bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of inflammatory cytokines on eradication and recurrence of Helicobacter pylori infection in children
Authors: Zhang Sisi , Zhang Yuanda , Chen Songsong , Teng Yongnan , Li Chen 
Published: August 2022

Objectives: To study the correlation of eradication and recurrence with IL-1 β, IL-6 and TNF-α levels in children with Helicobacter pylori (Hp) infection.
Methods: Children confirmed with Hp infection (n = 153) in our hospital from January to June 2019 and successfully followed up for one year were selected as the study subjects, and 73 healthy children of the same period were selected as the control group. The levels of IL-1 β, IL-6 and TNF-α in children confirmed with Hp infection and healthy children were detected, respectively.
Results: Results of triple therapy: 113 cases (73.9%) reexamined with negative 13C-urea breath test were included in Group-A; and 40 cases (26.1%) reexamined with positive 13C-urea breath test were included in Group-B. Follow up results: 23 cases (20.4%) positive in 13C-urea breath test in one year follow-up were included in Group-C; and 90 cases (79.6%) negative in 13C-urea breath test in one year follow-up were included in Group-D. Group-B showed significantly higher levels of IL-1β, IL-6 and TNF-α when compared with the Group-A and the control group, respectively (P < 0.05). Obviously higher levels of IL-1β, IL-6 and TNF-α were observed in Group-C and Group-D in comparison with the control group (P < 0.05). There was no significant difference in IL-1 β level between Group-C and Group-D (P > 0.05). IL-6 and TNF-α levels in Group-C were remarkably higher than those in Group-D (P < 0.05).
Conclusions: Higher levels of IL-1β, IL-6 and TNF-α may affect the eradication effect of triple therapy in Children with Hp infection, and increased levels of IL-6 and TNF-α may affect the recurrence rate of Hp infection in children.
doi: https://doi.org/10.12669/pjms.38.7.5281
How to cite this:Zhang S, Zhang Y, Chen S, Teng Y, Li C. Effects of inflammatory cytokines on eradication and recurrence of Helicobacter pylori infection in children. Pak J Med Sci. 2022;38(7):---------. doi: https://doi.org/10.12669/pjms.38.7.5281
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Publication audit & ever increasing problems faced by editors of Biomedical Journals
Authors: Jawaid Shaukat Ali 
Published: August 2022

doi: https://doi.org/10.12669/pjms.38.7.6920
How to cite this:Jawaid SA. Publication audit & ever increasing problems faced by editors of Biomedical Journals. Pak J Med Sci. 2022;38(7):---------. doi: https://doi.org/10.12669/pjms.38.7.6920
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries
Authors: Offornedo Queen , Menkir Abebe , Babalola Deborah , Gedil Melaku 
Published: August 2022

Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.
Immunoglobulin G isolation by fast protein liquid chromatography (FPLC): Method validation and implementation in patients with amyotrophic lateral sclerosis – a preliminary study
Authors: Aru Basak , Simsek Turkay , Ormeci Burcu , Gurel Gizem , Milićević Katarina , Radenović Lidija , Andjus Pavle , Yanikkaya Demirel Gulderen 
Published: August 2022

Amyotrophic lateral sclerosis (ALS) is a fatal, heterogenous neurodegenerative disease which is characterized by weakness and muscle atrophy. While more than 50 genes linked with the familial ALS have been identified, sporadic ALS accounts for the majority of cases and genetic factors contributing to the sporadic form of the disease remain largely elusive. Involvement of the immune system in disease progression, including presence of circulating autoimmune complexes, associations with other autoimmune diseases, as well as immunoglobulin (Igs) levels have been described. However, investigations involving immunoglobulins requires isolation of patient antibodies, while so far, there is no validated fast protein liquid chromatography (FPLC) protocol. For this purpose, we evaluated specificity, accuracy and precision parameters; limit of detection, limit of quantification and correlation coefficient were calculated from the calibration curve. Our results indicated the limit of detection and limit of quantification as 0.045 and 0.13 mg respectively, while r2 was calculated as 0.9992. Our preliminary data suggest that this protocol can be implemented for the isolation of IgGs of ALS patients’ sera samples for in vitro and in vivo analyses, while more studies involving larger patient groups are required.
The latest reports on biomarkers used in the diagnosis of ovarian cancer
Authors: Chałupnik Aleksandra , Chilimoniuk Zuzanna , Dobosz Maciej , Sobstyl Anna , Sobstyl Małgorzata 
Published: August 2022

Introduction: Ovarian cancer ranks seventh in terms of incidence and eighth in terms of mortality among women worldwide. It is divided into several subtypes. The epithelial type of ovarian cancer is responsible for 90% of cases. The clinical picture is usually an appendage tumor detected by palpation or during pelvic imaging. Symptoms are usually non-specific such as abdominal pushing or bloating.
State of knowledge: Ovarian cancer is usually detected at an advanced stage due to the long duration of absence of symptoms. Therefore, there is an urgent need to look at existing and identify potential biomarkers that can lead to the development of new and more effective predictors for the diagnosis and prognosis of ovarian cancer. The ability of these biomarkers to predict the existence and stages of ovarian cancer could improve early diagnosis and survival of ovarian cancer patients. Currently, the biomarkers CA-125 and HE4 play the most important role in diagnosis. However, there are an increasing number of reports on other biomarkers such as kallikreins, bikunin, VEGF, and mesothelin.
Summary: Partly due to the lack of effective screening, ovarian cancer is usually diagnosed in the final stages. This is why ongoing research into new biomarkers that could contribute to faster detection of the disease is so important. They would also increase the effectiveness of the therapies used and enable a better prognosis of the course of the disease.
Impact of neurological disorders occurring in neurodegenerative diseases on the conversation process and patients' quality of life
Authors: Mielniczek Katarzyna , Kowalska Aleksandra , Jóźwik Katarzyna , Lipiec Marta , Dołomisiewicz Diana 
Published: August 2022

Introduction : Dialogue, or conversation, is the ability to speak as well as listen. It plays a very important role in interpersonal relations.Speech disorders are a group of of disorders that includes various types of speech production difficulties. Speech production depends on the coordination of several motor acts: respiration, phonation, articulation, resonance and prosody. Phonation is the complex activity of producing sound by vibration of the vocal cords. Resonance is the amplification of sounds at specific frequencies through vibration in the chest, throat and sinuses. Prosody includes a set of phonetic features, such as tone, loudness, tempo, and the overall timbre of speech, which are designed to intended to preserve the meaning and character of speech. Disruption of any of these related elements results in motor speech disorders.
Material and method : An overview is presented of language disorders in diseases neurodegenerative diseases such as Parkinson's disease(PD) and Friedreich's ataxia (FRDA). Their impact on the conversation process and the patient's quality of life assessment was evaluated. The paper was based on scientific publications posted on the PubMed scientific platform.
Results : Speech and language disorders are the main symptoms of FRDA, which significantly affect the patients' quality of life. Patients often present with dysarthria, resulting from causes of central and peripheral and additional primary language disorders. The classic speech disorder in PD is hypokinetic dysarthria, manifested by hypophonia; monotonous, uneven and strained speech; reduced prosody (melodic voice); crowded articulation; inadequate pauses in speech; freezing of speech, unclear articulation.
Conclusions : The described disease entities show a significant impact on the deterioration of the process of of conversation by the patient, thus showing a significantly negative impact on the patients' quality of life.
Business Method Innovation in U.S. Manufacturing and Trade
Authors: Chan Tian Heong , Bharadwaj Anandhi , Varadarajan Deepa 
Published: August 2022

Problem definition: In what kinds of business method innovation do firms in the manufacturing and trade sectors engage? Does engaging in business method innovation create value for these firms? The present paper answers these questions using empirical evidence. Methodology/results: Using text analysis of business method patents, we show that business method innovation in the U.S. manufacturing and trade sectors is aimed primarily at improving the business operations that support the sales of tangible products—that is, how the firm targets customers, manages product delivery, or enhances the product through service offerings. We then evaluate the effect of having business method innovation, as evidenced by patents, on a firm’s value. Leveraging the exogenous shock of the State Street ruling, which first recognized business methods as a patentable category of innovation, we identify a set of firms that possess business method patents and a matched set of comparable firms without such patents. Then, using a difference-in-differences with firm fixed effects model on the matched sample, we show that the valuation of the former set of firms increased by 9% after State Street, as measured by Tobin’s q. We further show that (1) business method innovators in the manufacturing sector gained a 7% increase, whereas business method innovators in the trade sectors gained a 25% increase; and (2) only firms with broader innovation scope—that is, business method innovations covering the range of customer targeting, product delivery, and service support of products—experienced a significant (18%) value bump. Managerial implications: This research provides evidence that business method innovation in the manufacturing and trade sectors primarily involves innovating in business operations that support product sales. Our work also provides empirical support for the proposition that engaging in business method innovation drives manufacturing and trade firms’ market performance.Supplemental Material: The online appendices are available at https://doi.org/10.1287/msom.2022.1129 .
Development and validation of a gene signature predicting the risk of postmenopausal osteoporosis
Authors: Yuan Wei , Yang Maowei , Zhu Yue 
Published: August 2022

Aims We aimed to develop a gene signature that predicts the occurrence of postmenopausal osteoporosis (PMOP) by studying its genetic mechanism. Methods Five datasets were obtained from the Gene Expression Omnibus database. Unsupervised consensus cluster analysis was used to determine new PMOP subtypes. To determine the central genes and the core modules related to PMOP, the weighted gene co-expression network analysis (WCGNA) was applied. Gene Ontology enrichment analysis was used to explore the biological processes underlying key genes. Logistic regression univariate analysis was used to screen for statistically significant variables. Two algorithms were used to select important PMOP-related genes. A logistic regression model was used to construct the PMOP-related gene profile. The receiver operating characteristic area under the curve, Harrell’s concordance index, a calibration chart, and decision curve analysis were used to characterize PMOP-related genes. Then, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression of the PMOP-related genes in the gene signature. Results We identified three PMOP-related subtypes and four core modules. The muscle system process, muscle contraction, and actin filament-based movement were more active in the hub genes. We obtained five feature genes related to PMOP. Our analysis verified that the gene signature had good predictive power and applicability. The outcomes of the GSE56815 cohort were found to be consistent with the results of the earlier studies. qRT-PCR results showed that RAB2A and FYCO1 were amplified in clinical samples. Conclusion The PMOP-related gene signature we developed and verified can accurately predict the risk of PMOP in patients. These results can elucidate the molecular mechanism of RAB2A and FYCO1 underlying PMOP, and yield new and improved treatment strategies, ultimately helping PMOP monitoring. Cite this article: Bone Joint Res 2022;11(8):548–560.
Knowledge and Awareness of COVID-19 in Uttar Pradesh: An Exploratory Data Analysis
Authors: Sharma Prayas , Adichwal Nitesh Kumar , Singh Ashish Kumar 
Published: August 2022

Corona viruses, commonly called COVID-19, are a large family of viruses that can cause diseases ranging from the common cold to Severe Acute Respiratory Syndrome (SARS). Worldwide Covid-19 is affecting 210 countries and territories around the world and two international conveyances. As of 2 June 2020, there are 6,408,869 confirmed 2,935,368 recovered and 378,317 deaths cases has been reported in world of Coronavirus diseases, India is not untouched from this situation. Currently, it has reported infected 190,535 and 5,394 death cases due to COVID-19 in India. (https://covid19.who.int/region/searo/country/in). The COVID-19 pandemic was first confirmed in the Indian state of Uttar Pradesh on 4 March 2020, with the first positive case in Ghaziabad. As of 1 June 2020, the state has 8361 confirmed cases, resulting in 222 deaths and 5030 recoveries. The situation is getting worst day by day as COVID-19 outbreaks and patients are increasing by every minute and become the most important issue for the whole world and So accessing knowledge and awareness among the people is very important. The present study using the exploratory data analysis we tried to demonstrate the knowledge and awareness of individuals about the COVID-19 pandemic in Uttar Pradesh, the most populous state of India. The findings of the present study can be utilized by the researchers and policy makers to handle this worst situation.
Supply-side readiness to deliver HIV testing and treatment services in Indonesia: Going the last mile to eliminate mother-to-child transmission of HIV
Authors: Adawiyah Rabiah al , Boettiger David , Applegate Tanya L. , Probandari Ari , Marthias Tiara , Guy Rebecca , Wiseman Virginia 
Published: August 2022

IntroductionDespite national efforts to integrate Prevention of Mother-to-Child Transmission (PMTCT) of HIV services into antenatal care in Indonesia, the rate of mother-to-child transmission of HIV remains the highest in the world. A range of barriers to uptake and long-term engagement in care have been identified, but far less is known about health system preparedness to deliver PMTCT of HIV services. This study explored supply-side barriers to the delivery of PMTCT services in Indonesia and whether these factors are associated with the uptake of antenatal HIV testing.Materials and methodsAn ecological analysis was undertaken, linking data from the World Bank Quality Service and Delivery Survey (2016) with routine data from Indonesia’s HIV and AIDS case surveillance system and district health profile reports (2016). Supply-side readiness scores—generated from a readiness index that measures overall structural capacity and is often used as proxy for quality of care—were adapted from the WHO Service Availability and Readiness Assessment and presented by sector and geographic area. Univariate and multivariate regression analysis was used to explore factors associated with the uptake of antenatal HIV testing in public facilities.ResultsIn general, public facilities scored more highly in most inputs compared to private facilities. Facilities located in urban areas also scored more highly in the majority of inputs compared to ones in rural areas. Readiness scores were lowest for PMTCT services compared to Antenatal Care and HIV Care and Support services, especially for the availability of medicines such as zidovudine and nevirapine. The national composite readiness score for PMTCT was only 0.13 (based on a maximum score of 1) with a composite score of 0.21 for public facilities and 0.06 for private facilities. The multivariate analysis shows that the proportion of pregnant women tested for HIV was more likely to be greater than or equal to 10% in facilities with a higher readiness score and a higher number of trained counsellors available, and less likely in facilities located outside of Java-Bali and in facilities supporting a higher number of village midwives.DiscussionDespite targeted efforts by the Indonesian government and multinational agencies, significant gaps exist in the delivery of PMTCT that compromise the standard of care delivered in Indonesia. Future strategies should focus on improving the availability of tests and treatment, especially in the private sector and in rural areas.
Impact of Epstein-Barr virus co-infection on natural acquired Plasmodium vivax antibody response
Authors: Dias Michelle H. F. , Guimarães Luiz F. F. , Barcelos Matheus G. , Moreira Eduardo U. M. , do Nascimento Maria F. A. , de Souza Taís N. , Pires Camilla V. , Monteiro Talita A. F. , Middeldorp Jaap M. , Soares Irene S. , Fontes Cor J. F. , Ntumngia Francis B. , Adams John H. , Kano Flora S. , Carvalho Luzia H. 
Published: August 2022

BackgroundThe simultaneous infection ofPlasmodium falciparumand Epstein-Barr virus (EBV) could promote the development of the aggressive endemic Burkitt’s Lymphoma (eBL) in children living inP.falciparumholoendemic areas. While it is well-established that eBL is not related to other human malaria parasites, the impact of EBV infection on the generation of human malaria immunity remains largely unexplored. Considering that this highly prevalent herpesvirus establishes a lifelong persistent infection on B-cells with possible influence on malaria immunity, we hypothesized that EBV co-infection could have impact on the naturally acquired antibody responses toP.vivax, the most widespread human malaria parasite.Methodology/Principal findingsThe study design involved three cross-sectional surveys at six-month intervals (baseline, 6 and 12 months) among long-termP.vivaxexposed individuals living in the Amazon rainforest. The approach focused on a group of malaria-exposed individuals whose EBV-DNA (amplification ofbalf-5gene) was persistently detected in the peripheral blood (PersVDNA, n = 27), and an age-matched malaria-exposed group whose EBV-DNA could never be detected during the follow-up (NegVDNA, n = 29). During the follow-up period, the serological detection of EBV antibodies to lytic/ latent viral antigens showed that IgG antibodies to viral capsid antigen (VCA-p18) were significantly different between groups (PersVDNA> NegVDNA). A panel of blood-stageP.vivaxantigens covering a wide range of immunogenicity confirmed that in general PersVDNAgroup showed low levels of antibodies as compared with NegVDNA. Interestingly, more significant differences were observed to a novel DBPII immunogen, named DEKnull-2, which has been associated with long-term neutralizing antibody response. Differences between groups were less pronounced with blood-stage antigens (such as MSP1-19) whose levels can fluctuate according to malaria transmission.Conclusions/SignificanceIn a proof-of-concept study we provide evidence that a persistent detection of EBV-DNA in peripheral blood of adults in aP.vivaxsemi-immune population may impact the long-term immune response to major malaria vaccine candidates.
Prevalence of respiratory viruses among paediatric patients in acute respiratory illnesses in Malaysia
Authors: Low Yoke Lee , Wong Shin Yee , Lee Eric Kim Hor , Muhammed Mohd Hareeff 
Published: August 2022

Objectives
Acute respiratory infections (ARIs) are one of the leading causes of childhood morbidity and mortality worldwide. However, there is limited surveillance data on the epidemiological burden of respiratory pathogens in tropical countries like Malaysia. This study aims to estimate the prevalence of respiratory pathogens causing ARIs among children aged <18 years old in Malaysia and their epidemiological characteristics.

Methods
Nasopharyngeal swab specimens received at 12 laboratories located in different states of Malaysia from 2015–2019 were studied. Detection of 18 respiratory pathogens were performed using multiplex PCR.

Results
Data from a total of 23,306 paediatric patients who presented with ARI over a five-year period was studied. Of these, 18538 (79.5%) were tested positive. The most prevalent respiratory pathogens detected in this study were enterovirus/ rhinovirus (6837/ 23000; 29.7%), influenza virus (5176/ 23000; 22.5%) and respiratory syncytial virus (RSV) (3652/ 23000; 15.9%). Throughout the study period, RSV demonstrated the most pronounce seasonality; peak infection occurred during July to September. Whereas the influenza virus was detected year-round in Malaysia. No seasonal variation was noted in other respiratory pathogens. The risk of RSV hospitalisation was found to be significantly higher in children aged less than two years old, whereas hospitalisation rates for the influenza virus peaked at children aged between 3–6 years old.

Conclusion
This study provides insight into the epidemiology and the seasonality of the causative pathogens of ARI among the paediatric population in Malaysia. Knowledge of seasonal respiratory pathogens epidemiological dynamics will facilitate the identification of a target window for vaccination.