bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school
Authors: Scott Pippa , Zhang Ji , Anderson Trevor , Priest Patricia C. , Chambers Stephen , Smith Helen , Murdoch David R. , French Nigel , Biggs Patrick J. 
Published: October 2021

AbstractEpidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of “allelic differences”. We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.
On the statistical significance of communities from weighted graphs
Authors: He Zengyou , Chen Wenfang , Wei Xiaoqi , Liu Yan 
Published: October 2021

AbstractCommunity detection is a fundamental procedure in the analysis of network data. Despite decades of research, there is still no consensus on the definition of a community. To analytically test the realness of a candidate community in weighted networks, we present a general formulation from a significance testing perspective. In this new formulation, the edge-weight is modeled as a censored observation due to the noisy characteristics of real networks. In particular, the edge-weights of missing links are incorporated as well, which are specified to be zeros based on the assumption that they are truncated or unobserved. Thereafter, the community significance assessment issue is formulated as a two-sample test problem on censored data. More precisely, the Logrank test is employed to conduct the significance testing on two sets of augmented edge-weights: internal weight set and external weight set. The presented approach is evaluated on both weighted networks and un-weighted networks. The experimental results show that our method can outperform prior widely used evaluation metrics on the task of individual community validation.
Slow deep breathing modulates cardiac vagal activity but does not affect peripheral glucose metabolism in healthy men
Authors: Vosseler Andreas , Zhao Dongxing , Hummel Julia , Gholamrezaei Ali , Hudak Sarah , Kantartzis Konstantinos , Peter Andreas , Birkenfeld Andreas L. , Häring Hans-Ulrich , Wagner Robert , Preißl Hubert , Kullmann Stephanie , Heni Martin 
Published: October 2021

AbstractParasympathetic nervous system innervates peripheral organs including pancreas, hepatic portal system, and gastrointestinal tract. It thereby contributes to the regulation of whole-body glucose metabolism especially in the postprandial state when it promotes secretion of insulin and enhances its action in major target organs. We now aimed to evaluate the effect of parasympathetic modulation on human glucose metabolism. We used slow deep breathing maneuvers to activate the parasympathetic nervous system and tested for effects on metabolism during an oral glucose tolerance test in a randomized, controlled, cross-over trial in 15 healthy young men. We used projections towards the heart as a readout for parasympathetic activity. When analyzing heart rate variability, there was a significant increase of RMSSD (root mean square of successive differences) when participants performed slow deep breathing compared to the control condition, indicating a modulation of parasympathetic activity. However, no statistically significant effects on peripheral glucose metabolism or energy expenditure after the glucose tolerance test were detected. Of note, we detected a significant association between mean heart rate and serum insulin and C-peptide concentrations. While we did not find major effects of slow deep breathing on glucose metabolism, our correlational results suggest a link between the autonomic nervous system and insulin secretion after oral glucose intake. Future studies need to unravel involved mechanisms and develop potential novel treatment approaches for impaired insulin secretion in diabetes.
Weakly supervised learning for classification of lung cytological images using attention-based multiple instance learning
Authors: Teramoto Atsushi , Kiriyama Yuka , Tsukamoto Tetsuya , Sakurai Eiko , Michiba Ayano , Imaizumi Kazuyoshi , Saito Kuniaki , Fujita Hiroshi 
Published: October 2021

AbstractIn cytological examination, suspicious cells are evaluated regarding malignancy and cancer type.
To assist this, we previously proposed an automated method based on supervised learning that classifies cells in lung cytological images as benign or malignant. However, it is often difficult to label all cells. In this study, we developed a weakly supervised method for the classification of benign and malignant lung cells in cytological images using attention-based deep multiple instance learning (AD MIL). Images of lung cytological specimens were divided into small patch images and stored in bags. Each bag was then labeled as benign or malignant, and classification was conducted using AD MIL. The distribution of attention weights was also calculated as a color map to confirm the presence of malignant cells in the image. AD MIL using the AlexNet-like convolutional neural network model showed the best classification performance, with an accuracy of 0.916, which was better than that of supervised learning. In addition, an attention map of the entire image based on the attention weight allowed AD MIL to focus on most malignant cells. Our weakly supervised method automatically classifies cytological images with acceptable accuracy based on supervised learning without complex annotations.
Fibrinolytic system activation immediately following trauma was quickly and intensely suppressed in a rat model of severe blunt trauma
Authors: Hayakawa Mineji , Tsuchida Takumi , Honma Yoshinori , Mizugaki Asumi , Ooyasu Takayoshi , Yoshida Tomonao , Saito Tomoyo , Katabami Kenichi , Wada Takeshi , Maekawa Kunihiko 
Published: October 2021

AbstractIn severe trauma, excessive fibrinolytic activation is associated with an increase in the transfusion volume and mortality rate. However, in the first several hours after a blunt trauma, changes in fibrinolytic activation, suppression, and activation–suppression balance have not yet been elucidated, which the present study aimed to clarify. Anesthetized 9-week-old male Wistar S/T rats experienced severe blunt trauma while being placed inside the Noble–Collip drum. Rats were randomly divided into four groups of seven. The no-trauma group was not exposed to any trauma; the remaining groups were analysed 0, 60, and 180 min after trauma. Immediately following trauma, total tissue-plasminogen activator (tPA) levels significantly increased in the plasma, and the balance of active tPA and active plasminogen activator inhibitor-1 (PAI-1) significantly tipped toward fibrinolytic activation. After trauma, both tPA and PAI-1 levels increased gradually in various organs and active and total PAI-1 levels increased exponentially in the plasma. Total plasma tPA levels 60 min after trauma returned quickly to levels comparable to those in the no-trauma group. In conclusion, fibrinolytic activation was observed only immediately following trauma. Therefore, immediately after trauma, the fibrinolytic system was activated; however, its activation was quickly and intensely suppressed.
Plasma lipidomic profiles of kidney, breast and prostate cancer patients differ from healthy controls
Authors: Wolrab Denise , Jirásko Robert , Peterka Ondřej , Idkowiak Jakub , Chocholoušková Michaela , Vaňková Zuzana , Hořejší Karel , Brabcová Ivana , Vrána David , Študentová Hana , Melichar Bohuslav , Holčapek Michal 
Published: October 2021

AbstractEarly detection of cancer is one of the unmet needs in clinical medicine. Peripheral blood analysis is a preferred method for efficient population screening, because blood collection is well embedded in clinical practice and minimally invasive for patients. Lipids are important biomolecules, and variations in lipid concentrations can reflect pathological disorders. Lipidomic profiling of human plasma by the coupling of ultrahigh-performance supercritical fluid chromatography and mass spectrometry is investigated with the aim to distinguish patients with breast, kidney, and prostate cancers from healthy controls. The mean sensitivity, specificity, and accuracy of the lipid profiling approach were 85%, 95%, and 92% for kidney cancer; 91%, 97%, and 94% for breast cancer; and 87%, 95%, and 92% for prostate cancer. No association of statistical models with tumor stage is observed. The statistically most significant lipid species for the differentiation of cancer types studied are CE 16:0, Cer 42:1, LPC 18:2, PC 36:2, PC 36:3, SM 32:1, and SM 41:1 These seven lipids represent a potential biomarker panel for kidney, breast, and prostate cancer screening, but a further verification step in a prospective study has to be performed to verify clinical utility.
National-scale changes in crop diversity through the Anthropocene
Authors: Mariani Rachel O. , Cadotte Marc W. , Isaac Marney E. , Vile Denis , Violle Cyrille , Martin Adam R. 
Published: October 2021

AbstractExpansion of crops beyond their centres of domestication is a defining feature of the Anthropocene Epoch. This process has fundamentally altered the diversity of croplands, with likely consequences for the ecological functioning and socio-economic stability of agriculture under environmental change. While changes in crop diversity through the Anthropocene have been quantified at large spatial scales, the patterns, drivers, and consequences of change in crop diversity and biogeography at national-scales remains less explored. We use production data on 339 crops, grown in over 150 countries from 1961 to 2017, to quantify changes in country-level crop richness and evenness. Virtually all countries globally have experienced significant increases in crop richness since 1961, with the early 1980s marking a clear onset of a ~ 9-year period of increase in crop richness in countries worldwide. While these changes have increased the similarity of diversity of croplands among countries, only half of countries experienced increases in crop evenness through time. Ubiquitous increases in crop richness within nearly all countries between 1980 and 2000 are a unique biogeographical feature of the Anthropocene. At the same time, we detected opposing changes in crop evenness, and only modest signatures of increased homogenization of croplands among countries. Therefore context-dependent and, at least, national-scale assessments are needed to understand and predict how changes in crop diversity influence agricultural resistance and resilience to environmental change.
Interindividual variability of electric fields during transcranial temporal interference stimulation (tTIS)
Authors: von Conta Jill , Kasten Florian H. , Ćurčić-Blake Branislava , Aleman André , Thielscher Axel , Herrmann Christoph S. 
Published: October 2021

AbstractTranscranial temporal interference stimulation (tTIS) is a novel non-invasive brain stimulation technique for electrical stimulation of neurons at depth. Deep brain regions are generally small in size, making precise targeting a necessity. The variability of electric fields across individual subjects resulting from the same tTIS montages is unknown so far and may be of major concern for precise tTIS targeting. Therefore, the aim of the current study is to investigate the variability of the electric fields due to tTIS across 25 subjects. To this end, the electric fields of different electrode montages consisting of two electrode pairs with different center frequencies were simulated in order to target selected regions-of-interest (ROIs) with tTIS. Moreover, we set out to compare the electric fields of tTIS with the electric fields of conventional tACS. The latter were also based on two electrode pairs, which, however, were driven in phase at a common frequency. Our results showed that the electric field strengths inside the ROIs (left hippocampus, left motor area and thalamus) during tTIS are variable on single subject level. In addition, tTIS stimulates more focally as compared to tACS with much weaker co-stimulation of cortical areas close to the stimulation electrodes. Electric fields inside the ROI were, however, comparable for both methods. Overall, our results emphasize the potential benefits of tTIS for the stimulation of deep targets, over conventional tACS. However, they also indicate a need for individualized stimulation montages to leverage the method to its fullest potential.
Exosomal CD63 in critically ill patients with sepsis
Authors: Im Yunjoo , Yoo Hongseok , Ko Ryoung-Eun , Lee Jin Young , Park Junseon , Jeon Kyeongman 
Published: October 2021

AbstractCD63 is one of the tetraspanin protein family members that is ubiquitously expressed on exosomes and is involved in the signal transduction of various types of immune cells. It may thus contribute to immunometabolic mechanisms of cellular and organ dysfunction in sepsis. Nonetheless, the association of exosomal CD63 with the severity and mortality of sepsis is not well known. Therefore, in the present study, the overall levels of exosomal CD63 were evaluated to ascertain whether they were associated with organ failure and mortality in patients with sepsis. Exosomal CD63 was measured from prospectively enrolled critically-ill patients with sepsis (n = 217) and healthy control (n = 20). To detect and quantify exosomes in plasma, a commercially available enzyme-linked immunosorbent assay kit was used according to the manufacturer’s protocol. The total number of exosomal CD63 was determined by quantifying the immunoreactive CD63. The association between plasma levels of exosomal CD63 and sequential organ failure assessment (SOFA) score was assessed by a linear regression method. The best cut-off level of exosomal CD63 for 28-day mortality prediction was determined by Youden’s index. Among 217 patients with sepsis, 143 (66%) patients were diagnosed with septic shock. Trends of increased exosomal CD63 levels were observed in control, sepsis, and septic-shock groups (6.6 µg/mL vs. 42 µg/mL vs. 90 µg/mL, p < 0.001). A positive correlation between exosomal CD63 and SOFA scores was observed in patients with sepsis (r value = 0.35). When patients were divided into two groups according to the best cut-off level, the group with higher exosomal CD63 levels (more than 126 µg/mL) was significantly associated with 28-day and in-hospital mortality. Moreover, the Kaplan–Meier survival method showed a significant difference in 90-day survival between patients with high- and low-exosomal CD63 levels (log-rank p = 0.005). Elevated levels of exosomal CD63 were associated with the severity of organ failure and predictive of mortality in critically ill patients with sepsis.
Personalized behavior management as a replacement for medications for pain control and mood regulation
Authors: Davydov Dmitry M. , Galvez-Sánchez Carmen M. , Montoro Casandra Isabel , de Guevara Cristina Muñoz Ladrón , Reyes del Paso Gustavo A. 
Published: October 2021

AbstractA lack of personalized approaches in non-medication pain management has prevented these alternative forms of treatment from achieving the desired efficacy. One hundred and ten female patients with fibromyalgia syndrome (FMS) and 60 healthy women without chronic pain were assessed for severity of chronic or retrospective occasional pain, respectively, along with alexithymia, depression, anxiety, coping strategies, and personality traits. All analyses were conducted following a ‘resource matching’ hypothesis predicting that to be effective, a behavioral coping mechanism diverting or producing cognitive resources should correspond to particular mechanisms regulating pain severity in the patient. Moderated mediation analysis found that extraverts could effectively cope with chronic pain and avoid the use of medications for pain and mood management by lowering depressive symptoms through the use of distraction mechanism as a habitual (‘out-of-touch-with-reality’) behavior. However, introverts could effectively cope with chronic pain and avoid the use of medications by lowering catastrophizing through the use of distraction mechanism as a situational (‘in-touch-with-reality’) behavior. Thus, personalized behavior management techniques applied according to a mechanism of capturing or diverting the main individual ‘resource’ of the pain experience from its ‘feeding’ to supporting another activity may increase efficacy in the reduction of pain severity along with decreasing the need for pain relief and mood-stabilizing medications.
An examination of active inference in autistic adults using immersive virtual reality
Authors: Arthur Tom , Harris David , Buckingham Gavin , Brosnan Mark , Wilson Mark , Williams Genevieve , Vine Sam 
Published: October 2021

AbstractThe integration of prior expectations, sensory information, and environmental volatility is proposed to be atypical in Autism Spectrum Disorder, yet few studies have tested these predictive processes in active movement tasks. To address this gap in the research, we used an immersive virtual-reality racquetball paradigm to explore how visual sampling behaviours and movement kinematics are adjusted in relation to unexpected, uncertain, and volatile changes in environmental statistics. We found that prior expectations concerning ball ‘bounciness’ affected sensorimotor control in both autistic and neurotypical participants, with all individuals using prediction-driven gaze strategies to track the virtual ball. However, autistic participants showed substantial differences in visuomotor behaviour when environmental conditions were more volatile. Specifically, uncertainty-related performance difficulties in these conditions were accompanied by atypical movement kinematics and visual sampling responses. Results support proposals that autistic people overestimate the volatility of sensory environments, and suggest that context-sensitive differences in active inference could explain a range of movement-related difficulties in autism.
An experimental study on the relation between friction force and real contact area
Authors: Liang X. M. , Xing Y. Z. , Li L. T. , Yuan W. K. , Wang G. F. 
Published: October 2021

AbstractClassical laws of friction suggest that friction force is proportional to the normal load and independent of the nominal contact area. As a great improvement in this subject, it is now widely accepted that friction force is proportional to the real contact area, and much work has been conducted based on this hypothesis. In present study, this hypothesis will be carefully revisited by measuring the friction force and real contact area in-site and real-time at both normal loading and unloading stages. Our experiments reveal that the linear relation always holds between friction force and normal load. However, for the relation between friction force and real contact area, the linearity holds only at the loading stage while fails at the unloading stage. This study may improve our understanding of the origin of friction.
A novel temporary immersion bioreactor system for large scale multiplication of banana (Rasthali AAB—Silk)
Authors: Uma Subbaraya , Karthic Raju , Kalpana Sathiamoorthy , Backiyarani Suthanthiram , Saraswathi Marimuthu Somasundaram 
Published: October 2021

AbstractMusa sp. cultivar Rasthali (Silk AAB) is a choice variety of the Asian sub-continent. Its production and sustenance are threatened by Fusarium wilt, which affects the livelihoods of small and marginal farmers. The use of quality planting material is one of the strategies to manage the disease. Availability of quality planting material for varieties other than Grand Naine is limited. Large-scale micropropagation using existing technologies is laborious and expensive. Temporary immersion bioreactor system is emerging as a potential advancement in the micropropagation industry. In this study, a cost-effective temporary immersion bioreactor (TIB) system has been developed and an efficient micropropagation method has been standardized. Explants cultured in TIB with 250 ml of culture medium in a 2-min immersion frequency of 6 h were found to be efficient for shoot proliferation and rooting. Its efficacy has been compared with the semisolid culture method. At the end of the 6th subculture, 1496 ± 110 shoots per explant were obtained in TIB. Chlorophyll, carotenoid, stomatal index, and the number of closed stomata were examined to determine the physiological functions of the plants grown in TIB and compared with semisolid grown plantlets. Plantlets grown in TIB were genetically stable and were confirmed using inter-simple sequence repeat (ISSR) markers. The multiplication of shoots in TIB was 2.7-fold higher than the semisolid culture method, which is suitable for large-scale production of planting material for commercial applications.
Arabidopsis thaliana myosin XIK is recruited to the Golgi through interaction with a MyoB receptor
Authors: Perico Chiara , Gao Hongbo , Heesom Kate J. , Botchway Stanley W. , Sparkes Imogen A. 
Published: October 2021

AbstractPlant cell organelles are highly mobile and their positioning play key roles in plant growth, development and responses to changing environmental conditions. Movement is acto-myosin dependent. Despite controlling the dynamics of several organelles, myosin and myosin receptors identified so far in Arabidopsis thaliana generally do not localise to the organelles whose movement they control, raising the issue of how specificity is determined. Here we show that a MyoB myosin receptor, MRF7, specifically localises to the Golgi membrane and affects its movement. Myosin XI-K was identified as a putative MRF7 interactor through mass spectrometry analysis. Co-expression of MRF7 and XI-K tail triggers the relocation of XI-K to the Golgi, linking a MyoB/myosin complex to a specific organelle in Arabidopsis. FRET-FLIM confirmed the in vivo interaction between MRF7 and XI-K tail on the Golgi and in the cytosol, suggesting that myosin/myosin receptor complexes perhaps cycle on and off organelle membranes. This work supports a traditional mechanism for organelle movement where myosins bind to receptors and adaptors on the organelle membranes, allowing them to actively move on the actin cytoskeleton, rather than passively in the recently proposed cytoplasmic streaming model.