bluuebunny/crossref_metadata_2025 huggingface dataset:
The feasibility and reliability of actigraphy to monitor sleep in intensive care patients: an observational study
Authors: Delaney L. J. , Litton E. , Melehan K. L. , Huang H.-C. C. , Lopez V. , Van Haren F.
Published: January 2021

Background

Sleep amongst intensive care patients is reduced and highly fragmented which may adversely impact on recovery. The current challenge for Intensive Care clinicians is identifying feasible and accurate assessments of sleep that can be widely implemented. The objective of this study was to investigate the feasibility and reliability of a minimally invasive sleep monitoring technique compared to the gold standard, polysomnography, for sleep monitoring.

Methods

Prospective observational study employing a within subject design in adult patients admitted to an Intensive Care Unit. Sleep monitoring was undertaken amongst minimally sedated patients via concurrent polysomnography and actigraphy monitoring over a 24-h duration to assess agreement between the two methods; total sleep time and wake time.

Results

We recruited 80 patients who were mechanically ventilated (24%) and non-ventilated (76%) within the intensive care unit. Sleep was found to be highly fragmented, composed of numerous sleep bouts and characterized by abnormal sleep architecture. Actigraphy was found to have a moderate level of overall agreement in identifying sleep and wake states with polysomnography (69.4%;K = 0.386,p < 0.05) in an epoch by epoch analysis, with a moderate level of sensitivity (65.5%) and specificity (76.1%). Monitoring accuracy via actigraphy was improved amongst non-ventilated patients (specificity 83.7%; sensitivity 56.7%). Actigraphy was found to have a moderate correlation with polysomnography reported total sleep time (r = 0.359,p < 0.05) and wakefulness (r = 0.371,p < 0.05). Bland–Altman plots indicated that sleep was underestimated by actigraphy, with wakeful states overestimated.

Conclusions

Actigraphy was easy and safe to use, provided moderate level of agreement with polysomnography in distinguishing between sleep and wakeful states, and may be a reasonable alternative to measure sleep in intensive care patients.

Clinical Trial Registration numberACTRN12615000945527 (Registered 9/9/2015).
Evolutionary conservation and divergence of the human brain transcriptome
Authors: Pembroke William G. , Hartl Christopher L. , Geschwind Daniel H.
Published: January 2021

Background

Mouse models have allowed for the direct interrogation of genetic effects on molecular, physiological, and behavioral brain phenotypes. However, it is unknown to what extent neurological or psychiatric traits may be human- or primate-specific and therefore which components can be faithfully recapitulated in mouse models.

Results

We compare conservation of co-expression in 116 independent data sets derived from human, mouse, and non-human primate representing more than 15,000 total samples. We observe greater changes occurring on the human lineage than mouse, and substantial regional variation that highlights cerebral cortex as the most diverged region. Glia, notably microglia, astrocytes, and oligodendrocytes are the most divergent cell type, three times more on average than neurons. We show that cis-regulatory sequence divergence explains a significant fraction of co-expression divergence. Moreover, protein coding sequence constraint parallels co-expression conservation, such that genes with loss of function intolerance are enriched in neuronal, rather than glial modules. We identify dozens of human neuropsychiatric and neurodegenerative disease risk genes, such as COMT, PSEN-1, LRRK2, SHANK3, and SNCA, with highly divergent co-expression between mouse and human and show that 3D human brain organoids recapitulate in vivo co-expression modules representing several human cell types.

Conclusions

We identify robust co-expression modules reflecting whole-brain and regional patterns of gene expression. Compared with those that represent basic metabolic processes, cell-type-specific modules, most prominently glial modules, are the most divergent between species. These data and analyses serve as a foundational resource to guide human disease modeling and its interpretation.
A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis
Authors: Li Li , Ugalde Alejandro P. , Scheele Colinda L. G. J. , Dieter Sebastian M. , Nagel Remco , Ma Jin , Pataskar Abhijeet , Korkmaz Gozde , Elkon Ran , Chien Miao-Ping , You Li , Su Pin-Rui , Bleijerveld Onno B. , Altelaar Maarten , Momchev Lyubomir , Manber Zohar , Han Ruiqi , van Breugel Pieter C. , Lopes Rui , ten Dijke Peter , van Rheenen Jacco , Agami Reuven
Published: January 2021

Background

Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiveness. Although thousands of YAP/TEAD4 binding-sites are annotated, their functional importance is unknown. Here, we aim at further identification of enhancer elements that are required for YAP functions.

Results

We first apply genome-wide ChIP profiling of YAP to systematically identify enhancers that are bound by YAP/TEAD4. Next, we implement a genetic approach to uncover functions of YAP/TEAD4-associated enhancers, demonstrate its robustness, and use it to reveal a network of enhancers required for YAP-mediated proliferation. We focus on EnhancerTRAM2, as its target gene TRAM2 shows the strongest expression-correlation with YAP activity in nearly all tumor types. Interestingly, TRAM2 phenocopies the YAP-induced cell proliferation, migration, and invasion phenotypes and correlates with poor patient survival. Mechanistically, we identify FSTL-1 as a major direct client of TRAM2 that is involved in these phenotypes. Thus, TRAM2 is a key novel mediator of YAP-induced oncogenic proliferation and cellular invasiveness.

Conclusions

YAP is a transcription co-factor that binds to thousands of enhancer loci and stimulates tumor aggressiveness. Using unbiased functional approaches, we dissect YAP enhancer network and characterize TRAM2 as a novel mediator of cellular proliferation, migration, and invasion. Our findings elucidate how YAP induces cancer aggressiveness and may assist diagnosis of cancer metastasis.
Further evaluation and validation of the VETSCAN IMAGYST: in-clinic feline and canine fecal parasite detection system integrated with a deep learning algorithm
Authors: Nagamori Yoko , Sedlak Ruth Hall , DeRosa Andrew , Pullins Aleah , Cree Travis , Loenser Michael , Larson Benjamin S. , Smith Richard Boyd , Penn Cory , Goldstein Richard
Published: January 2021

Background

Fecal examinations in pet cats and dogs are key components of routine veterinary practice; however, their accuracy is influenced by diagnostic methodologies and the experience level of personnel performing the tests. The VETSCAN IMAGYST system was developed to provide simpler and easier fecal examinations which are less influenced by examiners’ skills. This system consists of three components: a sample preparation device, an automated microscope scanner, and analysis software. The objectives of this study were to qualitatively evaluate the performance of the VETSCAN IMAGYST system on feline parasites (AncylostomaandToxocara cati) and protozoan parasites (CystoisosporaandGiardia) and to assess and compare the performance of the VETSCAN IMAGYST centrifugal flotation method to reference centrifugal and passive flotation methods.

Methods

To evaluate the diagnostic performance of the scanning and algorithmic components of the VETSCAN IMAGYST system, fecal slides were prepared by the VETSCAN IMAGYST centrifugal flotation technique with pre-screened fecal samples collected from dogs and cats and examined by both an algorithm and parasitologists. To assess the performance of the VETSCAN IMAGYST centrifugal flotation technique, diagnostic sensitivity and specificity were calculated and compared to those of conventional flotation techniques.

Results

The performance of the VETSCAN IMAGYST algorithm closely correlated with evaluations by parasitologists, with sensitivity of 75.8–100% and specificity of 93.1-100% across the targeted parasites. For samples with 50 eggs or less per slide, Lin’s concordance correlation coefficients ranged from 0.70 to 0.95 across the targeted parasites. The results of the VETSCAN IMAGYST centrifugal flotation method correlated well with those of the conventional centrifugal flotation method across the targeted parasites: sensitivity of 65.7–100% and specificity of 97.6–100%. Similar results were observed for the conventional passive flotation method compared to the conventional centrifugal flotation method: sensitivity of 56.4–91.7% and specificity of 99.4–100%.

Conclusions

The VETSCAN IMAGYST scanning and algorithmic systems with the VETSCAN IMAGYST fecal preparation technique demonstrated a similar qualitative performance to the parasitologists’ examinations with conventional fecal flotation techniques. Given the deep learning nature of the VETSCAN IMAGYST system, its performance is expected to improve over time, enabling it to be utilized in veterinary clinics to perform fecal examinations accurately and efficiently.

Graphical Abstract
Structural changes in the sacroiliac joint on MRI and relationship to ASDAS inactive disease in axial spondyloarthritis: a 2-year study comparing treatment with etanercept in EMBARK to a contemporary control cohort in DESIR
Authors: Maksymowych Walter P. , Claudepierre Pascal , de Hooge Manouk , Lambert Robert G. , Landewé Robert , Molto Anna , van der Heijde Désirée , Bukowski Jack F. , Jones Heather , Pedersen Ron , Szumski Annette , Vlahos Bonnie , Dougados Maxime
Published: January 2021

Background

Limited information is available on the impact of treatment with a tumor necrosis factor inhibitor (TNFi) on structural lesions in patients with recent-onset axial spondyloarthritis (axSpA). We compared 2-year structural lesion changes on magnetic resonance imaging (MRI) in the sacroiliac joints (SIJ) of patients with recent-onset axSpA receiving etanercept in a clinical trial (EMBARK) to similar patients not receiving biologics in a cohort study (DESIR). We also evaluated the relationship between the Ankylosing Spondylitis Disease Activity Score (ASDAS) and change in MRI structural parameters.

Methods

The difference between etanercept (EMBARK) and control (DESIR) in the net percentage of patients with structural lesion change was determined using the SpondyloArthritis Research Consortium of Canada SIJ Structural Score, with and without adjustment for baseline covariates. The relationship between sustained ASDAS inactive disease, defined as the presence of ASDAS < 1.3 for at least 2 consecutive time points 6 months apart, and structural lesion change was evaluated.

Results

This study included 163 patients from the EMBARK trial and 76 from DESIR. The net percentage of patients with erosion decrease was significantly greater for etanercept vs control: unadjusted: 23.9% vs 5.3%; P = 0.01, adjusted: 23.1% vs 2.9%; P = 0.01. For the patients attaining sustained ASDAS inactive disease on etanercept, erosion decrease was evident in significantly more than erosion increase: 34/104 (32.7%) vs 5/104 (4.8%); P < 0.001. A higher proportion had erosion decrease and backfill increase than patients in other ASDAS status categories. However, the trend across ASDAS categories was not significant and decrease in erosion was observed even in patients without a sustained ASDAS response.

Conclusions

These data show that a greater proportion of patients achieved regression of erosion with versus without etanercept. However, the link between achieving sustained ASDAS inactive disease and structural lesion change on MRI could not be clearly established.

Trial registration

EMBARK: ClinicalTrials.gov identifier: NCT01258738, Registered 13 December 2010; DESIR: ClinicalTrials.gov identifier: NCT01648907, Registered 24 July 2012.
Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Authors: Zhu Mansheng , Liang Qixiang , Chen Tao , Kong Qian , Ye Gengtai , Yu Shitong , Li Xunjun , He Qinglie , Liu Hao , Hu Yanfeng , Yu Jiang , Li Guoxin
Published: January 2021

Background

The recent discovery of cancer/tissue specificity of miRNA has indicated its great potential as a therapeutic target. In Epstein–Barr virus-associated gastric cancer (EBVaGC), host genes are affected by extensive DNA methylation, including miRNAs. However, the role of methylated miRNA in the development of EBVaGC and immune cell infiltration has largely remained elusive.

Results

After crossmatching the DNA methylation and expression profile of miRNA and mRNA in the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas Research Network (TCGA), we discovered that miR-129-2-3p was significantly suppressed due to hypermethylation on its enhancer in EBVaGC. The differentially expressed genes (DEGs) added up to 30, among which AKAP12 and LARP6 were predicted to be the target genes of miR-129-2-3p and negatively correlated with patients’ survival. Accordingly, miR-129-2-3p was significantly down-regulated in tumor samples in 26 (65%) out of 40 cases in our cohort (P < 0.0001). The proliferation, migration and invasion functions of GC cells were significantly promoted when transfected with miR-129-2-3p inhibitor and suppressed when transfected with mimics or treated with 5-aza-2′-deoxycytidine. Moreover, a comprehensive regulation network was established by combining the putative transcription factors, miRNA-mRNA and protein–protein interaction (PPI) analysis. Pathway enrichment analysis showed that cytokine activity, especially CCL20, was the most prominent biological process in EBVaGC development. Immune cell infiltration analysis demonstrated CD4+ T cell, macrophage and dendritic cell infiltrates were significantly enriched for the prognostic-indicated hub genes.

Conclusion

This study has provided a comprehensive analysis of differentially expressed miRNAs and mRNAs associated with genome-wide DNA methylation by integrating multi-source data including transcriptome, methylome and clinical data from GEO and TCGA, QPCR of tumor samples and cell function assays. It also gives a hint on the relationships between methylated miRNA, DEGs and the immune infiltration. Further experimental and clinical investigations are warranted to explore the underlying mechanism and validate our findings.
Generation of dyskeratosis congenita-like hematopoietic stem cells through the stable inhibition of DKC1
Authors: Carrascoso-Rubio Carlos , Zittersteijn Hidde A. , Pintado-Berninches Laura , Fernández-Varas Beatriz , Lozano M. Luz , Manguan-Garcia Cristina , Sastre Leandro , Bueren Juan A. , Perona Rosario , Guenechea Guillermo
Published: January 2021

Dyskeratosis congenita (DC) is a rare telomere biology disorder, which results in different clinical manifestations, including severe bone marrow failure. To date, the only curative treatment for the bone marrow failure in DC patients is allogeneic hematopoietic stem cell transplantation. However, due to the toxicity associated to this treatment, improved therapies are recommended for DC patients. Here, we aimed at generating DC-like human hematopoietic stem cells in which the efficacy of innovative therapies could be investigated. Because X-linked DC is the most frequent form of the disease and is associated with an impaired expression of DKC1, we have generated DC-like hematopoietic stem cells based on the stable knock-down of DKC1 in human CD34+ cells with lentiviral vectors encoding for DKC1 short hairpin RNAs. At a molecular level, DKC1-interfered CD34+ cells showed a decreased expression of TERC, as well as a diminished telomerase activity and increased DNA damage, cell senescence, and apoptosis. Moreover, DKC1-interfered human CD34+ cells showed defective clonogenic ability and were incapable of repopulating the hematopoiesis of immunodeficient NSG mice. The development of DC-like hematopoietic stem cells will facilitate the understanding of the molecular and cellular basis of this inherited bone marrow failure syndrome and will serve as a platform to evaluate the efficacy of new hematopoietic therapies for DC.
Current use of inotropes in circulatory shock
Authors: Scheeren Thomas W. L. , Bakker Jan , Kaufmann Thomas , Annane Djillali , Asfar Pierre , Boerma E. Christiaan , Cecconi Maurizio , Chew Michelle S. , Cholley Bernard , Cronhjort Maria , De Backer Daniel , Dubin Arnaldo , Dünser Martin W. , Duranteau Jacques , Gordon Anthony C. , Hajjar Ludhmila A. , Hamzaoui Olfa , Hernandez Glenn , Kanoore Edul Vanina , Koster Geert , Landoni Giovanni , Leone Marc , Levy Bruno , Martin Claude , Mebazaa Alexandre , Monnet Xavier , Morelli Andrea , Payen Didier , Pearse Rupert M. , Pinsky Michael R. , Radermacher Peter , Reuter Daniel A. , Sakr Yasser , Sander Michael , Saugel Bernd , Singer Mervyn , Squara Pierre , Vieillard-Baron Antoine , Vignon Philippe , Vincent Jean-Louis , van der Horst Iwan C. C. , Vistisen Simon T. , Teboul Jean-Louis
Published: January 2021

Background

Treatment decisions on critically ill patients with circulatory shock lack consensus. In an international survey, we aimed to evaluate the indications, current practice, and therapeutic goals of inotrope therapy in the treatment of patients with circulatory shock.

Methods

From November 2016 to April 2017, an anonymous web-based survey on the use of cardiovascular drugs was accessible to members of the European Society of Intensive Care Medicine (ESICM). A total of 14 questions focused on the profile of respondents, the triggering factors, first-line choice, dosing, timing, targets, additional treatment strategy, and suggested effect of inotropes. In addition, a group of 42 international ESICM experts was asked to formulate recommendations for the use of inotropes based on 11 questions.

Results

A total of 839 physicians from 82 countries responded. Dobutamine was the first-line inotrope in critically ill patients with acute heart failure for 84% of respondents. Two-thirds of respondents (66%) stated to use inotropes when there were persistent clinical signs of hypoperfusion or persistent hyperlactatemia despite a supposed adequate use of fluids and vasopressors, with (44%) or without (22%) the context of low left ventricular ejection fraction. Nearly half (44%) of respondents stated an adequate cardiac output as target for inotropic treatment. The experts agreed on 11 strong recommendations, all of which were based on excellent (> 90%) or good (81–90%) agreement. Recommendations include the indications for inotropes (septic and cardiogenic shock), the choice of drugs (dobutamine, not dopamine), the triggers (low cardiac output and clinical signs of hypoperfusion) and targets (adequate cardiac output) and stopping criteria (adverse effects and clinical improvement).

Conclusion

Inotrope use in critically ill patients is quite heterogeneous as self-reported by individual caregivers. Eleven strong recommendations on the indications, choice, triggers and targets for the use of inotropes are given by international experts. Future studies should focus on consistent indications for inotrope use and implementation into a guideline for circulatory shock that encompasses individualized targets and outcomes.
Sign-changing solutions for Schrödinger–Kirchhoff-type fourth-order equation with potential vanishing at infinity
Authors: Guan Wen , Zhang Hua-Bo
Published: January 2021

The purpose of this paper is to study the existence of sign-changing solution to the following fourth-order equation:$$ \Delta ^{2}u- \biggl(a+ b \int _{\mathbb{R}^{N}} \vert \nabla u \vert ^{2}\,dx \biggr) \Delta u+V(x)u=K(x)f(u) \quad\text{in } \mathbb{R}^{N}, $$Δ2u−(a+b∫RN|∇u|2dx)Δu+V(x)u=K(x)f(u)in RN,where$5\leq N\leq 7$5≤N≤7,$\Delta ^{2}$Δ2denotes the biharmonic operator,$K(x), V(x)$K(x),V(x)are positive continuous functions which vanish at infinity, and$f(u)$f(u)is only a continuous function. We prove that the equation has a least energy sign-changing solution by the minimization argument on the sign-changing Nehari manifold. If, additionally,fis an odd function, we obtain that equation has infinitely many nontrivial solutions.
Sufficient and necessary conditions for oscillation of linear fractional-order delay differential equations
Authors: Meng Qiong , Jin Zhen , Liu Guirong
Published: January 2021

This paper studies the linear fractional-order delay differential equation$$ {}^{C}D^{\alpha }_{-}x(t)-px(t-\tau )= 0, $$D−αCx(t)−px(t−τ)=0,where$0<\alpha =\frac{\text{odd integer}}{\text{odd integer}}<1$0<α=odd integerodd integer<1,$p, \tau >0$p,τ>0,${}^{C}D_{-}^{\alpha }x(t)=-\Gamma ^{-1}(1-\alpha )\int _{t}^{\infty }(s-t)^{- \alpha }x'(s)\,ds$D−αCx(t)=−Γ−1(1−α)∫t∞(s−t)−αx′(s)ds. We obtain the conclusion that$$ p^{1/\alpha } \tau >\alpha /e $$p1/ατ>α/eis a sufficient and necessary condition of the oscillations for all solutions of Eq. (*). At the same time, some sufficient conditions are obtained for the oscillations of multiple delays linear fractional differential equation. Several examples are given to illustrate our theorems.
Study of composite fractional relaxation differential equation using fractional operators with and without singular kernels and special functions
Authors: Zafar Azhar Ali , Awrejcewicz Jan , Mazur Olga , Riaz Muhammad Bilal
Published: January 2021

Our aim in this article is to solve the composite fractional relaxation differential equation by using different definitions of the non-integer order derivative operator $D_{t}^{\alpha }$

D
t
α

, more specifically we employ the definitions of Caputo, Caputo–Fabrizio and Atangana–Baleanu of non-integer order derivative operators. We apply the Laplace transform method to solve the problem and express our solutions in terms of Lorenzo and Hartley’s generalised G function. Furthermore, the effects of the parameters involved in the model are graphically highlighted.
Investigation of Diagonal Strut Actions in Masonry-Infilled Reinforced Concrete Frames
Authors: Lee Seung-Jae , Eom Tae-Sung , Yu Eunjong
Published: January 2021

This study analytically investigated the behavior of reinforced concrete frames with masonry infills. For the analysis, VecTor2, a nonlinear finite element analysis program that implements the Modified Compression Field Theory and Disturbed Stress Field Model, was used. To account for the slip behavior at the mortar joints in the masonry element, the hyperbolic Mohr–Coulomb yield criterion, defined as a function of cohesion and friction angle, was used. The analysis results showed that the lateral resistance and failure mode of the infilled frames were significantly affected by the thickness of the masonry infill, cohesion on the mortar joint–brick interface, and poor mortar filling (or gap) on the masonry boundary under the beam. Diagonal strut actions developed along two or three load paths on the mortar infill, including the backstay actions near the tension column and push-down actions near the compression columns. Such backstay and push-down actions increased the axial and shear forces of columns, and ultimately affect the strength, ductility, and failure mode of the infilled frames.
Right place, right time? Making crime pattern theory time-specific
Authors: van Sleeuwen Sabine E. M. , Ruiter Stijn , Steenbeek Wouter
Published: January 2021

Objectives

Crime pattern theory and the related empirical research have remained rather a-temporal, as if the timing of routine activities and crime plays no role. Building on previous geography of crime research, we extend crime pattern theory and propose that an offender’s spatial knowledge acquired during daily routine activities is not equally applicable to all times of day.

Methods

We put this extended theory to a first empirical test by applying a discrete spatial choice model to detailed information from the Netherlands on 71 offences committed by 30 offenders collected through a unique online survey instrument. The offenders reported on their most important activity nodes and offence locations over the past year, as well as the specific times they regularly visited these locations.

Results

The results show that almost 40% of the offences are committed within the neighbourhoods of offenders’ activity nodes, increasing to 85% when including first-, second- and third-order neighbourhoods. Though not statistically significant in our small sample, the results further suggest that offenders are more likely to commit crime in neighbourhoods they have regularly visited at the same time of day than in neighbourhoods they have regularly visited at different times of day.

Conclusion

Our extension of crime pattern theory is only tentatively supported. We argue for replication research with larger samples before any firm conclusions are warranted.
Spatial differentiation of metabolism in prostate cancer tissue by MALDI-TOF MSI
Authors: Andersen Maria K. , Høiem Therese S. , Claes Britt S. R. , Balluff Benjamin , Martin-Lorenzo Marta , Richardsen Elin , Krossa Sebastian , Bertilsson Helena , Heeren Ron M. A. , Rye Morten B. , Giskeødegård Guro F. , Bathen Tone F. , Tessem May-Britt
Published: January 2021

Background

Prostate cancer tissues are inherently heterogeneous, which presents a challenge for metabolic profiling using traditional bulk analysis methods that produce an averaged profile. The aim of this study was therefore to spatially detect metabolites and lipids on prostate tissue sections by using mass spectrometry imaging (MSI), a method that facilitates molecular imaging of heterogeneous tissue sections, which can subsequently be related to the histology of the same section.

Methods

Here, we simultaneously obtained metabolic and lipidomic profiles in different prostate tissue types using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MSI. Both positive and negative ion mode were applied to analyze consecutive sections from 45 fresh-frozen human prostate tissue samples (N = 15 patients). Mass identification was performed with tandem MS.

Results

Pairwise comparisons of cancer, non-cancer epithelium, and stroma revealed several metabolic differences between the tissue types. We detected increased levels of metabolites crucial for lipid metabolism in cancer, including metabolites involved in the carnitine shuttle, which facilitates fatty acid oxidation, and building blocks needed for lipid synthesis. Metabolites associated with healthy prostate functions, including citrate, aspartate, zinc, and spermine had lower levels in cancer compared to non-cancer epithelium. Profiling of stroma revealed higher levels of important energy metabolites, such as ADP, ATP, and glucose, and higher levels of the antioxidant taurine compared to cancer and non-cancer epithelium.

Conclusions

This study shows that specific tissue compartments within prostate cancer samples have distinct metabolic profiles and pinpoint the advantage of methodology providing spatial information compared to bulk analysis. We identified several differential metabolites and lipids that have potential to be developed further as diagnostic and prognostic biomarkers for prostate cancer. Spatial and rapid detection of cancer-related analytes showcases MALDI-TOF MSI as a promising and innovative diagnostic tool for the clinic.
A survey on generative adversarial networks for imbalance problems in computer vision tasks
Authors: Sampath Vignesh , Maurtua Iñaki , Aguilar Martín Juan José , Gutierrez Aitor
Published: January 2021

Any computer vision application development starts off by acquiring images and data, then preprocessing and pattern recognition steps to perform a task. When the acquired images are highly imbalanced and not adequate, the desired task may not be achievable. Unfortunately, the occurrence of imbalance problems in acquired image datasets in certain complex real-world problems such as anomaly detection, emotion recognition, medical image analysis, fraud detection, metallic surface defect detection, disaster prediction, etc., are inevitable. The performance of computer vision algorithms can significantly deteriorate when the training dataset is imbalanced. In recent years, Generative Adversarial Neural Networks (GANs) have gained immense attention by researchers across a variety of application domains due to their capability to model complex real-world image data. It is particularly important that GANs can not only be used to generate synthetic images, but also its fascinating adversarial learning idea showed good potential in restoring balance in imbalanced datasets.

In this paper, we examine the most recent developments of GANs based techniques for addressing imbalance problems in image data. The real-world challenges and implementations of synthetic image generation based on GANs are extensively covered in this survey. Our survey first introduces various imbalance problems in computer vision tasks and its existing solutions, and then examines key concepts such as deep generative image models and GANs. After that, we propose a taxonomy to summarize GANs based techniques for addressing imbalance problems in computer vision tasks into three major categories: 1. Image level imbalances in classification, 2. object level imbalances in object detection and 3. pixel level imbalances in segmentation tasks. We elaborate the imbalance problems of each group, and provide GANs based solutions in each group. Readers will understand how GANs based techniques can handle the problem of imbalances and boost performance of the computer vision algorithms.
Temporal evolutions of $$\text {N}_2^+$$ Meinel (1,2) band near $$1.5.\,\upmu \text {m}$$ associated with aurora breakup and their effects on mesopause temperature estimations from OH Meinel (3,1) band
Authors: Nishiyama Takanori , Taguchi Makoto , Suzuki Hidehiko , Dalin Peter , Ogawa Yasunobu , Brändström Urban , Sakanoi Takeshi
Published: January 2021

We have carried out ground-based NIRAS (Near-InfraRed Aurora and airglow Spectrograph) observations at Syowa station, Antarctic ($$69.0^{\circ }\text {S}$$

69
.

0
∘

S

, $$39.6^{\circ }\text {E}$$

39
.

6
∘

E

) and Kiruna ($$67.8^{\circ }\text {N}$$

67
.

8
∘

N

, $$20.4^{\circ }\text {E}$$

20
.

4
∘

E

), Sweden for continuous measurements of hydroxyl (OH) rotational temperatures and a precise evaluation of auroral contaminations to OH Meinel (3,1) band. A total of 368-nights observations succeeded for 2 winter seasons, and 3 cases in which $$\text {N}_2^+$$

N
2
+

Meinel (1,2) band around $$1.5\,\mu \text {m}$$

1.5

μ
m

was significant were identified. Focusing on two specific cases, detailed spectral characteristics with high temporal resolutions of 30 s are presented. Intensities of $$\text {N}_2^+$$

N
2
+

band were estimated to be 228 kR and 217 kR just at the moment of the aurora breakup and arc intensification during pseudo breakup, respectively. At a wavelength of $$\text {P}_1(2)$$

P
1

(
2
)

line ($$\sim 1523 \,\text {nm}$$

∼
1523

nm

), $$\text {N}_2^+$$

N
2
+

emissions were almost equal to or greater than the OH line intensity. On the other hand, at a wavelength of $$\text {P}_1(4)$$

P
1

(
4
)

line ($$\sim 1542 \,\text {nm}$$

∼
1542

nm

), the OH line was not seriously contaminated and still dominant to $$\text {N}_2^+$$

N
2
+

emissions. Furthermore, we evaluated $$\text {N}_2^+$$

N
2
+

(1,2) band effects on OH rotational temperature estimations quantitatively for the first time. Auroral contaminations from $$\text {N}_2^+$$

N
2
+

(1,2) band basically lead negative bias in OH rotational temperature estimated by line-pair-ratio method with $$\text {P}_1(2)$$

P
1

(
2
)

and $$\text {P}_1(4)$$

P
1

(
4
)

lines in OH (3,1) band. They possibly cause underestimations of OH rotational temperatures up to 40 K. In addition, $$\text {N}_2^+$$

N
2
+

(1,2) band contaminations were temporally limited to a moment around the aurora breakup. This is consistent with proceeding studies reporting that enhancements of $$\text {N}_2^+$$

N
2
+

(1,2) band were observed associated with International Brightness Coefficient 2–3 auroras. It is also suggested that the contaminations would be neglected in the polar cap and the sub-auroral zone, where strong aurora intensification is less observed. Further spectroscopic investigations at these wavelengths are needed especially for more precise evaluations of $$\text {N}_2^+$$

N
2
+

(1,2) band contaminations. For example, simultaneous 2-D imaging observation and spectroscopic measurement with high spectral resolutions for airglow in OH (3,1) band will make great advances in more robust temperature estimations in the auroral zone.
Unusual enhancement of ~ 30 MeV proton flux in an ICME sheath region
Authors: Oka Mitsuo , Obara Takahiro , Nitta Nariaki V. , Yashiro Seiji , Shiota Daikou , Ichimoto Kiyoshi
Published: January 2021

In gradual Solar Energetic Particle (SEP) events, shock waves driven by coronal mass ejections (CMEs) play a major role in accelerating particles, and the energetic particle flux enhances substantially when the shock front passes by the observer. Such enhancements are historically referred to as Energetic Storm Particle (ESP) events, but it remains unclear why ESP time profiles vary significantly from event to event. In some cases, energetic protons are not even clearly associated with shocks. Here, we report an unusual, short-duration proton event detected on 5 June 2011 in the compressed sheath region bounded by an interplanetary shock and the leading edge of the interplanetary CME (or ICME) that was driving the shock. While < 10 MeV protons were detected already at the shock front, the higher-energy (> 30 MeV) protons were detected about four hours after the shock arrival, apparently correlated with a turbulent magnetic cavity embedded in the ICME sheath region.
Estimation of relative source locations from seismic amplitude: application to earthquakes and tremors at Meakandake volcano, eastern Hokkaido, Japan
Authors: Ogiso Masashi , Yomogida Kiyoshi
Published: January 2021

Although seismic amplitudes can be used to estimate event locations for volcanic tremors and other seismic events with unclear phase arrival times, the precision of such estimates is strongly affected by site amplification factors. Therefore, reduction of the influence of site amplification will allow more precise estimation of event locations by this method. Here, we propose a new method to estimate relative event locations using seismic amplitudes. We use the amplitude ratio between two seismic events at a given station to cancel out the effect of the site amplification factor at that station. By assuming that the difference between the hypocentral distances of these events is much smaller than their hypocentral distances themselves, we derive a system of linear equations for the differences in relative event locations. This formulation is similar to that of a master event location method that uses differences in phase arrival times. We applied our new method to earthquakes and tremors at Meakandake volcano, eastern Hokkaido, Japan. Comparison of the hypocentral distributions of volcano-tectonic earthquakes obtained thereby with those obtained from phase arrival times confirmed the validity of our new method. Moreover, our method clearly identified source migration among three source regions in the tremor on 16 November 2008, consistent with previous interpretations of other geophysical observations in our study area. Our method will thus be useful for detailed analyses of seismic events whose onset times are ambiguous.
Understanding the promoting effect of non-catalytic protein on enzymatic hydrolysis efficiency of lignocelluloses
Authors: Gong Zhenggang , Yang Guangxu , Song Junlong , Zheng Peitao , Liu Jing , Zhu Wenyuan , Huang Liulian , Chen Lihui , Luo Xiaolin , Shuai Li
Published: January 2021

Lignin deposits formed on the surface of pretreated lignocellulosic substrates during acidic pretreatments can non-productively adsorb costly enzymes and thereby influence the enzymatic hydrolysis efficiency of cellulose. In this article, peanut protein (PP), a biocompatible non-catalytic protein, was separated from defatted peanut flour (DPF) as a lignin blocking additive to overcome this adverse effect. With the addition of 2.5 g/L PP in enzymatic hydrolysis medium, the glucose yield of the bamboo substrate pretreated by phenylsulfonic acid (PSA) significantly increased from 38 to 94% at a low cellulase loading of 5 FPU/g glucan while achieving a similar glucose yield required a cellulase loading of 17.5 FPU/g glucan without PP addition. Similar promotion effects were also observed on the n-pentanol-pretreated bamboo and PSA-pretreated eucalyptus substrates. The promoting effect of PP on enzymatic hydrolysis was ascribed to blocking lignin deposits via hydrophobic and/or hydrogen-bonding interactions, which significantly reduced the non-productive adsorption of cellulase onto PSA lignin. Meanwhile, PP extraction also facilitated the utilization of residual DPF as the adhesive for producing plywood as compared to that without protein pre-extraction. This scheme provides a sustainable and viable way to improve the value of woody and agriculture biomass.

Peanut protein, a biocompatible non-catalytic protein, can block lignin, improve enzymatic hydrolysis efficiency and thereby facilitate the economics of biorefinery.

Graphical abstract
ICS/formoterol in the management of asthma in the clinical practice of pulmonologists: an international survey on GINA strategy
Authors: Cruz Álvaro A. , Barile Sara , Nudo Elena , Brogelli Laura , Guller Patricia , Papi Alberto
Published: January 2021

Background

The treatment with short-acting beta-2 agonists (SABA) alone is no longer recommended due to safety issues. Instead, the current Global Initiative for Asthma (GINA) Report recommends the use of the combination of inhaled corticosteroids (ICS) with the rapid/long-acting beta-2 agonist formoterol, although the use in steps 1 and 2 is still off-label in the EU and in many countries. It is important to understand clinicians’ knowledge and opinions on the issue with the ultimate goal to encourage the implementation of the new approach in clinical practice.

Methods

We performed an international survey, directed to pulmonologists interested in the management of patients with asthma.

Results

Most participants reported that SABA alone should not be used in GINA Step 1 asthma treatment. As-needed low-dose ICS/formoterol combination to patients in step 1, and as-needed low-dose ICS/formoterol as reliever therapy in any step were found to be of current use prescribed in their real-life settings. SABA alone was still prescribed to a proportion of patients, although the pulmonologists’ opinion was that it should no longer be used.

Conclusions

Most specialists are up to date and understand the relevance of the changes in GINA reports from 2019. Nevertheless, dissemination and implementation of GINA novel management strategy is still needed.
Detection of road cavities in urban cities by 3D ground-penetrating radar
Authors: Liu Hai , Shi Zhenshi , Li Jianhui , Liu Chao , Meng Xu , Du Yanliang , Chen Jie
Published: January 2021

Cavities under urban roads have increasingly become a great threat to traffic safety in many cities. As a quick, effective, and high-resolution geophysical method, ground-penetrating radar (GPR) has been widely used to detect and image near-surface objects. However, the interpretation of field GPR data remains challenging. For example, it is hard to distinguish reflections caused by road cavities or other urban utilities with a conventional 2D GPR survey. The superiority of 3D GPR in data interpretation is demonstrated by a laboratory experiment. Two pipes and a glass-made cavity buried in a sandpit show similar hyperbolic reflections in the 2D GPR profiles; thus, they are difficult to discriminate. In contrast, their geometric shapes and dimensions are readily identified in the 3D image reconstructed from the synthetic 3D GPR data set. Based on these ideas, we have developed a car-mounted 3D GPR system with two antenna arrays oriented in different polarization directions and have detected more than 100 cavities in three Chinese cities over the past year. The field data of two such cavities are presented. As a result, the cavity depth, horizontal size, and height can be accurately estimated from the 3D GPR data set. Laboratory and field experimental results indicate that 3D GPR possesses potential in the detection and recognition of road cavities and utilities in the complex urban environment.
Sparsity-promoting multiparameter pseudoinverse Born inversion in acoustic media
Authors: Farshad Milad , Chauris Hervé
Published: January 2021

Least-squares reverse time migration (RTM) has become the method of choice for quantitative seismic imaging. The main drawback of such a scheme is that it requires many migration/modeling cycles. The convergence of least-squares RTM can be accelerated by using a suitable preconditioner. In the context of an extended domain in variable-density acoustic media, the pseudoinverse Born operator is the recommended preconditioner, providing quantitative results within a single iteration. This method consists of two steps: application of the pseudoinverse Born operator and inversion of two parameters using an efficient weighted least-squares approach based on the Radon transform. As expected, crosstalk artifacts are generated in the second step due to limited acquisition. We have developed a variable-density pseudoinverse Born operator constrained with the [Formula: see text]-norm for each model parameter to suppress the artifacts. The fast iterative shrinkage-thresholding algorithm is used to carry out the optimization problem. In classic iterative least-squares migration, the [Formula: see text]-norm constraints would affect the whole imaging process. Because the imaging method is split into two steps, only the Radon transform part is modified, where no wave-based operators are involved. Through numerical experiments, we verify the robustness of our method against different migration artifacts including the parameter crosstalk, interfaces with abrupt truncations, sparse shot acquisition geometry, noisy data, and high-contrast complex structures.
Effects of Vitamin D3 Supplementation on Body Composition in the VITamin D and OmegA-3 TriaL (VITAL)
Authors: Chou Sharon H , Murata Elle M , Yu Cindy , Danik Jacqueline , Kotler Gregory , Cook Nancy R , Bubes Vadim , Mora Samia , Chandler Paulette D , Tobias Deirdre K , Copeland Trisha , Buring Julie E , Manson JoAnn E , LeBoff Meryl S
Published: January 2021

Context

Although observational studies show inverse associations between vitamin D status and body weight/adiposity, there are few large randomized controlled trials (RCTs) investigating this relationship.

Objective

To determine whether vitamin D3 supplementation lowers weight or improves body composition.

Design

The VITamin D and OmegA-3 TriaL (VITAL) was a double-blinded, placebo-controlled RCT including 25 871 US adults. This ancillary study was completed in a sub-cohort that underwent body composition assessments at baseline and 2-year follow-up (89% retention).

Setting

Harvard Clinical and Translational Science Center in Boston.

Participants

771 participants (men ≥ 50 and women ≥ 55 years).

Interventions

2 × 2 factorial design of supplemental vitamin D3 (2000 IU/day) and/or omega-3 fatty acids (1 g/day).

Main Outcome Measures

Endpoints were 2-year changes in weight, body mass index (BMI), waist circumference, and total and/or regional fat and lean tissue measures determined by dual-energy X-ray absorptiometry. Effect modification by clinical variables and total and free 25-hydroxyvitamin D (25[OH]D) levels was explored.

Results

There were no effects of supplemental vitamin D3vs placebo on weight, BMI, or measures of adiposity and lean tissue. Effects did not vary by sex, race/ethnicity, fat mass index, or baseline total or free 25(OH)D levels. Vitamin D3 supplementation did slightly improve body fat percentage in participants with normal BMI at baseline, but not in the overweight or obese (P for interaction = 0.04).

Conclusions

Daily vitamin D3 supplementation vs placebo in the general older population did not improve weight or body composition. Whether supplemental vitamin D3 may benefit individuals with normal BMI warrants further study.
Plasma Lipidomic Profiles and Risk of Diabetes: 2 Prospective Cohorts of HIV-Infected and HIV-Uninfected Individuals
Authors: Zhang Eric , Chai Jin Choul , Deik Amy A , Hua Simin , Sharma Anjali , Schneider Michael F , Gustafson Deborah , Hanna David B , Lake Jordan E , Rubin Leah H , Post Wendy S , Anastos Kathryn , Brown Todd , Clish Clary B , Kaplan Robert C , Qi Qibin
Published: January 2021

Objectives

Antiretroviral therapy (ART) use is associated with disrupted lipid and glucose metabolism in people with HIV infection. We aimed to identify plasma lipid species associated with risk of diabetes in the context of HIV infection.

Research Design and Methods

We profiled 211 plasma lipid species in 491 HIV-infected and 203 HIV-uninfected participants aged 35 to 55 years from the Women’s Interagency HIV Study and the Multicenter AIDS Cohort Study. Cox proportional hazards model was used to examine associations between baseline lipid species and incident diabetes (166 diabetes cases were identified during a median follow-up of 12.6 years).

Results

We identified 11 lipid species, representing independent signals for 8 lipid classes/subclasses, associated with risk of diabetes (P < 0.05 after FDR correction). After adjustment for multiple covariates, cholesteryl ester (CE) (22:4), lysophosphatidylcholine (LPC) (18:2), phosphatidylcholine (PC) (36:4), phosphatidylcholine plasmalogen (34:3), and phosphatidylethanolamine (PE) (38:2) were associated with decreased risk of diabetes (HRs = 0.70 to 0.82 per SD increment), while diacylglycerol (32:0), LPC (14:0), PC (38:3), PE (36:1), and triacylglycerol (50:1) were associated with increased risk of diabetes (HRs = 1.26 to 1.56 per SD increment). HIV serostatus did not modify any lipid-diabetes associations; however, most of these lipid species were positively associated with HIV and/or ART use, including 3 diabetes-decreased ( CE [22:4], LPC [18:2], PE [38:2]) and all 5 diabetes-increased lipid species.

Conclusions

This study identified multiple plasma lipid species associated with incident diabetes. Regardless of the directions of their associations with diabetes, most diabetes-associated lipid species were elevated in ART-treated people with HIV infection. This suggests a complex role of lipids in the link between ART and diabetes in HIV infection.