bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral pathogens of acute gastroenteritis in Egyptian children: role of the parechovirus
Authors: Mashaly Mervat El-Sayed , Alkasaby Nashwa M. , Bakr Asmaa , Zaki Maysaa El Sayed , Montasser Karim 
Published: June 2022

Abstract
Background and aim
Human parechovirus (HPeV) has emerged as a pathogen associated with acute gastroenteritis (AGE).

Aim
To detect the presence of HPeV in the stool samples from Egyptian children with AGE seeking care and the possibility of its co-infection with other enteric viruses.

Methodology
One hundred stool samples were collected from children attending Mansoura University Children's Hospital with AGE. HPeV and astrovirus were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). At the same time, detection of rotavirus antigen and norovirus was achieved by enzyme-linked immunosorbent assay and rapid immunochromatographic method, respectively.

Results
The most frequently detected virus was rotavirus (39%), followed by norovirus (27%), HPeV (19%), and astrovirus (12%). Interestingly, the single infection with HPeV was 5%. Among the 19 HPeV positive samples, the co-infection of HPeV with other enteric viruses was detected in 9(43.9%) for rotavirus, 7(36.8%) for norovirus, 2(10.5%) for astrovirus, in 3(15.8%) for rotavirus and norovirus and 1(5.3%) for norovirus and astrovirus. Regarding the clinical presentation, there was no significant difference between children infected with HPeV alone and those infected with viruses other than HPeV alone; fever (p = 0.3), vomiting (p = 0.12), abdominal pain (p = 0.12), and grades of severity (P = 0.82). HPeV alone infected children were of mild severity (60%), and their main presenting symptom was fever (60%).

Conclusions
Detection of HPeV as a single viral pathogen in the stool of some children with AGE showed that this virus could be a causative agent of AGE in Egyptian children. Therefore, HPeV could be included as one of the viruses screened for AGE diagnosis in children in Egypt.
A nomogram based on A-to-I RNA editing predicting overall survival of patients with lung squamous carcinoma
Authors: Liu Li , Liu Jun , Deng Xiaoliang , Tu Li , Zhao Zhuxiang , Xie Chenli , Yang Lei 
Published: June 2022

Abstract
Background
Adenosine-to-inosine RNA editing (ATIRE) is characterized as non-mutational epigenetic reprogramming hallmark of cancer, while little is known about its predictive role in cancer survival.

Methods
To explore survival-related ATIRE events in lung squamous cell carcinoma (LUSC), ATIRE profile, gene expression data, and corresponding clinical information of LUSC patients were downloaded from the TCGA database. Patients were randomly divided into a training (n = 134) and validation cohort (n = 94). Cox proportional hazards regression followed by least absolute shrinkage and selection operator algorithm were performed to identify survival-related ATIRE sites and to generate ATIRE risk score. Then a nomogram was constructed to predict overall survival (OS) of LUSC patients. The correlation of ATIRE level and host gene expression and ATIREs’ effect on transcriptome expression were analyzed.

Results
Seven ATIRE sites that were TMEM120B chr12:122215052A > I, HMOX2 chr16:4533713A > I, CALCOCO2 chr17:46941503A > I, LONP2 chr16:48388244A > I, ZNF440 chr19:11945758A > I, CLCC1 chr1:109474650A > I, and CHMP3 chr2:86754288A > I were identified to generate the risk score, of which high levers were significantly associated with worse OS and progression-free survival in both the training and validation sets. High risk-score was also associated with advanced T stages and worse clinical stages. The nomogram performed well in predicting OS probability of LUSC. Moreover, the editing of ATIRE sites exerted a significant association with expression of host genes and affected several cancer-related pathways.

Conclusions
This is the first comprehensive study to analyze the role of ATIRE events in predicting LUSC survival. The AITRE-based model might serve as a novel tool for LUSC survival prediction.
Evaluating patient data quality in South Africa’s National Health Laboratory Service Data Warehouse, 2017-2020: implications for monitoring child health programmes
Authors: Radebe Lebohang , Haeri Mazanderani Ahmad , Sherman Gayle G. 
Published: June 2022

Abstract
Background
South Africa’s National Health Laboratory Service (NHLS), the only clinical laboratory service in the country’s public health sector, is an important resource for monitoring public health programmes.

Objectives
We describe NHLS data quality, particularly patient demographics among infants, and the effect this has on linking multiple test results to a single patient.

Methods
Retrospective descriptive analysis of NHLS data from 1st January 2017—1st September 2020 was performed. A validated probabilistic record-linking algorithm linked multiple results to individual patients in lieu of a unique patient identifier. Paediatric HIV PCR data was used to illustrate the effect on monitoring and evaluating a public health programme. Descriptive statistics including medians, proportions and inter quartile ranges are reported, with Chi-square univariate tests for independence used to determine association between variables.

Results
During the period analysed, 485 300 007 tests, 98 217 642 encounters and 35 771 846 patients met criteria for analysis. Overall, 15.80% (n = 15 515 380) of all encounters had a registered national identity (ID) number, 2.11% (n = 2 069 785) were registered without a given name, 63.15% (n = 62 020 107) were registered to women and 32.89% (n = 32 304 329) of all folder numbers were listed as either the patient’s date of birth or unknown. For infants tested at < 7 days of age (n = 2 565 329), 0.099% (n = 2 534) had an associated ID number and 48.87% (n = 1 253 620) were registered without a given name. Encounters with a given name were linked to a subsequent encounter 40.78% (n = 14 180 409 of 34 775 617) of the time, significantly more often than the 21.85% (n = 217 660 of 996 229) of encounters registered with a baby-derivative name (p-value < 0.001).

Conclusion
Unavailability and poor capturing of patient demographics, especially among infants and children, affects the ability to accurately monitor routine health programmes. A unique national patient identifier, other than the national ID number, is urgently required and must be available at birth if South Africa is to accurately monitor programmes such as the Prevention of Mother-to-Child Transmission of HIV.
The cascade of hypertension care in Cambodia: evidence from a cross-sectional population-based survey
Authors: Chham Savina , Buffel Veerle , Van Olmen Josefien , Chhim Srean , Ir Por , Wouters Edwin 
Published: June 2022

Abstract
Background
Hypertension (HTN) is a leading cause of cardiovascular diseases and deaths globally. To respond to the high HTN prevalence (23.5% among adults aged 40–69 years in 2016) in Cambodia, the government (and donors) established innovative interventions to improve access to screening, care, and treatment at different public health system and community levels. We assessed the effectiveness of these interventions and resulting health outcomes through a cascade of HTN care and explored key determinants.

Methods
We performed a population-based survey among 5070 individuals aged ≥ 40 years to generate a cascade of HTN care in Cambodia. The cascade, built with conditional approach, shows the patients’ flow in the health system and where they are lost (dropped out) along the steps: (i) prevalence, (ii) screening, (iii) diagnosis, (iv) treatment in the last twelve months, (v) treatment in the last three months, and (vi) HTN being under control. The profile of people dropping out from each bar of the cascade was determined by multivariate logistic regression.

Results
The prevalence of HTN (i) among study participants was 35.2%, of which 81.91% had their blood pressure (BP) measured in the last three years (ii). Over 63.72% of those screened were diagnosed by healthcare professionals as hypertensive patients (iii). Among these, 56.19% received treatment in the last twelve months (iv) and 54.26% received follow-up treatment in the last three months (v). Only 35.8% of treated people had their BP under control (vi). Males, those aged ≥ 40 years, and from poorer households had lower odds to receive screening, diagnosis, and treatment. Lower odds to have their BP under-control were found in males, those from poor and rich quintiles, having HTN < five years, and receiving treatment at a private facility.

Conclusions
Overall, people with HTN are lost along the cascade, suggesting limited access to appropriate screening, diagnosis, and treatment and resulting poor health outcomes, especially among those who are male, aged 40–49 years, from poorer households, and visiting a private facility. Efforts to improve the quality of facility-based and community-based interventions are needed to prevent inequitable drops along the cascade of care.
Dynamic rewiring of biological activity across genotype and lineage revealed by context-dependent functional interactions
Authors: Kim Eiru , Novak Lance C. , Lin Chenchu , Colic Medina , Bertolet Lori L. , Gheorghe Veronica , Bristow Christopher A. , Hart Traver 
Published: June 2022

Abstract
Background
Coessentiality networks derived from CRISPR screens in cell lines provide a powerful framework for identifying functional modules in the cell and for inferring the roles of uncharacterized genes. However, these networks integrate signal across all underlying data and can mask strong interactions that occur in only a subset of the cell lines analyzed.

Results
Here, we decipher dynamic functional interactions by identifying significant cellular contexts, primarily by oncogenic mutation, lineage, and tumor type, and discovering coessentiality relationships that depend on these contexts. We recapitulate well-known gene-context interactions such as oncogene-mutation, paralog buffering, and tissue-specific essential genes, show how mutation rewires known signal transduction pathways, including RAS/RAF and IGF1R-PIK3CA, and illustrate the implications for drug targeting. We further demonstrate how context-dependent functional interactions can elucidate lineage-specific gene function, as illustrated by the maturation of proreceptors IGF1R and MET by proteases FURIN and CPD.

Conclusions
This approach advances our understanding of context-dependent interactions and how they can be gleaned from these data. We provide an online resource to explore these context-dependent interactions at diffnet.hart-lab.org.
Mantle cell lymphoma negative for t(11,14) involving the kidneys: a case report
Authors: Nassereldine Hasan , Mohty Razan , Awada Hussein , Abou Dalle Iman , El-Cheikh Jean , Bazarbachi Ali 
Published: June 2022

Abstract
Background
Mantle cell lymphoma is the rarest subtype of non-Hodgkin’s lymphoma. It can exhibit diverse extranodal manifestations. However, renal involvement is uncommon, and if it occurs, it usually only gets detected postmortem. There are several mechanisms by which mantle cell lymphoma can damage the kidneys. Renal failure is a potential complication, and prompt evaluation and diagnosis are critical steps to prevent long-term complications.

Case presentation
We present the case of a 75-year-old non-Hispanic White male with past medical history significant for hypertension and dyslipidemia, presenting with fever, weight loss, and night sweats. Work-up showed markedly elevated white blood cells, multiple enlarged lymph nodes, and a kidney mass. The patient was diagnosed with mantle cell lymphoma with kidney involvement confirmed with a kidney biopsy. His disease was positive for cyclin D1 overexpression despite t(11; 14) absence. The patient received six cycles of alternating vincristine, rituximab, cyclophosphamide, doxorubicin, and prednisone then dexamethasone, high-dose cytarabine, and oxaliplatin, after which he was maintained on ibrutinib and rituximab, with resolution of symptoms and disease regression.

Conclusion
We present a case of a rare presentation of Mantle cell lymphoma while describing the clinical presentation and diagnostic and treatment approaches. This case report can assist physicians in the clinical work-up and treatment of patients with similar diagnosis or presentation.
Exploring the roles of information search and information evaluation literacy and pre-service teachers’ ICT self-efficacy in teaching
Authors: Peciuliauskiene Palmira , Tamoliune Giedre , Trepule Elena 
Published: June 2022

AbstractThis study analyzes the relationship between pre-service teachers’ information search and information evaluation literacy and their information and communication technology (ICT) self-efficacy in teaching. Theoretical analysis confirmed a direct relation between information literacy and pre-service teachers’ ICT self-efficacy in teaching. However, there is insufficient understanding regarding the effect that specific components of information literacy, i.e., information search and evaluation, have on teachers’ ICT self-efficacy in teaching. Data were collected using an online survey of students in teacher training programs who were engaged as research participants. The analysis disclosed that perceived information evaluation literacy has a more strongly expressed indirect impact on teachers’ ICT self-efficacy than a direct impact, while perceived information search literacy has a stronger direct impact on teachers’ ICT self-efficacy in teaching. Therefore, for teacher educators, it is important to develop a sufficient level of information literacy and ensure a positive experience with information search and evaluation, which are related to higher pre-service teachers’ ICT self-efficacy in teaching. This finding may help support calls for teacher training and/or professional development programs with a focus on information literacy, which might increase teachers’ ICT self-efficacy in teaching and improve ICT use in teaching.
Green synthesis, characterization and antibacterial, antifungal, larvicidal and anti-termite activities of copper nanoparticles derived from Grewia asiatica L.
Authors: Tahir Arifa , Quispe Cristina , Herrera-Bravo Jesús , Iqbal Hafsa , ul Haq Zia , Anum Faiza , Javed Zeeshan , Sehar Anam , Sharifi-Rad Javad 
Published: June 2022

Abstract
Background
The current study was conducted to find out an eco-friendly and cost-efficient way to prepare copper nanoparticles (CuNPs) by utilizing Grewia asiatica L. leaf extract, which was found to be a very effective antimicrobial and larvicidal chemical.

Methods
Characterization of nanoparticles was also carried out by utilizing Fourier transform infrared spectroscopy (FTIR) analysis, scanning electron microscope along with X-ray diffraction analysis (XRD). The artificially prepared nanoparticles in the laboratory were approximately in the range of 2 µm in size and crystalline in nature. The CuNPs were tested for their antimicrobial activity against different types of fungi and bacteria, also some mosquito and termite. All the results and observations were tested with a one-way analysis of variance keeping the probability level at < 0.0001.

Results
The copper nanoparticles exhibit significant antibacterial and antifungal activities and are also found lethal for many mosquito and termite species. Antibacterial activity was checked against Escherichia coli and Bacillus subtilis, their zone of inhibition was 17 nm and 20 nm, respectively. The antifungal potential was checked against Aspergillus niger and Aspergillus oryzae and the zone of inhibition was recorded at 20 mm and 23 mm, respectively. CuNPs were also found lethal for many mosquitoes and maximum efficacy of CuNPs against Aedes aegypti larva was observed at 100 mg/ml after 24 h. Termite species such as Heterotermes indicola were exposed to CuNPs and the highest mortality rate in termites was seen at 100 ppm concentration of CuNPs. Current research provides the first investigation of CuNPs of G. asiatica as a larvicidal and as an anti-termite. G. asiatica garden-fresh leaves were collected from Railway colony Mughalpura.

Conclusions
This study proves that CuNPs have a toxic effect on insects and can also be utilized as a biological control of insects. By using such a scientific approach, the scientists can lower the costs of chemical usage and a biodegradable alternative could be provided.
Toxicological exposure to phthalates mixtures and human health risk assessment of drinking water and fruit drinks packaged in plastics and tetra pak cartons
Authors: Adegunwa Abiodun Odunlami , Adegunwa Aderibigbe Kola , Oyatoyinbo Rokeebat Motunrayo 
Published: June 2022

Abstract
Background
This study estimates the migration and levels of phthalate esters in drinking water and fruit drinks packed in plastics and tetra pak cartons that are regularly available for consumption in Nigeria. The probable human health risk from the long-term consistent ingestion of the drinking water and fruit drinks products were also investigated.

Results
Nine (9) phthalates were detected in the analyzed samples and they all showed varying concentrations. The results showed that the total mean concentration of the analyzed phthalates in the drinking water and fruit drinks packed in plastic container were found with the range of 1740–2370 µg/L and 1340–2220 µg/L respectively while fruit drinks packed in tetra pak container showed comparatively low concentration range of 385–450 µg/L. Also, the health hazard (HQ) values for the exposure via oral ingestion by adults were recorded at 505.974, 390.353 and 64.161 respectively for water and, fruit drinks packed in plastics and tetra pak containers. Correspondingly, very high values of HQ were observed in children (2529.80, 2187.39 and 355.92). The overall carcinogenic risks estimated owing to oral ingestion in adults were 0.01, 0.02 and 3.3 × 10–4 for drinking water and fruit drinks packaged with plastics and tetra pak container respectively while higher carcinogenic (CR) values of 0.04, 0.08 and 0.02 were observed in children.

Conclusions
The result obtained showed comparatively low concentrations of phthalates in fruits drinks packaged in Tetra Pak cartons than drinking water and fruit drinks in plastics containers. The high values of hazard index (HI) and CR observed in drinking water and fruit drink packaged in plastics is an indication of future health challenges relating to carcinogenic effects on the favorite consumer of the drinks in which children are more vulnerable. In view of this, packages like tetra pak product and less toxic materials could be adopted for packing drinking water and fruit drinks to avoid exposing consumers to phthalates present in plastics containers which have attendant negative health effect.
Cataloging targetable dependencies of head and neck cancer cell lines in the DepMap CRISPR screens.
Authors: Basu Devraj , Cao Austin , Raghav Lovely , Rajagopalan Pavithra , Brody Robert , Gimotty Phyllis A. 
Published: June 2022

6056 Background: The DepMap genome-wide loss of function CRISPR screens offer new insight into gene dependencies in HPV(-) head and neck squamous cell carcinoma (HNSCC) cell lines. We aimed to leverage this data to guide preclinical studies by cataloging targetable dependencies and identifying ones predicted to offer a therapeutic window. We also aimed to identify targets representing potential synthetic lethalities by testing for associations between genetic alterations and dependency profile. Methods: DepMap was queried for gene probability and effect scores in cell lines from 77 tumors, including 62 HPV(-) HNSCCs plus 15 ESCCs, which have comparable etiology, genetic features, and tissue of origin. A probability score of ≥ 0.5 was used as the threshold for essentiality. Essential genes were selected for analysis by 3 criteria: (1) presence in ≥10% cell lines, (2) lack of dependency in CRISPR screens of normal human cell lineages, and (3) designation as druggable by the Drug-Gene Interaction Database. Gene set enrichment analysis was performed using the Hallmark Gene Sets. DepMap gene effect scores were used to prioritize targets likely to have a useful therapeutic window based on median scores greater than for EGFR (0.676), a target with established albeit modest utility for HNSCC. The Open Targets platform was used to identify targets with inhibitors used in trials for other cancers and/or nonmalignant diseases. Associations between dependencies and genetic alterations were defined using two-sample t-tests, with filter conditions of p < 0.05 and effect size ≥1. Results: The 231 genes meeting selection criteria had a median gene effect score of 0.56. The criteria captured targets of standard therapeutic agents including TYMS (5-FU), tubulin genes (paclitaxel), EGFR (cetuximab), plus known oncogenes like PIK3CA. GSEA showed enrichment of known oncogenic signaling pathways including PI3K/AKT and JAK/STAT, as well as hallmark cancer processes like DNA repair and apoptosis. 90% were not known oncogenes cataloged in the OncoKB Database. 45 genes had a median gene effect score between that of EGFR and the median for common essential genes, including 7 without known cancer-promoting roles: OTOP1, DHRSX, UTP11, MBTPS1, SLC25A3, PPIAL4G, and RBM10. 17% had inhibitors that reached a non-HNSCC phase II trial, including 10 targets not previously tested in cancer. Novel associations between dependencies and genetic alterations included DDX3X with NOTCH1mut, ITGB1 with CDKN2Amut, and ATP1A1 with HRASmut. Conclusions: We catalog targetable dependencies in cell line models of HNSCC. While well-studied targets were captured, many genes lacked known roles in malignancy. Targets of inhibitors tested in other diseases provide new tools to guide preclinical studies. Association of some dependencies with known molecular subgroups in HNSCC may enhance use of cell line models to personalize therapy.