bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling dependency structures in 450k DNA methylation data
Authors: Nustad Haakon E , Steinsland Ingelin , Ollikainen Miina , Cazaly Emma , Kaprio Jaakko , Benjamini Yuval , Gervin Kristina , Lyle Robert 
Published: November 2021

Abstract

Motivation
DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences in dependency structure between individuals.

Results
We modeled spatial dependency with a flexible framework to quantify the dependency structure, focusing on inter-individual differences by exploring the association between dependency parameters and technical and biological variables. The model was applied to a subset of the Finnish Twin Cohort study (N = 1611 individuals). The estimates of the dependency parameters varied considerably across individuals, but were generally consistent across chromosomes within individuals. The variation in dependency parameters was associated with bisulfite conversion plate, zygosity, sex and age. The age differences presumably reflect accumulated environmental exposures and/or accumulated small methylation differences caused by stochastic mitotic events, establishing recognizable, individual patterns more strongly seen in older individuals.

Availability and implementation
The twin dataset used in the current study are located in the Biobank of the National Institute for Health and Welfare, Finland. All the biobanked data are publicly available for use by qualified researchers following a standardized application procedure (https://thl.fi/en/web/thl-biobank/for-researchers). A R-script for fitting the dependency structure to publicly available DNA methylation data with the software used in this article is provided in supplementary data.

Supplementary information
Supplementary data are available at Bioinformatics online.
Co-administration of platelet-rich plasma and small intestinal submucosa is more beneficial than their individual use in promoting acute skin wound healing
Authors: Lei Xiaoxuan , Cheng Liuhanghang , Yang Yu , Pang Mengru , Dong Yunqing , Zhu Xuanru , Chen Caihong , Yao Zexin , Wu Gang , Cheng Biao , Forouzanfar Tymour 
Published: November 2021

Abstract

Background
Acute skin wounds may compromise the skin barrier, posing a risk of infection. Small intestinal submucosa (SIS) is widely used to treat acute and chronic wounds. However, the efficacy of SIS to accelerate wound healing still needs to be improved to meet clinical demands. To tackle this problem, platelet-rich plasma (PRP) is used due to its potency to promote proliferation, migration and adhesion of target cells. In this study, we applied PRP and SIS to skin wounds to explore their effects on wound healing by evaluating re-epithelialization, collagen production, angiogenesis and the inflammatory response.

Methods
A 1 × 1-cm full-thickness skin defect was established in mice. Sixty mice were divided into four treatment groups: PRP + SIS, PRP, SIS and control. On days 3, 5, 7, 10 and 14 post-surgery, tissue specimens were harvested. Haematoxylin and eosin, Masson’s trichrome, immunohistochemical and immunofluorescence double staining were used to visualize epidermal thickness, collagen and vascular regeneration and inflammation.

Results
Wound contraction in the PRP and PRP + SIS groups was significantly greater, compared with the other groups, on days 3 and 5 post-surgery. A histological analysis showed higher collagen expression in the PRP and PRP + SIS groups on day 7, which was associated with a thicker epidermal layer on day 14. In addition, immunohistochemical staining showed that CD31-positive blood vessels and vascular endothelial growth factor expression in the PRP + SIS and PRP groups were significantly higher, compared with the control group. Furthermore, immunofluorescence double staining showed that the number of M1 and M2 macrophages in the PRP + SIS and PRP groups was higher, compared with the control and SIS groups alone, on day 3. However, on day 7, the number of M1 macrophages dramatically decreased in the PRP + SIS and PRP groups. The ratio of M2 to M1 macrophages in the PRP + SIS and PRP groups was 3.97 and 2.93 times that of the control group and 4.56 and 3.37 times that of the SIS group, respectively.

Conclusion
Co-administration of SIS and PRP has a better effect on promoting angiogenesis, re-epithelialization and collagen regeneration in managing acute wound healing than either agent alone.
The developmental changes in intrinsic and synaptic properties of prefrontal neurons enhance local network activity from the second to the third postnatal weeks in mice
Authors: Kalemaki Katerina , Velli Angeliki , Christodoulou Ourania , Denaxa Myrto , Karagogeos Domna , Sidiropoulou Kyriaki 
Published: November 2021

Abstract
The prefrontal cortex (PFC) is characterized by protracted maturation. The cellular mechanisms controlling the early development of prefrontal circuits are still largely unknown. Our study delineates the developmental cellular processes in the mouse medial PFC (mPFC) during the second and the third postnatal weeks and characterizes their contribution to the changes in network activity. We show that spontaneous inhibitory postsynaptic currents (sIPSC) are increased, whereas spontaneous excitatory postsynaptic currents (sEPSC) are reduced from the second to the third postnatal week. Drug application suggested that the increased sEPSC frequency in mPFC at postnatal day 10 (P10) is due to depolarizing γ-aminobutyric acid (GABA) type A receptor function. To further validate this, perforated patch-clamp recordings were obtained and the expression levels of K–Cl cotransporter 2 (KCC2) protein were examined. The reversal potential of IPSCs in response to current stimulation was significantly more depolarized at P10 than P20 while KCC2 expression is decreased. Moreover, the number of parvalbumin-expressing GABAergic interneurons increases and their intrinsic electrophysiological properties significantly mature in the mPFC from P10 to P20. Using computational modeling, we show that the developmental changes in synaptic and intrinsic properties of mPFC neurons contribute to the enhanced network activity in the juvenile compared with neonatal mPFC.
Spatial probability maps of the segments of the postcentral sulcus in the human brain
Authors: Zlatkina Veronika , Sprung-Much Trisanna , Petrides Michael 
Published: November 2021

Abstract
The postcentral sulcus is the posterior boundary of the postcentral gyrus where the somatosensory cortex is represented. In the human brain, the postcentral sulcus is composed of five distinct segments that are related to the somatosensory representation of different parts of the body. Segment 1 of the postcentral sulcus, located near the dorsomedial boundary of each hemisphere, is associated with toe/leg representations, segment 2 with arm/hand representations, segment 3 with blinking, and segments 4 and 5, which are near the lateral fissure and the parietal operculum, with the mouth and tongue representations. The variability in location and spatial extent of these five segments were quantified in 40 magnetic resonance imaging (MRI) anatomical brain scans registered to the stereotaxic space of the Montreal Neurological Institute (MNI space), in the form of volumetric (using MINC Toolkit) and surface (using FreeSurfer) spatial probability maps. These probability maps can be used by researchers and clinicians to improve the localization of the segments of the postcentral sulcus in MRI images of interest and also to improve the interpretation of the location of activation peaks generated in functional neuroimaging studies investigating somatosensory cortex.
The effective connectivity of the human hippocampal memory system
Authors: Rolls Edmund T , Deco Gustavo , Huang Chu-Chung , Feng Jianfeng 
Published: November 2021

Abstract
Effective connectivity measurements in the human hippocampal memory system based on the resting-state blood oxygenation-level dependent signal were made in 172 participants in the Human Connectome Project to reveal the directionality and strength of the connectivity. A ventral “what” hippocampal stream involves the temporal lobe cortex, perirhinal and parahippocampal TF cortex, and entorhinal cortex. A dorsal “where” hippocampal stream connects parietal cortex with posterior and retrosplenial cingulate cortex, and with parahippocampal TH cortex, which, in turn, project to the presubiculum, which connects to the hippocampus. A third stream involves the orbitofrontal and ventromedial-prefrontal cortex with effective connectivity with the hippocampal, entorhinal, and perirhinal cortex. There is generally stronger forward connectivity to the hippocampus than backward. Thus separate “what,” “where,” and “reward” streams can converge in the hippocampus, from which back projections return to the sources. However, unlike the simple dual stream hippocampal model, there is a third stream related to reward value; there is some cross-connectivity between these systems before the hippocampus is reached; and the hippocampus has some effective connectivity with earlier stages of processing than the entorhinal cortex and presubiculum. These findings complement diffusion tractography and provide a foundation for new concepts on the operation of the human hippocampal memory system.
Impact of Isolation and Exclusion as a Public Health Strategy to Contain Measles Virus Transmission During a Measles Outbreak
Authors: Banerjee Emily , Paul Prabasaj , Griffith Jayne , Laine Ellen , Como-Sabetti Kathryn , Gastañaduy Paul A 
Published: November 2021

Abstract
Responding to measles outbreaks in the United States puts a considerable strain on public health resources, and limited research exists about the effectiveness of containment strategies. In this paper we quantify the impact of isolation, contact tracing, and exclusion in reducing transmission during a measles outbreak in an under-vaccinated community.
Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection Associates With Unstable Housing and Occurs in the Presence of Antibodies
Authors: Bean David J , Monroe Janet , Turcinovic Jacquelyn , Moreau Yvetane , Connor John H , Sagar Manish 
Published: November 2021

Abstract

Background
The factors associated with severe acute respiratory coronavirus 2 (SARS-CoV-2) reinfection remain poorly defined.

Methods
We identified patients with SARS-CoV-2 infection and at least 1 repeat reverse transcription polymerase chain reaction result a minimum of 90 days after the initial positive test and before 21 January 2021. Those with a repeat positive test were deemed to have reinfection (n = 75), and those with only negative tests were classified as convalescents (n = 1594). Demographics, coronavirus disease 2019 (COVID-19) severity, and treatment histories were obtained from the Boston Medical Center electronic medical record. Humoral responses were analyzed using SARS-CoV-2–specific enzyme-linked immunosorbent assays and pseudovirus neutralizations in a subset of reinfection (n = 16) and convalescent samples (n = 32). Univariate, multivariate, and time to event analyses were used to identify associations.

Results
Individuals with reinfection had more frequent testing at shorter intervals compared with the convalescents. Unstable housing was associated with more than 2-fold greater chance of reinfection. Preexisting comorbidities and COVID-19 severity after the initial infection were not associated with reinfection. SARS-CoV-2 immunoglobulin G levels and pseudovirus neutralization were not different within the early weeks after primary infection and at a timepoint at least 90 days later in the 2 groups. In the convalescents, but not in those with reinfection, the late as compared with early humoral responses were significantly higher.

Conclusions
Reinfection associates with unstable housing, which is likely a marker for virus exposure, and reinfection occurs in the presence of SARS-CoV-2 antibodies.
A Novel Generation Method for Diverse Privacy Image Based on Machine Learning
Authors: Niu Weina , Luo Yuheng , Ding Kangyi , Zhang Xiaosong , Wang Yanping , Li Beibei 
Published: November 2021

AbstractIn recent years, deep neural networks have been extensively applied in various fields, and face recognition is one of the most important applications. Artificial intelligence has reached or even surpassed human capabilities in many fields. However, while artificial intelligence application provides convenience to the human lives, it also leads to the risk of privacy leaking. At present, the privacy protection technology for human faces has received extensive attention. Research goals of face privacy protection technology mainly include providing face anonymization and data availability protection. Existing methods usually have insufficient anonymity and they are not easy to control the degree of image distortion, which makes it difficult to achieve the purpose of privacy protection. Moreover, they do not explicitly perform diversity preservation of attributes such as emotions, expressions and ethnicities, so they cannot perform data analysis tasks on non-identity attributes. This paper proposes a diverse privacy face image generation algorithm based on machine learning, called DIVFGEN. This algorithm comprehensively considers image distortion, identity mapping distance loss and emotion classification loss; transforms the privacy protection target into the problem of generating adversarial examples based on the recognition model; and uses an adaptive optimization algorithm to generate anonymity and diversity of privacy images. The experimental results show that on the Cohn-Kanade+ dataset, our algorithm can reduce the probability of facial recognition by the neural network when it accurately classifies sentiment, from 98.6% to 4.8%.
A New Approach for Resource Recommendation in the Fog-Based IoT Using a Hybrid Algorithm
Authors: Xu Zhiwang , Qin Huibin , Yang Shengying , Arefzadeh Seyedeh Maryam 
Published: November 2021

AbstractInternet of things (IoT) is an architecture of connected physical objects; these objects can communicate with each other and transmit and receive data. Also, fog-based IoT is a distributed platform that provides reliable access to virtualized resources based on various technologies such as high-performance computing and service-oriented design. A fog recommender system is an intelligent engine that suggests suitable services for fog users with less answer time and more accuracy. With the rapid growth of files and information sharing, fog recommender systems’ importance is also increased. Besides, the resource management problem appears challenging in fog-based IoT because of the fog’s unpredictable and highly variable environment. However, many current methods suffer from the low accuracy of fog recommendations. Due to this problem’s Non-deterministic Polynomial-time (NP)-hard nature, a new approach is presented for resource recommendation in the fog-based IoT using a hybrid optimization algorithm. To simulate the suggested method, the CloudSim simulation environment is used. The experimental results show that the accuracy is optimized by about 1–8% compared with the Cooperative Filtering method utilizing Smoothing and Fusing and Artificial Bee Colony algorithm. The outcomes of the present paper are notable for scholars, and they supply insights into subsequent study domains in this field.
Outcomes and Long-Term Effects of COVID-19 in Patients with Inflammatory Bowel Diseases – A Danish Prospective Population-Based Cohort Study with Individual-Level Data
Authors: Attauabi Mohamed , Dahlerup Jens Frederik , Poulsen Anja , Hansen Malte Rosager , Vester-Andersen Marianne Kajbæk , Eraslan Sule , Prahm August Pilegaard , Pedersen Natalia , Larsen Lone , Jess Tine , Neumann Anders , Haderslev Kent V , Molazahi Akbar , Lødrup Anders Berg , Glerup Henning , Oppfeldt Asser Mathiassen , Jensen Michael Dam , Theede Klaus , Kiszka-Kanowitz Marianne , Seidelin Jakob Benedict , Burisch Johan 
Published: November 2021

AbstractBackground and AimsThe health consequences of coronavirus disease 2019 [COVID-19] among patients with ulcerative colitis [UC] and Crohn’s disease [CD] remain largely unknown. We aimed to investigate the outcomes and long-term effects of COVID-19 in patients with UC or CD.MethodsWe conducted a prospective, population-based study covering all Danish patients with CD or UC and confirmed COVID-19 between January 28, 2020 and April 1, 2021, through medical records and questionnaires.ResultsAll 319 patients with UC and 197 patients with CD who developed COVID-19 in Denmark were included in this study and compared with the Danish background population with COVID-19 [N = 230 087]. A significantly higher risk of COVID-19-related hospitalization was observed among patients with UC (N = 46 [14.4%], relative risk [RR] = 2.49 [95% confidence interval, CI, 1.91–3.26]) and CD (N = 24 [12.2%], RR = 2.11 [95% CI 1.45–3.07]) as compared with the background population (N = 13 306 [5.8%]). A similar pattern was observed for admission to intensive care (UC: N = 8 [2.51%], RR = 27.88 [95% CI 13.88–56.00]; CD: N = 3 [1.52%], RR = 16.92 [95% CI 5.46–52.46]). After a median of 5.1 months (interquartile range [IQR] 4.5–7.9), 58 [42.3%] and 39 [45.9%] patients with UC and CD, respectively, reported persisting symptoms which were independently associated with discontinuation of immunosuppressive therapies during COVID-19 (odds ratio [OR] = 1.50 [95% CI 1.07–10.22], p = 0.01) and severe COVID-19 (OR = 2.76 [95% CI 1.05–3.90], p = 0.04), but not with age or presence of comorbidities.ConclusionIn this population-based study of 516 patients with IBD and COVID-19, 13.6% needed hospitalization and 2.1% required intensive care. Furthermore, sequelae were frequent, affecting 43.7% of COVID-19-infected patients. These findings might have implications for planning the healthcare of patients in the post-COVID-19 era.
Modeling the Influence of Abiotic and Biotic Factors on Spatial and Temporal Fluctuations of Prostephanus truncatus (Coleoptera: Bostrichidae) Populations in Mozambique
Authors: Muatinte Bernardo L , Van den Berg Johnnie 
Published: November 2021

Abstract
The larger grain borer, Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), is a serious pest of stored maize in Mozambique and in other African countries. This study investigated the influence of abiotic and biotic factors on populations of P. truncatus at four sites over a two-year period (2013–2014) in Mozambique. Fourteen 250 × 250 m quadrants were selected at each site. Plant species diversity, temperature, precipitation, and relative humidity data were recorded. Pheromone-baited Uni-traps were used to monitor P. truncatus inside each quadrant. In addition, plant species were identified using visual observation and measurement of morphological features of leaves and fruits, and quantified, after which the percentage of host plant species of P. truncatus was determined out of all species in each quadrant. Multiple regression analysis and generalized linear models showed that host plant species dominance, maximum and minimum temperature, relative humidity, and rainfall influenced the variations in P. truncatus abundance. The development of these models of P. truncatus flight activity provides a baseline for further studies predicting dispersal and potential areas of invasion by this pest.
Moderate aortic stenosis: importance of symptoms and left ventricular ejection fraction
Authors: Stassen Jan , Ewe See Hooi , Butcher Steele C , Amanullah Mohammed R , Hirasawa Kensuke , Singh Gurpreet K , Sin Kenny Y K , Ding Zee P , Pio Stephan M , Sia Ching-Hui , Chew Nicholas W S , Kong William K F , Poh Kian Keong , Cohen David J , Généreux Philippe , Leon Martin B , Marsan Nina Ajmone , Delgado Victoria , Bax Jeroen J 
Published: November 2021

Abstract

Aims
The aim of this study is to investigate the independent determinants of survival in patients with moderate aortic stenosis (AS), stratified by severity of symptoms and left ventricular ejection fraction (LVEF).

Methods and results
Patients with a first diagnosis of moderate AS (aortic valve area &gt;1.0 and ≤1.5 cm2) were identified. Patients were stratified by New York Heart Association (NYHA) functional class (NYHA I, NYHA II, or NYHA III–IV) and LVEF (LVEF ≥60%, LVEF 50–59%, or LVEF &lt;50%) at the time of moderate AS diagnosis. The primary endpoint was all-cause mortality, while the secondary endpoint included all-cause mortality and aortic valve replacement. Of 1961 patients with moderate AS (mean age 73 ± 10 years, 51% men), 1108 (57%) patients were in NYHA class I, while 527 (27%) and 326 (17%) patients had symptoms of NYHA class II and III–IV, respectively. Regarding LVEF, 1032 (53%) had LVEF ≥60%, 544 (28%) LVEF 50–59%, and 385 (20%) LVEF &lt;50%. During a median follow-up of 50 (23–82) months, 868 (44%) patients died. On multivariable analysis, NYHA class II [hazard ratio (HR): 1.633; 95% confidence interval (CI): 1.431–1.864; P &lt; 0.001], NYHA class III–IV (HR: 2.084; 95% CI: 1.797–2.417; P &lt; 0.001), LVEF 50–59% (HR: 1.194; 95% CI: 1.013–1.406; P = 0.034), and LVEF &lt;50% (HR: 1.694; 95% CI: 1.417–2.026; P &lt; 0.001) were independently associated with increased mortality.

Conclusion
Moderate AS is associated with poor long-term survival. Baseline symptom severity and LVEF are associated with worse outcomes in these patients. Patients with low-normal LVEF (&lt;60%) and mild symptoms (NYHA II) already have an increased risk of adverse events.
Miniseries 2—Septal and paraseptal accessory pathways—Part III: Mid-paraseptal accessory pathways—revisiting bypass tracts crossing the pyramidal space
Authors: Farré Jerónimo , Anderson Robert H , Rubio José-Manuel , García-Talavera Camila , Sánchez-Quintana Damián , Bansal Raghav , Lokhandwala Yash , Cabrera José-Angel , Wellens Hein J J , Back Sternick Eduardo 
Published: November 2021

Abstract
The mid-paraseptal region corresponds to the portion of the pyramidal space whose right atrial aspect is known as the triangle of Koch. The superior area of this mid-paraseptal region is also para-Hisian, and is close to the compact atrioventricular node and the His bundle. The inferior sector of the mid-paraseptal area is unrelated to the normal atrioventricular conduction pathways. It is, therefore, a safe zone in which, if necessary, to perform catheter ablation. The middle part of the mid-paraseptal zone may, however, in some patients, house components of the compact atrioventricular node. This suggests the need for adopting a prudent attitude when considering catheter ablation in this area. The inferior extensions of the atrioventricular node, which may represent the substrate for the slow atrioventricular nodal pathway, take their course through the middle, and even the inferior, sectors of the mid-paraseptal region. In this review, we contend that the middle and inferior areas of the mid-paraseptal region correspond to what, in the past, was labelled by most groups as the ‘midseptal’ zone. We describe the electrocardiographic patterns observed during pre-excitation and orthodromic reciprocating tachycardia in patients with pathways ablated in the middle or inferior sectors of the region. We discuss the modification of the ventriculo-atrial conduction times during tachycardia after the development of bundle branch block aberrancy. We conclude that the so-called ‘intermediate septal’ pathways, as described in the era of surgical ablation, were insufficiently characterized. They should not be considered the surrogate of the ‘midseptal’ pathways defined using endocardial catheter electrode mapping.