bluuebunny/crossref_metadata_2025_split huggingface dataset:
CTMC Analyzing NAFLD Progression (Small Model)
Authors: Attia Iman M. 
Published: February 2022

Abstract
In this article, I tackle the problem of non-alcoholic fatty liver disease (NAFLD) from the statistical point of view. Using the multistate model, in the form of the continuous time Markov chains, helps the statistical analysis of the progression of the disease over time. The simplest model of the health-disease-death process is applied to the NAFLD. The model is composed of 8 pdfs and 5 rates that need to be estimated. Maximum likelihood and quasi-Newton methods are applied to estimate the transition rates among states. Exponentiation of this estimated rate matrix yields the transition probability matrix. This transition probability matrix can also be estimated from solving the forward Kolmogorov differential equations. Testing time homogeneity of this CTMC that model the disease process is also discussed by the author. This can be achieved by finding an empirical probability matrix that equates the exponentiation of the transition rate matrix, which is thoroughly investigated in the chapter. Also the embedding problem that may arise when trying to find the transition rate matrix from the transition probability matrix of the corresponding discrete time model is clarified. Testing Markovian property of the chain is also presented. Some remarks are also highlighted as regard the state probability distribution and the stationary probability distribution.
Effects of social restrictions on people with dementia and carers during the pre-vaccine phase of the COVID-19 pandemic: experiences of IDEAL cohort participants
Authors: Pentecost Claire , Collins Rachel , Stapley Sally , Victor Christina , Quinn Catherine , Hillman Alexandra , Litherland Rachael , Allan Louise , Clare Linda 
Published: February 2022

Abstract

This qualitative study was designed to understand the impact of social distancing measures on people with dementia and carers living in the community during a period of ongoing restrictions before the COVID-19 vaccination roll-out in England and Wales. We conducted semi-structured interviews with 11 people with dementia and 10 carers (including 3 dyads) living in the community in England and Wales. Participants were recruited during November and December 2020. We used framework analysis to identify issues and elicit suggestions for potential solutions. We identified three interrelated themes. People with dementia experienced a fear of decline in capabilities or mood and attempted to mitigate this. Carers were aware of changes in the person with dementia and an increase in caring responsibilities and for some, there was a change in the relationship. Subsequently, reduced confidence in capabilities to navigate a new and hostile environment created a cyclical dilemma of returning to ‘normal’ where not returning to usual activities made things worse. People with dementia and carers had feelings of neglect and being alone in their struggle, alongside feeling socially excluded during the pandemic when comparing themselves to others in society, and there was little optimism associated with the upcoming vaccine programme. People found their own solutions to reduce the effects of isolation by keeping busy and socially active and practising skills deemed to help reduce the progression of dementia. This and some limited local public initiatives for the general public facilitated feelings of social inclusion. This study adds understanding to existing evidence about the longer-term experience of social isolation several months into the pandemic highlighting the importance of health and community groups and how services can find ways to support, include and interact with people with dementia and carers during and after social restrictions.
A New Approach to Estimate the Critical Shear Stress of Stiffened Plate Girder
Authors: Hamed Asmaa Y 
Published: February 2022

Abstract
Despite years of studies on critical bucking stresses, choosing the perfect boundary conditions at the junction between the web plate and flange & stiffener is still a question of engineering judgment. A conservative design criterion is adopted by all current codes of practice and standards at this juncture, based on the simply supported boundary conditions. However, in this study, we have proved Two theoretical methods were employed to investigate such situation that the boundary conditions along the junction between the webs and the flanges as built-in and the other boundary conditions along the position of the vertical stiffeners are assumed to be simply supported due to the relatively small stiffness of the stiffeners could be reached. The first method using the minimum potential energy concept to obtain a semi-exact equation from which the interaction equation can be deduced. The second method is performed by using a finite element technique (ANSYS software) to investigate the effects of the geometric parameters on the boundary conditions at the juncture.
ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
Authors: Mixão Verónica , Pinto Miguel , Gomes João Paulo , Borges Vitor 
Published: February 2022

Abstract

Genomics-informed pathogen surveillance strengthens public health decision-making, thus playing an important role in infectious diseases’ prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time consuming and difficult to reproduce. For this reason, we developed ReporTree, an automated surveillance-oriented pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance threshold(s) of a tree, identify regions of cluster stability (key step in nomenclature design), and further characterize them according to any relevant feature, such as timespan, geography or clinical status. To validate ReporTree, we reproduced a large-scale study on genetic clustering and linkage to antibiotic resistance data in Neisseria gonorrhoeae. Also, we show how this tool can be a useful asset in genomics-informed routine surveillance and outbreak detection of a wide variety of species, providing examples for SARS-CoV-2 virus and the foodborne bacterial pathogen Listeria monocytogenes. In summary, ReporTree facilitates and accelerates the production of surveillance-oriented reports, thus contributing to a sustainable and efficient public health genomics-informed pathogen surveillance.Availability and implementation: ReporTree is implemented in python 3.6 and is freely available at https://github.com/insapathogenomics/ReporTree.
Outcomes of Heavily Experienced HIV-Infected Patients Receiving Salvage Raltegravir-Based Therapy
Authors: Escarcina Jesús Enrique Patiño , Netto Eduardo Martins , Brites Carlos 
Published: February 2022

Abstract
Objectives
To assess real-life virologic success, long-term survival, and adverse events in treatment-experienced patients initiating either raltegravir or other third-line drugs (darunavir/ritonavir, maraviroc or etravirine) for salvage regimens in a Brazilian cohort of heavily treated patients.
Results
We included 168 patients initiating salvage regimens, 123 on raltegravir and 45 on other drugs (darunavir/ritonavir, maraviroc or etravirine). Of these, 90 patients were matched by Propensity score (PS) methods to account for clinical differences at the time of the switch from failing ART regimens, 45 patients from each group. During follow-up, virologic suppression (PVL<50 copies/mL) was similar for both groups (77.8% vs. 82.2%, p=0.73). During a mean follow-up of 1.09 (SD = 0.32) years, mortality rates (4.04 vs 6.18 persons per 100 person-years; p=0.67), drug toxicity (0.00 vs 2.06 persons per 100 person-years; p=0.49), treatment interruption (8.07 vs 0.00 persons per 100 person-years; p=0.06), virologic failure (2.02 vs 4.12 persons per 100 person-years; p=0.61) and loss of follow-up (6.05 vs 4.12 persons per 100 person-years; p=0.70) were similar for both groups. Our findings suggest similar survival and virologic success rates for raltegravir and other drugs for salvage regimens, with similar drug toxicity rates, treatment interruption, virologic failure, and loss of follow-up.
Identification of methylation driven biomarkers for diagnosis and prognosis in colorectal cancer by Integrative Analysis of TCGA, GTEx, and GEO database
Authors: Cao Lichao , Li Tong , Ba Ying , Chen Erfei , Yang Jin , Zhang Hezi 
Published: February 2022

Abstract
Background: This work investigates the use of methylation driven biomarkers for diagnosis and prognosis in colorectal cancer (CRC) by mining DNA methylation and gene expression data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), and the Gene Expression Omnibus (GEO).
Methods: The differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were screened using mRNA expression and DNA methylation data from TCGA, respectively. The methylation driven genes (MDGs) of CRC were further identified using the MethylMix R package. Subsequently, the MDGs were analyzed with Random Forest (RF), support vector machine (SVM), and logistic regression (LR) algorithms to establish diagnosis prediction models as independent indicators using mRNA expression data from TCGA and GTEx. The RF algorithm was determined to be the most suitable and used to construct the diagnostic model with the combined MDGs, which was then validated by GSE39582 from GEO. Prognostic biomarkers were used to establish the risk score model, which was generated by univariate and multivariate Cox regression analyses. Moreover, we constructed and validated a nomogram that integrated the risk score and clinical information, including age, gender, and tumor stage.
Results: 9 out of 10 MDGs performed well as independent diagnostic predictors, and STK33 and EPHX4 were also found to be associated with overall survival (OS). The results of the nomogram suggest that it is a better predictive model for prognosis than the risk score model.
Conclusion: Our findings suggest that the identified MDGs could be biomarkers for diagnosis and prognosis of CRC.
Jelajah Pemikiran Josef Prijotomo terhadap Arsitektur Nusantara (Tahun 1999-2020): Kajian Sejarah Pemikiran
Authors: Octavia Linda 
Published: February 2022

Title: Exploration on Josef Prijotomo Thinking towards Nusantara Architecture (1999-2020): A History of Thought Studies

The Indonesian historical journey in which showing the traces of architectural discourse is still on its way. One of the strong discourses in forming the foundation of thinking is Nusantara Architecture. Nusantara Architecture, as suggested by Prijotomo, is an architecture in which its perspective, concepts, and theories are developed based on Mother Nature. Prijotomo has been working in the formation of this Thinking and it evolves in time. It is important to understand this journey as well as to understand Nusantara Architecture The study of the exploration of Prijotomo’s thinking about Nusantara Architecture (1999-2020) aims to identify the shift of Prijotomo’s way of thinking from Traditional Architecture to Nusantara Architecture, as well as identifying the impacts or implications of Prijotomo’s thinking in the recent era. The study uses a historical research method using documents and oral sources. The document sources used are the original ones including books and articles written by Prijotomo within 1999-2020, while the oral sources are the direct conversation with Prijotomo. Through the exploration, it can be concluded that using Nusantara Architecture thinking, Prijotomo has attempted to make the base thought of Mother Nature equal to Western Architecture (European and American). This study serves as a starter to place Nusantara Architecture as architectural knowledge that is ‘liyan (the other)’ in relation to Western Architecture (European and American). The thoughts in seeking the base foundations for architects of (in) Indonesia are still ongoing. However, the offer and even the basis initiated and proposed in a series of Prijotomo’s deep thinking struggle are crucial and relevant. Emendation and purification by Prijotomo should be used and sustained by the various Architecture stakeholders in Indonesia.
Black Phosphorous Aptamer-based Platform for Biomarker Detection
Authors: Nene Ajinkya , Geng Shengyong , Zhou Wenhua , Yu Xue-Feng , Luo Hongrong , Ramakrishna Seeram 
Published: February 2022

Abstract:
Black phosphorus nanostructures (nano-BPs) mainly include BP nanosheets
(BP NSs), BP quantum dots (BPQDs), and other nano-BPs-based particles at nanoscale.
Firstly discovered in 2014, nano-BPs are one of the most popular nanomaterials. Different
synthesis methods are discussed in short to understand the basic concepts and developments
in synthesis. Exfoliated nano-BPs, i.e. nano-BPs possess high surface area, high
photothermal conversion efficacy, excellent biocompatibility, high charge carrier mobility
(~1000 cm2V-1s-1), thermal conductivity of 86 Wm-1K-1; and these properties make it a
highly potential candidate for fabrication of biosensing platform. These properties enable
nano-BPs to be promising photothermal/drug delivery agents as well as in electrochemical
data storage devices and sensing devices; and in super capacitors, photodetectors, photovoltaics
and solar cells, LEDs, super-conductors, etc. Early diagnosis is very critical in
the health sector scenarios. This review attempts to highlight the attempts made towards
attaining stable BP, BP-aptamer conjugates for successful biosensing applications. BP-aptamer-
based platforms are reviewed to highlight the significance of BP in detecting biological
and physiological markers of cardiovascular diseases and cancer; to be useful in
disease diagnosis and management.
Neoteric Direct Physical Approaches in TDDS: A Boon for Permeation
Enhancement
Authors: Palekar Shanbhag Pradnya , Jain Ronak 
Published: February 2022

Abstract:
Human skin has been tremendously explored for decades as a potential route for the delivery of various substances. It has shown great applications to deliver drugs to systemic circulation as well as has provided adequate advantages to treat local manifestations over the skin. However, the rigid stratum corneum layer has served as the biggest barrier in transdermal drug delivery; various methods have been designed to overcome the stratum corneum layer and make the molecule pass through this. These methods were then broadly classified into chemical and physical approaches. The below study is an overall review of the physical approaches being used in transdermal drug delivery for overcoming the stratum corneum layer. Physical approaches also include direct and indirect methods; we will be physically considering the direct approaches herein.
Epigenetic Modifications by Estrogen and Androgen in Alzheimer’s
Disease
Authors: Kumar Rajnish , Fatima Faiza , Yadav Garima , Singh Simran , Haldar Subhagata , Alexiou Athanasios , Ashraf Ghulam Md 
Published: February 2022

Abstract:
For the development and maintenance of neuron networks in the brain, epigenetic mechanisms
are necessary, as indicated by recent findings. This includes some of the high-order brain processes,
such as behavior and cognitive functions. Epigenetic mechanisms could influence the pathophysiology
or etiology of some neuronal diseases, altering disease susceptibility and therapy responses.
Recent studies support epigenetic dysfunctions in neurodegenerative and psychiatric conditions,
such as Alzheimer's disease (AD). These dysfunctions in epigenetic mechanisms also play crucial
roles in the transgenerational effects of the environment on the brain and subsequently in the inheritance
of pathologies. The possible role of gonadal steroids in the etiology and progression of neurodegenerative
diseases, including Alzheimer’s disease, has become the subject of a growing body of
research over the last 20 years. Recent scientific findings suggest that epigenetic changes, driven by
estrogen and androgens, play a vital role in brain functioning. Therefore, exploring the role of estrogen
and androgen-based epigenetic changes in the brain is critical for the deeper understanding of AD.
This review highlights the epigenetic modifications caused by these two gonadal steroids and the possible
therapeutic strategies for AD.
Characterization of Human-malarial Parasite Species based on DHFR and
GST Targets Resulting in Changes in Anti-malarial Drug Binding
Conformations
Authors: Sakpal Shrutika , Kothari Shanker Lal , Bastikar Virupaksha 
Published: February 2022

Background:
In this study, we focused primarily on three anti-malarial drugs that were tested against two malarial targets. Anti-malarial drugs like chloroquine, mefloquine, proguanil were chosen, while DHFR and GST targets from human malaria parasites such as Plasmodium falciparum, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax were considered for the study.

Objective:
The purpose of this study was to determine the sequence and structural similarity of proteins DHFR and GST among four Plasmodium species as well as to discover in silico interactions with aforementioned drug candidates.

Methods:
To conduct research, many bioinformatics databases like PDB, UniProt, DrugBank, PubChem; tools, and software’s like Phyre 2.0, Clustal O (1.2.4), and AutoDock 4, AutoDock vina, Discovery studio visualizer were used to determine the evolutionary significance of Plasmodium species.

Result:
Hence that variation has shown a difference in the binding patterns of drugs with target proteins. Our findings revealed Plasmodium spp divergence or convergence as well as how structurally and sequentially they share similar or dissimilar features

Conclusion:
As a result of the diversity, variations in protein-drug binding patterns have emerged.
Applications and User Perceptions of Smart Glasses in Emergency Medical Services: Semistructured Interview Study
Authors: Zhang Zhan , Joy Karen , Harris Richard , Ozkaynak Mustafa , Adelgais Kathleen , Munjal Kevin 
Published: February 2022

Background
Smart glasses have been gaining momentum as a novel technology because of their advantages in enabling hands-free operation and see-what-I-see remote consultation. Researchers have primarily evaluated this technology in hospital settings; however, limited research has investigated its application in prehospital operations.

Objective
The aim of this study is to understand the potential of smart glasses to support the work practices of prehospital providers, such as emergency medical services (EMS) personnel.

Methods
We conducted semistructured interviews with 13 EMS providers recruited from 4 hospital-based EMS agencies in an urban area in the east coast region of the United States. The interview questions covered EMS workflow, challenges encountered, technology needs, and users’ perceptions of smart glasses in supporting daily EMS work. During the interviews, we demonstrated a system prototype to elicit more accurate and comprehensive insights regarding smart glasses. Interviews were transcribed verbatim and analyzed using the open coding technique.

Results
We identified four potential application areas for smart glasses in EMS: enhancing teleconsultation between distributed prehospital and hospital providers, semiautomating patient data collection and documentation in real time, supporting decision-making and situation awareness, and augmenting quality assurance and training. Compared with the built-in touch pad, voice commands and hand gestures were indicated as the most preferred and suitable interaction mechanisms. EMS providers expressed positive attitudes toward using smart glasses during prehospital encounters. However, several potential barriers and user concerns need to be considered and addressed before implementing and deploying smart glasses in EMS practice. They are related to hardware limitations, human factors, reliability, workflow, interoperability, and privacy.

Conclusions
Smart glasses can be a suitable technological means for supporting EMS work. We conclude this paper by discussing several design considerations for realizing the full potential of this hands-free technology.
Interlanguage, Simplified English and Two-Word Structures
Authors: Ford Kevin 
Published: February 2022

English is widely used as a Second Language. Papua New Guinea (PNG) in the 1990s (during my residence) had a population of approximately 4 million people who used slightly more than 800 languages. Many PNG people, through exogamy, have both a mother and a father language; they use Tok Pisin (a major dialect of Neo-Melanesian Creole English) for everyday communication outside their neighbourhood group; and they use English officially and for schooling. They are expert multilinguals. India is a vast, multilingual country with 427 languages, with English used officially and for education, and it is geographically remote from PNG. Both peoples were found to simplify English in similar ways, as an aid to learning the language, specifically by these means: - rule-generalization (disregarding exceptions)- giving a regular semantic basis to the prepositions (in, into, for, on, etc.),which have a basis in regularity with reference to location, direction and time, but are, overall, highly irregular in Standard English (SE)- reducing the system of article determiners (the, a, zero) to the zero option- exploiting the use of two-word verb+preposition and verb+noun combinations like play up, play down, and do banking, do repairs, make_progress.This congruence implies systematic processes and a universal basis, suggesting that other learners could profit from this approach, with the further implication that this type of English is a true interlanguage.
Nasopharyngeal Carcinoma with Dural Metastasis Masquerading as Meningioma
Authors: Mohamad Nur saadah , Ramli Ramiza Ramza 
Published: February 2022

Nasopharyngeal carcinoma (NPC) is one of the commonest head and neck malignancies in South East Asia. The tumor arises from epithelial layer of the nasopharynx, found most frequently at the Fossa of Rosenmuller (FOR). NPC can spread to its adjacent structures and cause distant metastasis. However, the occurrence of dura metastasis is uncommon despite being closely located. Consequently, a lesion of the dura may be misdiagnosed as meningioma, especially when it presents with a dural tail sign in the Magnetic Resonance Image (MRI). We reported a case of a 48-year-old lady with progressive right eye diplopia and blurry of vision which later on MRI noted an extensive base of skull mass at the petroclival, suprasellar and orbital apex with adural tail Meningioma was the primary diagnosis until tissue biopsy of the nasopharynx and posterior part of inferior turbinate later revealed as nasopharyngeal carcinoma, non-keratinizing type.