bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antemortem detection of Parkinson’s disease pathology in peripheral biopsies using artificial intelligence
Authors: Signaevsky Maxim , Marami Bahram , Prastawa Marcel , Tabish Nabil , Iida Megan A. , Zhang Xiang Fu , Sawyer Mary , Duran Israel , Koenigsberg Daniel G. , Bryce Clare H. , Chahine Lana M. , Mollenhauer Brit , Mosovsky Sherri , Riley Lindsey , Dave Kuldip D. , Eberling Jamie , Coffey Chris S. , Adler Charles H. , Serrano Geidy E. , White Charles L. , Koll John , Fernandez Gerardo , Zeineh Jack , Cordon-Cardo Carlos , Beach Thomas G. , Crary John F. 
Published: February 2022

AbstractThe diagnosis of Parkinson’s disease (PD) is challenging at all stages due to variable symptomatology, comorbidities, and mimicking conditions. Postmortem assessment remains the gold standard for a definitive diagnosis. While it is well recognized that PD manifests pathologically in the central nervous system with aggregation of α-synuclein as Lewy bodies and neurites, similar Lewy-type synucleinopathy (LTS) is additionally found in the peripheral nervous system that may be useful as an antemortem biomarker. We have previously found that detection of LTS in submandibular gland (SMG) biopsies is sensitive and specific for advanced PD; however, the sensitivity is suboptimal especially for early-stage disease. Further, visual microscopic assessment of biopsies by a neuropathologist to identify LTS is impractical for large-scale adoption. Here, we trained and validated a convolutional neural network (CNN) for detection of LTS on 283 digital whole slide images (WSI) from 95 unique SMG biopsies. A total of 8,450 LTS and 35,066 background objects were annotated following an inter-rater reliability study with Fleiss Kappa = 0.72. We used transfer learning to train a CNN model to classify image patches (151 × 151 pixels at 20× magnification) with and without the presence of LTS objects. The trained CNN model showed the following performance on image patches: sensitivity: 0.99, specificity: 0.99, precision: 0.81, accuracy: 0.99, and F-1 score: 0.89. We further tested the trained network on 1230 naïve WSI from the same cohort of research subjects comprising 42 PD patients and 14 controls. Logistic regression models trained on features engineered from the CNN predictions on the WSI resulted in sensitivity: 0.71, specificity: 0.65, precision: 0.86, accuracy: 0.69, and F-1 score: 0.76 in predicting clinical PD status, and 0.64 accuracy in predicting PD stage, outperforming expert neuropathologist LTS density scoring in terms of sensitivity but not specificity. These findings demonstrate the practical utility of a CNN detector in screening for LTS, which can translate into a computational tool to facilitate the antemortem tissue-based diagnosis of PD in clinical settings.
Differential protein expression in the hippocampi of resilient individuals identified by digital spatial profiling
Authors: Walker Jamie M. , Kazempour Dehkordi Shiva , Fracassi Anna , Vanschoiack Alison , Pavenko Anna , Taglialatela Giulio , Woltjer Randall , Richardson Timothy E. , Zare Habil , Orr Miranda E. 
Published: February 2022

AbstractClinical symptoms correlate with underlying neurodegenerative changes in the vast majority of people. However, an intriguing group of individuals demonstrate neuropathologic changes consistent with Alzheimer disease (AD) yet remain cognitively normal (termed “resilient”). Previous studies have reported less overall neuronal loss, less gliosis, and fewer comorbidities in these individuals. Herein, NanoString GeoMx™ Digital Spatial Profiler (DSP) technology was utilized to investigate protein expression differences comparing individuals with dementia and AD neuropathologic change to resilient individuals. DSP allows for spatial analysis of protein expression in multiple regions of interest (ROIs) on formalin-fixed paraffin-embedded sections. ROIs in this analysis were hippocampal neurofibrillary tangle (NFT)-bearing neurons, non-NFT-bearing neurons, and their immediate neuronal microenvironments. Analyses of 86 proteins associated with CNS cell-typing or known neurodegenerative changes in 168 ROIs from 14 individuals identified 11 proteins displaying differential expression in NFT-bearing neurons of the resilient when compared to the demented (including APP, IDH1, CD68, GFAP, SYP and Histone H3). In addition, IDH1, CD68, and SYP were differentially expressed in the environment of NFT-bearing neurons when comparing resilient to demented. IDH1 (which is upregulated under energetic and oxidative stress) and PINK1 (which is upregulated in response to mitochondrial dysfunction and oxidative stress) both displayed lower expression in the environment of NFT-bearing neurons in the resilient. Therefore, the resilient display less evidence of energetic and oxidative stress. Synaptophysin (SYP) was increased in the resilient, which likely indicates better maintenance of synapses and synaptic connections. Furthermore, neurofilament light chain (NEFL) and ubiquitin c-terminal hydrolase (Park5) were higher in the resilient in the environment of NFTs. These differences all suggest healthier intact axons, dendrites and synapses in the resilient. In conclusion, resilient individuals display protein expression patterns suggestive of an environment containing less energetic and oxidative stress, which in turn results in maintenance of neurons and their synaptic connections.
Shell isolated nanoparticle enhanced Raman spectroscopy for mechanistic investigation of electrochemical reactions
Authors: Haryanto Andi , Lee Chan Woo 
Published: February 2022

AbstractElectrochemical conversion of abundant resources, such as carbon dioxide, water, nitrogen, and nitrate, is a remarkable strategy for replacing fossil fuel-based processes and achieving a sustainable energy future. Designing an efficient and selective electrocatalysis system for electrochemical conversion reactions remains a challenge due to a lack of understanding of the reaction mechanism. Shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) is a promising strategy for experimentally unraveling a reaction pathway and rate-limiting step by detecting intermediate species and catalytically active sites that occur during the reaction regardless of substrate. In this review, we introduce the SHINERS principle and its historical developments. Furthermore, we discuss recent SHINERS applications and developments for investigating intermediate species involved in a variety of electrocatalytic reactions.
A multicentre simulation study of planar whole-body bone scintigraphy in Sweden
Authors: Gustafsson Agnetha , Örndahl Eva , Minarik David , Cederholm Kerstin , Frantz Sophia , Hagerman Jessica , Johansson Lena , Lindqvist Johan Fredén , Jonsson Cathrine 
Published: February 2022

Abstract
Background
Whole-body bone scintigraphy is a clinically useful non-invasive and highly sensitive imaging method enabling detection of metabolic changes at an early stage of disease, often earlier than with conventional radiologic procedures. Bone scintigraphy is one of the most common nuclear medicine methods used worldwide. Therefore, it is important that the examination is implemented and performed in an optimal manner giving the patient added value in the subsequent care process. The aim of this national multicentre survey was to investigate Swedish nuclear medicine departments compliance with European practice guidelines for bone scintigraphy. In addition, the effect of image acquisition parameters on the ability to detect metabolic lesions was investigated.

Methods
Twenty-five hospital sites participated in the study. The SIMIND Monte Carlo (MC) simulation and the XCAT phantom were used to simulate ten fictive patient cases with increased metabolic activity distributed at ten different locations in the skeleton. The intensity of the metabolic activity was set into six different levels. Individual simulations were performed for each site, corresponding to their specific camera system and acquisition parameters. Simulated image data sets were then sent to each site and were visually evaluated in terms of if there was one or several locations with increased metabolic activity relative to normal activity.

Result
There is a high compliance in Sweden with the EANM guidelines regarding image acquisition parameters for whole-body bone scintigraphy. However, up to 40% of the participating sites acquire lower count density in the images than recommended. Despite this, the image quality was adequate to maintain a stable detection level. None of the hospital sites or individual responders deviated according to the statistical analysis. There is a need for at least 2.5 times metabolic activity compared to normal for a lesion to be detected.

Conclusion
The imaging process is well harmonized throughout the country and there is a high compliance with the EANM guidelines. There is a need for at least 2.5 times the normal metabolic activity for a lesion to be detected as abnormal.
Ultrasound-assessed diaphragmatic dysfunction as a predictor of weaning outcome in mechanically ventilated patients with sepsis in intensive care unit
Authors: Saad Mohamed Ahmed , Nashed Sherif Wadie , El-Shaer Ahmed Nagah , Elagamy Ashraf Elsayed , El derh Maha Sadek 
Published: February 2022

Abstract
Background
Weaning from mechanical ventilation is one of the most common challenges in the intensive care unit (ICU). Most of predictive indices of weaning from mechanical ventilation are often inaccurate. This study was performed to assess the accuracy of diaphragmatic ultrasonography for predicting weaning outcome in mechanically ventilated patients with sepsis in ICU.

Results
Sixty patients with sepsis in medical ICU were prospectively enrolled. All patients were ventilated in pressure support. Patients underwent a spontaneous breathing trial (SBT) on T-piece when they met all the following criteria: FiO2 < 0.6, PEEP ≤5 cmH2O, PaO2/FiO2 > 200, respiratory rate <30 breaths per minute, absence of fever, alert and cooperative, hemodynamic stability without or with low-dose vasoactive therapy support, and rapid shallow breathing index (RSBI)<105. During the trial, the patient was instructed to perform deep breathing to total lung capacity (TLC) and then exhaling to residual volume (RV) and the diaphragm was visualized in the 8th or 9th intercostal space between anterior and mid-axillary lines using a 3–5-MHz curved ultrasound probe to measure diaphragmatic excursion (DE) and a 7–11-MHz linear ultrasound probe to measure diaphragmatic thickness (DT) at TLC and RV, and the diaphragmatic thickness fraction (DTF) was calculated as percentage from the following formula (thickness at end inspiration—thickness at end expiration)/thickness at end expiration. According to weaning outcome, patients were divided into 2 groups: successful weaning group and weaning failure group. Weaning failure was defined as the inability to maintain spontaneous breathing for at least 48 h, without any form of ventilatory support.
In the present study, right DTF of more than 37% and DE during deep breathing of more than 6.1 and 5.4 cm on the Rt and Lt side, respectively, were associated with successful weaning from MV. In the study, the sensitivities for right and left DE and DTF were 58.33, 62.5, and 58.33%, respectively, and the pooled specificities were 83.33, 83.33, and 100%, respectively, with p value = 0.032, 0.028, and 0.001, respectively. The area under curve (AUC) for Rt, Lt DE, and DTF were 0.701, 0.712, and 0.840, respectively. The present data indicate a satisfactory diagnostic accuracy in predicting extubation outcome.

Conclusions
Ultrasonography-based determination of diaphragm function by assessing DTF and DE can be used as predictor of weaning outcome in mechanically ventilated patients with sepsis.
Genome-editing opportunities to enhance cattle productivity in the tropics
Authors: de Almeida Camargo Luiz Sergio , Pereira Jorge Fernando 
Published: February 2022

AbstractThe livestock performance in tropical regions has been limited by environmental conditions that causes heat stress and favors the development of parasites and diseases, impairing animal health. Heat stress disturbs animal homeostasis and affects animal production and fertility, with negative impacts on meat and milk quality. Flies and ticks proliferate easily under hot-humid weather, which makes difficult the control of their population, resulting in an increased parasitism. Tropical pastures usually have high dry matter production, but it is challenging to keep high production and quality under different environmental conditions throughout the year, constraining animal performance. Several strategies have been adopted in an attempt to overcome such hurdles in the tropical regions, but definitive solutions are yet to be implemented. In the last 20 years, biotechnologies, such as in vitro embryo production and genomic selection, have played an important role on cattle production in tropical countries. Genome editing (GnEd) is the novel tool in the toolbox for cattle production. GnEd with genomic selection offers the opportunity to boost the genetic gain in breeding programs of tropical cattle in fewer generations. It can be applied for disease resistance, to control parasite population, and to improve pasture quality and tolerance to biotic and abiotic stresses, favoring animal health and nutrition. Moreover, there is a perspective for the use of GnEd to control cattle methane emission by editing genes of methanogens present in the rumen. Although GnEd can already be applied to improve some traits, studies are still required for the identification of candidate genes in animals, tropical pastures, parasites, and microorganisms that can be targeted by gene editing in order to offer a robust contribution to the improvement of cattle production in the hot regions. Some examples of the use of GnEd are presented in this review, focusing on new perspectives of using GnEd to increase cattle production under the challenges of the tropical environments.
Architectural typology of rural housing in Jaen, Peru
Authors: Peña-Huaman Floiran , Sifuentes-Rivera Diego , Yarasca-Aybar Cristian 
Published: February 2022

AbstractJaén is one of the most important cities in the northern highlands of Peru due to its strategic location, commerce, and agricultural activities. Jaén has more than 185 thousand inhabitants, of which 48% live in rural areas, representing approximately 31 thousand rural housing. This research aims to determine the types of rural housing in Jaén, showing the possible variations and architectural manifestations due to the territorial and cultural characteristics. A field observation sheet has been used to study the rural dwellings of populated centres previously classified by altitudinal regions. The results show six architectural types of rural housing classified into two groups: “rural-residential housing” and “rural-agricultural housing”. These architectural types are generally located near water sources, within agricultural plots, and on hillsides. The architectural program is characterised by agricultural activity and family composition, which has grown over time. The most commonly used construction systems are “pirca” and “quincha”, using natural materials such as “ichu” and adobe. There is also evidence of cultural traditions rooted in the construction, such as “cambio de fuerzas”, “paracaico”, and “minga”. Therefore, the relevance of Jaén’s rural housing is its geographical reading of the territory through the architectural and cultural legacy of these buildings.
Microfluidic systems for modeling human development
Authors: Bonner Makenzie G. , Gudapati Hemanth , Mou Xingrui , Musah Samira 
Published: February 2022

ABSTRACT
The proper development and patterning of organs rely on concerted signaling events emanating from intracellular and extracellular molecular and biophysical cues. The ability to model and understand how these microenvironmental factors contribute to cell fate decisions and physiological processes is crucial for uncovering the biology and mechanisms of life. Recent advances in microfluidic systems have provided novel tools and strategies for studying aspects of human tissue and organ development in ways that have previously been challenging to explore ex vivo. Here, we discuss how microfluidic systems and organs-on-chips provide new ways to understand how extracellular signals affect cell differentiation, how cells interact with each other, and how different tissues and organs are formed for specialized functions. We also highlight key advancements in the field that are contributing to a broad understanding of human embryogenesis, organogenesis and physiology. We conclude by summarizing the key advantages of using dynamic microfluidic or microphysiological platforms to study intricate developmental processes that cannot be accurately modeled by using traditional tissue culture vessels. We also suggest some exciting prospects and potential future applications of these emerging technologies.
An Intelligent Superhydrophilic/Underwater Superoleophobic Temperature Sensitive Switch Device with Excellent Targeted Oil-Water Separation Performance
Authors: Li Congcong , Feng Huixia , Xu Haidong , Chen Baiyi , Yang Tiantian 
Published: February 2022

Abstract
Oil/water separation has become a global challenge as more and more oily wastewater is generated from oil spills and industrial wastewater. Super-wetting fuctional materials in oil-water separation has obvious advantages such as high efficiency, simple craft and potential to intelligentialize. But traditional superhydrophobic/superlipophilic oil-water separation material is easily blocked and damaged by oil. Here, a temperature-sensitive superhydrophilic/underwater superoleophobic switch device (TS-PNIPAM-Ni) was prepared using a poly-N-isopropylacrylamide (PNIPAM) hydrogel and magnetic hydrophobic foamed nickel through a one-step solution dipping method. The separation efficiency of TS-PNIPAM-Ni to dichloroethane-water can reach up to 100% and maintain a separation efficiency of more than 99.9% after the completion of 10 separation cycles, and the oil-water separation stops above 34 °C and captures water droplets intelligently. The micro-morphology, micro-structure and components of TS-PNIPAM-Ni and PNIPAM were analyzed with FTIR, SEM and EDS. The TS-PNIPAM-Ni shows excellent superhydrophilic/underwater superoleophobicity, good temperature sensitivity and magnetic navigation function.
Vessel masking and Hough transform for optic disc localisation from retinal images
Authors: Ali Aziah , Wan Zaki Wan Mimi Diyana , Hussain Aini , Hashim Noramiza , Mohd Isa Wan Noorshahida 
Published: February 2022

Background: Retinal images can be considered as one of the reliable indicators for symptoms of many ocular diseases such as diabetic retinopathy, macular degeneration and glaucoma. By analysing and tracking changes of important structures on a retinal image, symptoms of ocular diseases can be detected in a timely manner which helps physicians plan early treatment for better disease control. One of the important landmarks on a retinal image is the optic disc (OD), which must be localised to estimate retinal vessel parameters such as vessel width and tortuosity. This paper proposes a method for automatic OD localisation from a retinal image. Methods: A retinal image is first pre-processed and thresholded to produce a binary image that highlights most retinal vessels on the image. Next, a discrete cosine transform-based smoothing method is employed to replace the detected vessel pixel values on the pre-processed image with values closer to the surrounding neighbour pixel values, effectively masking most vessels on the image. Hough transform is then applied to the vessel-masked image to detect the circle representing the OD on the image, producing the estimated location of the OD center and its estimated diameter. Results: Applying the proposed method to three different public databases, namely Digital Retinal Images for Vessel Extraction (DRIVE), High-Resolution Fundus (HRF) and Methods to Evaluate Segmentation and Indexing Techniques in the field of Retinal Ophthalmology (MESSIDOR) resulted in an overall detection rate of 99.53%. Conclusions: The achieved performance by the proposed method is superior to many published methods of OD localization, with a processing time of less than one second for each image. While this has only been validated on one type of retinal images, future investigations may include validation on other types such as angiograms or scanning laser ophthalmoscopy.
New Discovery of Covid-19 Natural-Based Potential Antivirus Herbal Supplement Products from Pinang Yaki (Areca vestiaria) Extract: A Preliminary Study by Untargeted Metabolomic Profiling
Authors: Simbala Herny Emma Inonta , Nurkolis Fahrul , Mayulu Nelly , Rotty Linda Wilhelma Ancella 
Published: February 2022

Background: Pinang yaki has bioactive compounds that have potential as a new herbal supplement. A better understanding of the bioactive compounds of pinang yaki using untargeted metabolomic profiling studies will provide clearer insight into the health benefits of pinang yaki and in particular its potential for the therapy and prevention of Covid-19. Methods: Fresh samples of pinang yaki (Areca vestiaria) are obtained from forests in North Sulawesi Province, Indonesia. Samples were used for untargeted metabolomics analysis by UPLC-MS. Results: Based on an untargeted metabolomic profiling study of pinang yaki, 2504 compounds in ESI- and 2645 compounds in ESI+ were successfully obtained. After the analysis, 356 compounds in ESI- and 543 compounds in ESI+ were identified successfully. Major compounds Alpha-Chlorohydrin (PubChem ID: 7290) and Tagatose (PubChem ID: 439312) were found in ESI+ and ESI-. Discussion: The Top 10 metabolites from pinang yaki extract (ESI+) juga have been indicated in preventing SARS Cov2 infection and have exhibited good neuroprotective immunity. Benzothiazole (PubChem ID: 7222), L-isoleucine (PubChem ID: 6306), D-glucono-delta-lactone (PubChem ID: 736), Diethylpyrocarbonate (PubChem ID: 3051), Bis(2-Ethylhexyl) amine (PubChem ID: 7791), Cinnamic acid (PubChem ID: 444539), and Trigonelline (PubChem ID: 5570) also had potential effects as an antiviral, anti-inflammatory, and anti-Covid19. Conclusion: Untargeted metabolomic profiling showed many bioactive compounds contained in pinang yaki (Areca vestiaria) extract. The top 10 compounds have been identified and explored for their potential benefits as anti-Covid19 supplement products. This is a preliminary study which still needs further research such as preclinical and clinical trials.