HIV+ had higher heart (P = .0160) and respiratory (P = .0374) rates. Thirty-six percent of PH/HIV+ and 15% of PH/HIV− presented with pulmonary arterial hypertension (PAH) (P = .0084), whereas 36% of PH/HIV+ and 72% of PH/HIV− exhibited PH due to left heart disease (PHLHD) (P = .0009). Pulmonary hypertension due to lung diseases and hypoxia (PHLD) was frequent in PH/HIV+ (36% versus 15%) but did not reach statistical significance. Human immunodeficiency virus-associated PAH tended to have a poorer survival rate compared with PHLHD/PHLD in HIV-infected patients.

Conclusions
The PH/HIV + patients were younger and commonly had previous tuberculosis compared to PH/HIV− patients. Despite a better 6MWD at presentation, they had more signs and symptoms of early onset heart failure and a worse survival rate. Early echocardiography assessment should be performed in HIV-infected patients with history of tuberculosis who present with signs and symptoms of heart failure or posttuberculosis lung disease.
Emission characteristics of gadolinium ions in a water Cherenkov detector
Authors: Iwata Y , Sekiya H , Ito C 
Published: November 2022

Abstract
To observe supernova relic neutrino events, 13 tons of gadolinium sulfate octahydrate (Gd2(SO4)3·8H2O), corresponding to 0.01% Gd solution, was dissolved in the Super-Kamiokande water Cherenkov detector in 2020. The aim is to improve the detection efficiency of neutrons from inverse β decay involving electron antineutrinos. However, Gd3+ ions can be excited by the Cherenkov light from cosmic muons, and the subsequent emission at 312 nm is a possible background (BG) source for Cherenkov signal detection. In this work, we constructed an experimental setup based on time-resolved laser-induced luminescence spectroscopy to investigate the emission characteristics of Gd3+ ions in water. The excitation laser wavelength was tuned in the range of 245–255 nm, and large resonant peaks were observed at 246.2 nm and 252.3 nm with measured emission lifetimes of around 3 ms. Good linearity was observed between Gd concentration and emission intensity for these two wavelengths, indicating that our setup is useful for remote monitoring of Gd concentration. According to the simulation results using our spectroscopic data and reference values, the Gd3+ emission BG rate from cosmic muons is expected to be 10−1 counts/μs or less, which seems small but not negligible.
A comprehensive study of the vector leptoquark with U(1)B3-L2 on the B-meson and muon g − 2 anomalies
Authors: Ban Kayoung , Jho Yongsoo , Kwon Youngjoon , Park Seong Chan , Park Seokhee , Tseng Po-Yan 
Published: November 2022

Abstract
Recently reported anomalies in various B-meson decays and also in the anomalous magnetic moment of muon (g − 2)μ motivate us to consider a particular extension of the standard model incorporating new interactions in the lepton and quark sectors simultaneously. Our minimal choice would be the leptoquark. In particular, we take the vector leptoquark (U1) and comprehensively study all related observables including ${(g-2)_{\mu }},\ R_{K^{(*)}},\ R_{D^{(*)}}$, B → (K)ℓℓ′, where ℓℓ′ are various combinations of μ and τ, and also lepton flavor violation in the τ decays. We find that a hybrid scenario with an additional $U(1)_{B_3-L_2}$ gauge boson provides a common explanation for all these anomalies.
Can agricultural policy achieve environmental goals through an indicator-based direct payment system?
Authors: Gilgen Anina , Drobnik Thomas , Mann Stefan , Flury Christian , Mack Gabriele , Ritzel Christian , Roesch Andreas , Gaillard Gérard 
Published: November 2022

Abstract
Indicator-based frameworks for assessing farms’ environmental performance have become a resource for environmental knowledge regarding the impacts of agricultural practices. The present study explores whether a novel indicator-based direct payment system, which focuses on the farms’ environmental impact, could better target Swiss agricultural policy and help achieve its environmental goals. The system covers the environmental topics of biodiversity, nutrients and climate, plant protection products, and soil. Despite high direct payments, simulations with an agent-based agricultural sector model show that such indicator-based payments have a limited impact. For example, the decrease in the animal population is only moderate. Though direct payments alone can hardly lead to the desired reduction in Switzerland's environmental pollution, they could help make important contributions to a more targeted distribution of environmentally oriented direct payments and steer agricultural production in a more environmentally friendly way.
Measuring quality of gout management in residential aged care facilities
Authors: Nguyen Amy D , Lind Kimberly E , Day Richard O , Ross Daniel , Raban Magdalena Z , Georgiou Andrew , Westbrook Johanna I 
Published: November 2022

Abstract

Objective
Gout, a common form of arthritis, can be controlled successfully with pharmacotherapy and is thus an ideal model for examining chronic disease management. Our aim was to examine treatment of gout evaluated in accordance with general management guidelines for gout as applied to Australian residential aged care facilities.

Methods
Electronic health record data linked with aged care clinical notes and electronic medication administration information (11 548 residents in 68 residential aged care facilities, &gt;65 years of age) were interrogated to identify people with gout, other chronic conditions and gout medication use. The outcomes examined were the proportion receiving urate-lowering therapy (ULT; preventative medication) and/or colchicine/non-steroidal anti-inflammatory drug (NSAID) (to treat gout flares), the number of ULT and colchicine/NSAID treatment episodes (periods of continuous days of medication use) and the duration of these treatment episodes.

Results
The cohort included 1179 residents with gout, of whom 62% used a ULT, with a median of one episode of use for a very short duration [median = 4 days, median of use in total (i.e. repeated use) = 52 days]. Among residents with gout, 9% also used colchicine or an NSAID. Female residents were less likely to receive ULT and for shorter periods.

Conclusion
Nearly one-third of residents with gout did not receive ULT. In those receiving ULT, recurrent short courses were common. Overall, management of gout in aged care residents appears to be suboptimal, largely owing to intermittent and short exposure to ULT, and with female residents at greater risk of poor gout management.