bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurocognitive status and risk of mortality among people living with human immunodeficiency virus: an 18-year retrospective cohort study
Authors: Naveed Zaeema , Fox Howard S. , Wichman Christopher S. , Alam Morshed , May Pamela , Arcari Christine M. , Meza Jane , Totusek Steven , Baccaglini Lorena 
Published: February 2021

AbstractHIV-related neurocognitive impairment (NCI) may increase the risk of death. However, a survival disadvantage for patients with NCI has not been well studied in the post-combination antiretroviral therapy (cART) era. Specifically, limited research has been conducted considering the reversible nature and variable progression of the impairment and this area demands further evaluation. We performed multivariable Cox proportional hazards modeling to assess the association between baseline NCI (global T scores) and mortality. A joint modeling approach was then used to model the trajectory of global neurocognitive functioning over time and the association between neurocognitive trajectory and mortality. Among the National NeuroAIDS Tissue Consortium’s (NNTC) HIV-infected participants, we found a strong negative association between NCI and mortality in the older age groups (e.g., at age = 55, HR = 0.79; 95% CI 0.64–0.99). Three neurocognitive sub-domains (abstraction and executive functioning, speed of information processing, and motor) had the strongest negative association with mortality. Joint modelling indicated a 33% lower hazard for every 10-unit increase in global T scores (HR = 0.67; 95% CI 0.56–0.80). The study identified older HIV-infected individuals with NCI as a group needing special attention for the longevity of life. The study has considerable prognostic utility by not only predicting mortality hazard, but also future cognitive status.
Investigation of skin microbiota reveals Mycobacterium ulcerans-Aspergillus sp. trans-kingdom communication
Authors: Hammoudi N. , Cassagne C. , Million M. , Ranque S. , Kabore O. , Drancourt M. , Zingue D. , Bouam A. 
Published: February 2021

AbstractMycobacterium ulcerans secrete a series of non-ribosomal-encoded toxins known as mycolactones that are responsible for causing a disabling ulceration of the skin and subcutaneous tissues named Buruli ulcer. The disease is the sole non-contagion among the three most common mycobacterial diseases in humans. Direct contact with contaminated wetlands is a risk factor for Buruli ulcer, responsible for M. ulcerans skin carriage before transcutaneous inoculation with this opportunistic pathogen. In this study, we analysed the bacterial and fungal skin microbiota in individuals exposed to M. ulcerans in Burkina Faso. We showed that M. ulcerans-specific DNA sequences were detected on the unbreached skin of 6/52 (11.5%) asymptomatic farmers living in Sindou versus 0/52 (0%) of those living in the non-endemic region of Tenkodogo. Then, we cultured the skin microbiota of asymptomatic M. ulcerans carriers and negative control individuals, all living in the region of Sindou. A total of 84 different bacterial and fungal species were isolated, 21 from M. ulcerans-negative skin samples, 31 from M. ulcerans-positive samples and 32 from both. More specifically, Actinobacteria, Aspergillus niger and Aspergillus flavus were significantly associated with M. ulcerans skin carriage. We further observed that in vitro, mycolactones induced spore germination of A. flavus, attracting the fungal network. These unprecedented observations suggest that interactions with fungi may modulate the outcome of M. ulcerans skin carriage, opening new venues to the understanding of Buruli ulcer pathology, prophylaxis and treatment of this still neglected tropical infection.
Ingestion of probiotic (Lactobacillus helveticus and Bifidobacterium longum) alters intestinal microbial structure and behavioral expression following social defeat stress
Authors: Partrick Katherine A. , Rosenhauer Anna M. , Auger Jérémie , Arnold Amanda R. , Ronczkowski Nicole M. , Jackson Lanaya M. , Lord Magen N. , Abdulla Sara M. , Chassaing Benoit , Huhman Kim L. 
Published: February 2021

AbstractSocial stress exacerbates anxious and depressive behaviors in humans. Similarly, anxiety- and depressive-like behaviors are triggered by social stress in a variety of non-human animals. Here, we tested whether oral administration of the putative anxiolytic probiotic strains Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 reduces the striking increase in anxiety-like behavior and changes in gut microbiota observed following social defeat stress in Syrian hamsters. We administered the probiotic at two different doses for 21 days, and 16S rRNA gene amplicon sequencing revealed a shift in microbial structure following probiotic administration at both doses, independently of stress. Probiotic administration at either dose increased anti-inflammatory cytokines IL-4, IL-5, and IL-10 compared to placebo. Surprisingly, probiotic administration at the low dose, equivalent to the one used in humans, significantly increased social avoidance and decreased social interaction. This behavioral change was associated with a reduction in microbial richness in this group. Together, these results demonstrate that probiotic administration alters gut microbial composition and may promote an anti-inflammatory profile but that these changes may not promote reductions in behavioral responses to social stress.
Inclusion of genetic variants in an ensemble of gradient boosting decision trees does not improve the prediction of citalopram treatment response
Authors: Shumake Jason , Mallard Travis T. , McGeary John E. , Beevers Christopher G. 
Published: February 2021

AbstractIdentifying in advance who is unlikely to respond to a specific antidepressant treatment is crucial to precision medicine efforts. The current work leverages genome-wide genetic variation and machine learning to predict response to the antidepressant citalopram using data from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) trial (n = 1257 with both valid genomic and outcome data). A confirmatory approach selected 11 SNPs previously reported to predict response to escitalopram in a sample different from the current study. A novel exploratory approach selected SNPs from across the genome using nested cross-validation with elastic net logistic regression with a predominantly lasso penalty (alpha = 0.99). SNPs from each approach were combined with baseline clinical predictors and treatment response outcomes were predicted using a stacked ensemble of gradient boosting decision trees. Using pre-treatment clinical and symptom predictors only, out-of-fold prediction of a novel treatment response definition based on STAR*D treatment guidelines was acceptable, AUC = .659, 95% CI [0.629, 0.689]. The inclusion of SNPs using confirmatory or exploratory selection methods did not improve the out-of-fold prediction of treatment response (AUCs were .662, 95% CI [0.632, 0.692] and .655, 95% CI [0.625, 0.685], respectively). A similar pattern of results were observed for the secondary outcomes of the presence or absence of distressing side effects regardless of treatment response and achieving remission or satisfactory partial response, assuming medication tolerance. In the current study, incorporating SNP variation into prognostic models did not enhance the prediction of citalopram response in the STAR*D sample.
Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
Authors: Sjaarda Calvin P. , Rustom Nazneen , Evans Gerald A. , Huang David , Perez-Patrigeon Santiago , Hudson Melissa L. , Wong Henry , Sun Zhengxin , Guan T. Hugh , Ayub Muhammad , Soares Claudio N. , Colautti Robert I. , Sheth Prameet M. 
Published: February 2021

AbstractThe emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18–30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.
Chitosan increases Pinus pinaster tolerance to the pinewood nematode (Bursaphelenchus xylophilus) by promoting plant antioxidative metabolism
Authors: Nunes da Silva Marta , Santos Carla S. , Cruz Ana , López-Villamor Adrián , Vasconcelos Marta W. 
Published: February 2021

AbstractThe pine wilt disease (PWD), for which no effective treatment is available at the moment, is a constant threat to Pinus spp. plantations worldwide, being responsible for significant economic and environmental losses every year. It has been demonstrated that elicitation with chitosan increases plant tolerance to the pinewood nematode (PWN) Bursaphelenchus xylophilus, the causal agent of the PWD, but the biochemical and genetic aspects underlying this response have not been explored. To understand the influence of chitosan in Pinus pinaster tolerance against PWN, a low-molecular-weight (327 kDa) chitosan was applied to mock- and PWN-inoculated plants. Nematode population, malondialdehyde (MDA), catalase, carotenoids, anthocyanins, phenolic compounds, lignin and gene expression related to oxidative stress (thioredoxin 1, TRX) and plant defence (defensin, DEF, and a-farnesene synthase, AFS), were analysed at 1, 7, 14, 21 and 28 days post-inoculation (dpi). At 28 dpi, PWN-infected plants elicited with chitosan showed a sixfold lower nematode population when compared to non-elicited plants. Higher levels of MDA, catalase, carotenoids, anthocyanins, phenolic compounds, and lignin were detected in chitosan-elicited plants following infection. The expression levels of DEF gene were higher in elicited plants, while TRX and AFS expression was lower, possibly due to the disease containment-effect of chitosan. Combined, we conclude that chitosan induces pine defences against PWD via modulation of metabolic and transcriptomic mechanisms related with plant antioxidant system.
Midgut development in rat embryos using microcomputed tomography
Authors: Ginzel Marco , Martynov Illya , Haak Rainer , Lacher Martin , Kluth Dietrich 
Published: February 2021

AbstractThe development of the mammalian gut was first described more than a century ago. Since then, it has been believed that a series of highly orchestrated developmental processes occur before the intestine achieves its final formation. The key steps include the formation of the umbilicus, the so-called “physiological herniation” of the midgut into the umbilical cord, an intestinal “rotation”, and the “return of the gut” into the abdominal cavity. However, this sequence of events is predominantly based on histological sections of dissected embryos, a 2D technique with methodological limitations. For a better understanding of spatial relationships in the embryo, we utilized microcomputed tomography (µCT), a nondestructive 3D imaging method. Here, we show the detailed processes and mechanisms of intestinal development in rat embryos, including the development of the umbilicus, the formation of loops inside the umbilical coelom, and the subsequent shift of these loops into the abdominal cavity. Our 3D datasets of developing intestines will substantially advance the understanding of normal mammalian midgut embryology and offer new possibilities to reveal unknown mechanisms in the pathogenesis of congenital disorders.
Mitochondrial ubiquitin ligase alleviates Alzheimer’s disease pathology via blocking the toxic amyloid-β oligomer generation
Authors: Takeda Keisuke , Uda Aoi , Mitsubori Mikihiro , Nagashima Shun , Iwasaki Hiroko , Ito Naoki , Shiiba Isshin , Ishido Satoshi , Matsuoka Masaaki , Inatome Ryoko , Yanagi Shigeru 
Published: February 2021

AbstractMitochondrial pathophysiology is implicated in the development of Alzheimer’s disease (AD). An integrative database of gene dysregulation suggests that the mitochondrial ubiquitin ligase MITOL/MARCH5, a fine-tuner of mitochondrial dynamics and functions, is downregulated in patients with AD. Here, we report that the perturbation of mitochondrial dynamics by MITOL deletion triggers mitochondrial impairments and exacerbates cognitive decline in a mouse model with AD-related Aβ pathology. Notably, MITOL deletion in the brain enhanced the seeding effect of Aβ fibrils, but not the spontaneous formation of Aβ fibrils and plaques, leading to excessive secondary generation of toxic and dispersible Aβ oligomers. Consistent with this, MITOL-deficient mice with Aβ etiology exhibited worsening cognitive decline depending on Aβ oligomers rather than Aβ plaques themselves. Our findings suggest that alteration in mitochondrial morphology might be a key factor in AD due to directing the production of Aβ form, oligomers or plaques, responsible for disease development.
Fast and sensitive diffuse correlation spectroscopy with highly parallelized single photon detection
Authors: Liu Wenhui , Qian Ruobing , Xu Shiqi , Chandra Konda Pavan , Jönsson Joakim , Harfouche Mark , Borycki Dawid , Cooke Colin , Berrocal Edouard , Dai Qionghai , Wang Haoqian , Horstmeyer Roarke 
Published: February 2021

Diffuse correlation spectroscopy (DCS) is a well-established method that measures rapid changes in scattered coherent light to identify blood flow and functional dynamics within a tissue. While its sensitivity to minute scatterer displacements leads to a number of unique advantages, conventional DCS systems become photon-limited when attempting to probe deep into the tissue, which leads to long measurement windows (∽1 sec). Here, we present a high-sensitivity DCS system with 1024 parallel detection channels integrated within a single-photon avalanche diode array and demonstrate the ability to detect mm-scale perturbations up to 1 cm deep within a tissue-like phantom at up to a 33 Hz sampling rate. We also show that this highly parallelized strategy can measure the human pulse at high fidelity and detect behaviorally induced physiological variations from above the human prefrontal cortex. By greatly improving the detection sensitivity and speed, highly parallelized DCS opens up new experiments for high-speed biological signal measurement.
A single historical substitution drives an increase in acetylcholine receptor complexity
Authors: Emlaw Johnathon R. , Tessier Christian J. G. , McCluskey Gregory D. , McNulty Melissa S. , Sheikh Yusuf , Burkett Kelly M. , Musgaard Maria , daCosta Corrie J. B. 
Published: February 2021

Significance
Human muscle-type acetylcholine receptors are heteropentameric ion channels formed from four evolutionarily related subunits, which assemble with a specific stoichiometry and arrangement. It has long been thought that each of the modern-day subunits are required for function. We dispel this notion by first showing that an ancestral β-subunit can replace both the β- and δ-subunits in human acetylcholine receptors. We then identify a single historical amino acid substitution that eliminates the ability of the ancestral β-subunit to functionally replace the human δ-subunit. Our work experimentally demonstrates how acetylcholine receptor subunit complexity could have evolved and uncovers a form of contingency that is unique to heteromeric protein complexes, in which mutations that “lock in” individual subunits determine future evolutionary paths.
Design of A Freight Transport System for Highway Rest Areas
Authors: Wen Hao , Liu Yufeng , Lu Sichao , Fei Su 
Published: February 2021

Abstract
The rest area is an important place for travelers to have a rest. Therefore, it should be replenished with a variety of goods in time. This article introduces a freight transport system for highway rest areas, including conceptual framework, a mathematical model and its algorithm. The model has two objective functions which aim to minimize transport time as well as maximizing the priority value of highway rest areas. To solve this multi-objective optimization problem, a discrete firefly algorithm which was proposed to solve the multi-temperature joint distribution is extended. To validate the performance of the algorithm, simulation experiments are carried out and the experimental results show that the discrete firefly algorithm is effective for the problem.
Air traffic complexity evaluation with novel complexity features and mRMR-XGBoost
Authors: Zhang Minghua , xie Hua , Ge Jiaming , Zhang Dongfang 
Published: February 2021

Abstract
Air traffic complexity evaluation is a critical problem in air traffic system operation, especially for air traffic safety and air traffic controller deployment. Many researches focus on using mathematical modeling or machine learning methods to evaluate air traffic complexity. However, there are still challenges in accurate evaluation, which is affected by lack of effective complexity related features and complicated feature-complexity relationship. Based on the existing complexity features, this paper proposes additional domain features, time-dependent features and data distribution features to construct a novel air traffic complexity feature set. A mRMR method for feature selection is then applied to filter out redundant features. Finally, the filtered feature set and corresponding air traffic complexity level are input into XGBoost model for learning the relationship, so as to achieve high-performance evaluation of air traffic complexity in the face of new air traffic data. The experimental results show that the proposed features are beneficial to the evaluation of air traffic complexity, and the XGBoost model with mRMR method can effectively select the important features and mine the relationships within air traffic complexity data, resulting in an improvement in overall evaluation performance by at least 5% while using less than half of the original number of features.
Safety Level Analysis of Waterway Traffic Based on Trend Test in the Yangtze River
Authors: Wang Guobo , Hu Yahan , Hu Yuchang 
Published: February 2021

Abstract
In order to improve the safety of waterway traffic in the Yangtze River, comprehensively integrate the current status of waterway traffic safety at home and abroad. Analogy and MK trend analysis methods are used to analyze the current status and development trend of safety level of waterway traffic in the Yangtze River. The results show that there are significant differences in F-N indicators for waterway traffic safety in different countries. The U.S. has an outstanding ability to respond quickly to accidents, and can maintain a low level of F-N indicators even with a large number of accidents. The safety level of waterway traffic in the Yangtze River is relatively low. In particular, there is still a big gap of the rescue capability between China and developed countries. The safety level of water traffic on the Yangtze River is constantly improving, and the changing trend of waterway traffic safety level shows a more significant growth.
Compare between rotational and translational seismic response spectra
Authors: Liu YueWei , Zheng JingYun , Wu Zhitang 
Published: February 2021

Abstract
Rotational response spectra are still absent due to the substantial lack of direct measurements of rotational seismic waves. The work develops a relationship between rotational response spectra and translational ones. By the elastic wave theory, seismic rotations can be calculated form translational waves. In this paper, 113 translational waves are used to calculating rotational waves. And then the translational response spectra and rotational response spectra are calculated and compared. Factors such as the site condition and frequency are considered. The results show that from lower frequency to higher frequency, the ratio of normalized response spectra between rotational and translational waves increases. The ratios are also related to the site condition.
Analysis and Prediction of Subway Settlement Deformation Based on Grey Model
Authors: Shufen Zheng , Jing Wen 
Published: February 2021

Abstract
In this paper, the monitoring data of settlement and deformation along the western section of a metro in H city are collated and analyzed, the actual situation of settlement and deformation is grasped, and the long-term settlement and deformation trend are predicted by using grey prediction model. In the process of forecasting, a non-equidistant grey forecasting model is established by using the data of the first several groups of monitoring points, and the predicted values are compared with the last group of monitoring data to verify the reliability of the model and further optimize the model. Then, the optimized model is used to predict the long-term settlement deformation of the subway, which provides a basis for the deformation control and management of the subway.
Study on blasting vibration characteristics of metro tunnel based on wavelet packet technology
Authors: Jiang Shibin , Zhao Chen , Gao Shang , Ji Xinyu , Lv Xianpeng , Sun Hao , Chen Jihui 
Published: February 2021

Abstract
Wavelet packet technology has been widely applied in the study on blasting vibration transmission law of overlapping tunnels. The previous research focused on vibration transmission law of the distant area---a range more than 20m, but for the close area---a range less than 10m, research seldom has been carried out. Therefore, this paper, based on a overlapping tunnel project in Qingdao, reveals the blasting vibration transmission law of the close field as well as how the numbers of free surfaces affect the law. Firstly, at the site,the blasting vibration data both in front and rear of the working faces including the cutting area (a free face) and the spreading area (two free faces) in a newly-built tunnel are obtained; Secondly, the wavelet packet technology is applied to analyze the data of blasting vibration frequency and energy distribution characteristics. Finally, it is concluded that different free facing with different numbers can lead to different main frequency distribution range and different law of main frequency band changing with distance when blasting vibration transmit within the close field; and the vibration signal energy in front and rear of the working face in cutting area and spreading area is differently distributed in the directions of 3 channels. Combining blasting vibration signal frequence with energy factors, this paper puts forward the constructive suggestions on the safety protection of existing tunnels and provides reference for studying the law of blasting vibration transmission of overlapping tunnels.
CLC classification number: 0389 TD235 Document identification code: A