bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bayesian network based study on determining the relationship between job stress and safety climate factors in occurrence of accidents
Authors: Khoshakhlagh Amir Hossein , Yazdanirad Saeid , Kashani Masoud Motalebi , Khatooni Elham , Hatamnegad Yaser , Kabir Sohag 
Published: December 2021

Abstract
Background
Job stress and safety climate have been recognized as two crucial factors that can increase the risk of occupational accidents. This study was performed to determine the relationship between job stress and safety climate factors in the occurrence of accidents using the Bayesian network model.

Methods
This cross-sectional study was performed on 1530 male workers of Asaluyeh petrochemical company in Iran. The participants were asked to complete the questionnaires, including demographical information and accident history questionnaire, NIOSH generic job stress questionnaire, and Nordic safety climate questionnaire. Also, work experience and the accident history data were inquired from the petrochemical health unit. Finally, the relationships between the variables were investigated using the Bayesian network model.

Results
A high job stress condition could decrease the high safety climate from 53 to 37% and increase the accident occurrence from 72 to 94%. Moreover, a low safety climate condition could increase the accident occurrence from 72 to 93%. Also, the concurrent high job stress and low safety climate could raise the accident occurrence from 72 to 93%. Among the associations between the job stress factor and safety climate dimensions, the job stress and worker’s safety priority and risk non-acceptance (0.19) had the highest mean influence value.

Conclusion
The adverse effect of high job stress conditions on accident occurrence is twofold. It can directly increase the accident occurrence probability and in another way, it can indirectly increase the accident occurrence probability by causing the safety climate to go to a lower level.
Deep learning computer-aided detection system for pneumonia in febrile neutropenia patients: a diagnostic cohort study
Authors: Hwang Eui Jin , Lee Jong Hyuk , Kim Jae Hyun , Lim Woo Hyeon , Goo Jin Mo , Park Chang Min 
Published: December 2021

Abstract
Background
Diagnosis of pneumonia is critical in managing patients with febrile neutropenia (FN), however, chest X-ray (CXR) has limited performance in the detection of pneumonia. We aimed to evaluate the performance of a deep learning-based computer-aided detection (CAD) system in pneumonia detection in the CXRs of consecutive FN patients and investigated whether CAD could improve radiologists’ diagnostic performance when used as a second reader.

Methods
CXRs of patients with FN (a body temperature ≥ 38.3 °C, or a sustained body temperature ≥ 38.0 °C for an hour; absolute neutrophil count < 500/mm3) obtained between January and December 2017 were consecutively included, from a single tertiary referral hospital. Reference standards for the diagnosis of pneumonia were defined by consensus of two thoracic radiologists after reviewing medical records and CXRs. A commercialized, deep learning-based CAD system was retrospectively applied to detect pulmonary infiltrates on CXRs. For comparing performance, five radiologists independently interpreted CXRs initially without the CAD results (radiologist-alone interpretation), followed by the interpretation with CAD. The sensitivities and specificities for detection of pneumonia were compared between radiologist-alone interpretation and interpretation with CAD. The standalone performance of the CAD was also evaluated, using area under the receiver operating characteristic curve (AUC), sensitivity, and specificity. Moreover, sensitivity and specificity of standalone CAD were compared with those of radiologist-alone interpretation.

Results
Among 525 CXRs from 413 patients (52.3% men; median age 59 years), pneumonia was diagnosed in 128 (24.4%) CXRs. In the interpretation with CAD, average sensitivity of radiologists was significantly improved (75.4% to 79.4%, P = 0.003) while their specificity remained similar (75.4% to 76.8%, P = 0.101), compared to radiologist-alone interpretation. The CAD exhibited AUC, sensitivity, and specificity of 0.895, 88.3%, and 68.3%, respectively. The standalone CAD exhibited higher sensitivity (86.6% vs. 75.2%, P < 0.001) and lower specificity (64.8% vs. 75.4%, P < 0.001) compared to radiologist-alone interpretation.

Conclusions
In patients with FN, the deep learning-based CAD system exhibited radiologist-level performance in detecting pneumonia on CXRs and enhanced radiologists’ performance.
Bone damage after chemotherapy for lymphoma: a real-world experience
Authors: Mancuso S. , Scaturro Dalila , Santoro M. , Di Gaetano G. , Vitagliani F. , Falco V. , Siragusa S. , Gonnelli S. , Mauro G. Letizia 
Published: December 2021

AbstractBackgroundDespite recent improvements in survival due to advances in treatment, the quality of life of patients with lymphoma may be compromised by the long-term complications of chemotherapy and steroid therapy. Among these, a potentially relevant problem is bone loss and the development of fragility fractures.AimTo provide further evidence of clinical or subclinical skeletal complications in correlation with biological variables and markers of bone disease in patients with complete response to therapy.MethodA cross-sectional observational study was conducted on subjects diagnosed with lymphoma with subsequent antineoplastic treatment, disease status after therapy defined as complete response disease for at least a year now. We performed: blood chemistry tests, imaging techniques and screening tools for the assessment of functional status and quality of life (SARC-F and mini-Osteoporosis Quality of Life).ResultsApproximately 50% of patients had osteoporosis, with a prevalence of vertebral fractures of 65.5%. In most patients, we found hypovitaminosis D and high levels of parathyroid hormone (PTH). Furthermore, a statistically significant association was observed between high PTH levels and previous lymphoma treatment. Finally, the Mini-Osteoporosis Quality of life (mini-OQLQ) questionnaire demonstrated a loss of quality of life as a consequence of the change in bone status.ConclusionsPatient treatment design for personalized chemotherapy would be desirable to reduce late effects on bone. Also, early prevention programs need to be applied before starting treatment. The most benefited subpopulations could be not only elderly but also young patients.
Aesthetic monitoring-based assessment of oncological safety of oncoplastic management of breast cancer: a multi-center research study
Authors: Awad Selmy , Tarabay Ahmed , Qahtani Fahad H. , Alsulaimani Faisal S. , Shaat Mohamed M. , Ali Mazin A. , Khalid Ahmad H. , Alharthi Qasem M. , ALThomali Musab A. , Althobaiti Shabab S. , AlAmri Nadiah G. , Alturkistani Abdullah M. , Alshamrani Abdullah A. , Ali Amal A. , Alsufyani Ahmed H. , AlSofyani Fahad M. , Alghuraybi Abdullah A. , Alnefaie Amer M. , Alharthi Shuruq A. , Almalki Abdulrahman A. , Alghamdi Abdulrahman S. , Alzahrani Azzah , Yehia Ashraf , Abou Sheishaa Mohamed Samir 
Published: December 2021

Abstract
Background
Oncoplastic Breast surgeries (OBS) in breast cancer have evolved to preserve the cancerous breast rather than its amputation to improve postoperative cosmetic results. The lack of evidence to support the oncological safety and benefits of OBS is questionable. In this study, we evaluate various aspects of oncoplastic surgeries with a focused monitoring of aesthetic results and oncological safety.

Methods
This was a multi-center observational study focused on the statistics of data collected from cases who underwent oncoplastic surgeries from the cohort of breast cancer candidates at Mansoura University Hospitals/Egypt and King Faisal Medical Complex/KSA from January 2015 to June 2018. All data were analyzed carefully using SPSS v-26.

Results
Eighty cases who underwent different oncoplastic surgeries were included and reviewed for the aesthetic outcome and oncological safety. The recurrence rate was found to be 2.5%. The breast impact treatment scale assessment method was used to analyze the aesthetic outcomes, and average scores were accepted in 90% of patients.

Conclusions
The oncoplastic breast surgeries are feasible and they had a high rate of oncological safety with the maintenance of good aesthetic outcomes and patient satisfaction.
Integrated mRNA-miRNA transcriptome analysis of bladder biopsies from patients with bladder pain syndrome identifies signaling alterations contributing to the disease pathogenesis
Authors: Gheinani Ali Hashemi , Akshay Akshay , Besic Mustafa , Kuhn Annette , Keller Irene , Bruggmann Rémy , Rehrauer Hubert , Adam Rosalyn M. , Burkhard Fiona C. , Monastyrskaya Katia 
Published: December 2021

Abstract
Background
Interstitial cystitis, or bladder pain syndrome (IC/BPS), is a chronic bladder disorder characterized by lower abdominal pain associated with the urinary bladder and accompanied by urinary frequency and urgency in the absence of identifiable causes. IC/PBS can be separated into the classic Hunner’s ulcerative type and the more prevalent non-ulcerative disease. Our aim was to unravel the biological processes and dysregulated cell signaling pathways leading to the bladder remodeling in non-ulcerative bladder pain syndrome (BPS) by studying the gene expression changes in the patients’ biopsies.

Methods
We performed paired microRNA (miRNA) and mRNA expression profiling in the bladder biopsies of BPS patients with non-Hunner interstitial cystitis phenotype, using comprehensive Next-generation sequencing (NGS) and studied the activated pathways and altered biological processes based on the global gene expression changes. Paired mRNA-miRNA transcriptome analysis delineated the regulatory role of the dysregulated miRNAs by identifying their targets in the disease-induced pathways.

Results
EIF2 Signaling and Regulation of eIF4 and p70S6K Signaling, activated in response to cellular stress, were among the most significantly regulated processes during BPS. Leukotriene Biosynthesis nociceptive pathway, important in inflammatory diseases and neuropathic pain, was also significantly activated. The biological processes identified using Gene Ontology over-representation analysis were clustered into six main functional groups: cell cycle regulation, chemotaxis of immune cells, muscle development, muscle contraction, remodeling of extracellular matrix and peripheral nervous system organization and development. Compared to the Hunner’s ulcerative type IC, activation of the immune pathways was modest in non-ulcerative BPS, limited to neutrophil chemotaxis and IFN-γ-mediated signaling. We identified 62 miRNAs, regulated and abundant in BPS and show that they target the mRNAs implicated in eIF2 signalling pathway.

Conclusions
The bladders of non-ulcerative BPS patients recruited in this study had alterations consistent with a strong cell proliferative response and an up-regulation of smooth muscle contractility, while the contribution of inflammatory processes was modest. Pathway analysis of the integrated mRNA-miRNA NGS dataset pinpointed important regulatory miRNAs whose dysregulation might contribute to the pathogenesis. Observed molecular changes in the peripheral nervous system organization and development indicate the potential role of local bladder innervation in the pain perceived in this type of BPS.
Antibacterial effect of cerium oxide nanoparticle against Pseudomonas aeruginosa
Authors: Zamani Khosro , Allah-Bakhshi Noushin , Akhavan Faezeh , Yousefi Mahdieh , Golmoradi Rezvan , Ramezani Moazzameh , Bach Horacio , Razavi Shabnam , Irajian Gholam-Reza , Gerami Mahyar , Pakdin-Parizi Ali , Tafrihi Majid , Ramezani Fatemeh 
Published: December 2021

Abstract
Background
Antibiotics have been widely used for the treatment of bacterial infections for decades. However, the rapid emergence of antibiotic-resistant bacteria has created many problems with a heavy burden for the medical community. Therefore, the use of nanoparticles as an alternative for antibacterial activity has been explored. In this context, metal nanoparticles have demonstrated broad-spectrum antimicrobial activity. This study investigated the antimicrobial activity of naked cerium oxide nanoparticles dispersed in aqueous solution (CNPs) and surface-stabilized using Pseudomonas aeruginosa as a bacterial model.

Methods
Gelatin-polycaprolactone nanofibers containing CNPs (Scaffold@CNPs) were synthesized, and their effect on P. aeruginosa was investigated. The minimum inhibitory and bactericidal concentrations of the nanoparticls were determined in an ATCC reference strain and a clinical isolate strain. To determine whether the exposure to the nanocomposites might change the expression of antibiotic resistance, the expression of the genes shv, kpc, and imp was also investigated. Moreover, the cytotoxicity of the CNPs was assessed on fibroblast using flow cytometry.

Results
Minimum bactericidal concentrations for the ATCC and the clinical isolate of 50 µg/mL and 200 µg/mL were measured, respectively, when the CNPs were used. In the case of the Scaffold@CNPs, the bactericidal effect was 50 µg/mL and 100 µg/mL for the ATCC and clinical isolate, respectively. Interestingly, the exposure to the Scaffold@CNPs significantly decreased the expression of the genes shv, kpc, and imp.

Conclusions
A concentration of CNPs and scaffold@CNPs higher than 50 μg/mL can be used to inhibit the growth of P. aeruginosa. The fact that the scaffold@CNPs significantly reduced the expression of resistance genes, it has the potential to be used for medical applications such as wound dressings.
Oral cancer among Khat users: finding evidence from DNA analysis of nine cancer-related gene mutations
Authors: Alshahrani Sawsan Abdullah , Al-Qahtani Wedad Saeed , Almufareh Nawaf Abdulrahman , Domiaty Dalia Mostafa , Albasher Gadah Ibraheem , Safhi Fatmah Ahmed , AlQassim Fatima Abdullah , Alotaibi Mashael Alhumaidi , Al-Hazani Tahani Mohamed , Almutlaq Bassam Ahmed 
Published: December 2021

AbstractBackgroundKhat leaves contain the alkaloid cathinone. Research shows that khat might provoke toxicity, mutagenicity, as well as carcinogenicity.MethodsTwo groups were identified as khat abusers and were categorized by abuse time and diagnosis of oral squamous cell carcinoma (OSCC). Here, 41 participants from Group 2 were short-term khat users, and 42 participants were long-term khat users. The control group included 30 healthy individuals.The coding exons included nine cancer-related genes and were analysed. The histopathological research was conducted with H&E staining along with the TP53 protein expression by implementing immunohistochemical analyses.ResultsHere, 41 short-term khat users carried seven somatic mutations in four out of nine cancer-related genes: 29/41(70.73%)ARID1A, 24/41(58.53%)MLH1, 34/41(82.92%)PIK3CAand 36/41(87.80%)TP53. The 42 long-term khat users incorporated nine somatic mutations in five out of nin ecancer-related genes: 40/42(95.23%)ARID1A, 36/42(85.71%)ARID2, 29/42(69.04%)PIK3CA, 27/42(64.28%)MLH1, and 35/42(83.33%)TP53. Every khat user had somatic mutations related to OSCC affecting the gingiva and the lower lip. TP53 protein expression was confirmed in all immunohistochemical oral tests. Carcinoma was also positive in the histopathological analysis.ConclusionsKhat is a mutagenic and carcinogenic plant that provoked OSCC among short-term khat users (<15 years of use) and long-term users (>15 years of use).
An in vitro study on the effects of serum proteins on Enterococcus faecalis adhesion to three types of root sealers and gutta-percha
Authors: Lin Xinwei , Chi Danlu , Gong Qimei , Tong Zhongchun 
Published: December 2021

Abstract
Background
The extrusion of overfilled materials that extend beyond the apical foramina into the periradicular tissue may serve as a reservoir for bacterial adhesion and further affect recovery from periapical diseases. The aim of this study was to evaluate the effects of serum proteins on Enterococcus faecalis adhesion and survival on the surface of a calcium hydroxide-based root canal sealer (Apexit Plus), an epoxy resin sealer (AH-Plus) and a bioceramic sealer (iRoot SP).

Methods
Apexit Plus, AH-Plus and iRoot SP were evenly coated on gutta-percha, using gutta-percha alone as the control. After root canal sealer setting, the number of E. faecalis adhering to the root canal sealers and gutta-percha was counted in fetal bovine serum (FBS) or tryptic soy broth supplemented with 1% glucose (TSBG) by viable cell plate counts. The morphology of 7-day-old E. faecalis biofilms in FSB and TSBG was observed by scanning electron microscopy (SEM). Furthermore, E. faecalis biofilms on the three root canal sealers were labeled with a LIVE/DEAD BacLight™ Bacterial Viability Kit, and the ratios of viable to dead cells were analyzed using laser scanning microscopy operative software (Zen software).

Results
In the assays, after 1 and 7 days, the number of E. faecalis adhering to the root canal sealers or gutta-percha in FBS were significantly lower than those in TSBG (P < 0.05). In FBS, E. faecalis adhesion to iRoot SP and gutta-percha was reduced to a greater extent than that adhered to Apexit Plus and AH-Plus. Few E. faecalis accumulated on iRoot SP in FBS, whereas many bacteria assembled on iRoot SP and formed biofilms in TSBG. The ratio of viable cells in the E. faecalis biofilm on iRoot SP was the lowest.

Conclusions
Calcium hydroxide-based root canal sealers, epoxy resin sealers and bioceramic sealers may provide a substrate for E. faecalis adhesion, and the bioceramic sealer in this study showed the least E. faecalis adhesion in the presence of serum proteins compared to the other two sealers.
Effects of prolonged incubation period and centralized quarantine on the COVID-19 outbreak in Shijiazhuang, China: a modeling study
Authors: Zhu Wenlong , Zhang Mengxi , Pan Jinhua , Yao Ye , Wang Weibing 
Published: December 2021

Abstract
Background
From 2 January to 14 February 2021, a local outbreak of COVID-19 occurred in Shijiazhuang, the capital city of Hebei Province, with a population of 10 million. We analyzed the characteristics of the local outbreak of COVID-19 in Shijiazhuang and evaluated the effects of serial interventions.

Methods
Publicly available data, which included age, sex, date of diagnosis, and other patient information, were used to analyze the epidemiological characteristics of the COVID-19 outbreak in Shijiazhuang. The maximum likelihood method and Hamiltonian Monte Carlo method were used to estimate the serial interval and incubation period, respectively. The impact of incubation period and different interventions were simulated using a well-fitted SEIR+q model.

Results
From 2 January to 14 February 2021, there were 869 patients with symptomatic COVID-19 in Shijiazhuang, and most cases (89.6%) were confirmed before 20 January. Overall, 40.2% of the cases were male, 16.3% were aged 0 to 19 years, and 21.9% were initially diagnosed as asymptomatic but then became symptomatic. The estimated incubation period was 11.6 days (95% CI 10.6, 12.7 days) and the estimated serial interval was 6.6 days (0.025th, 0.975th: 0.6, 20.0 days). The results of the SEIR+q model indicated that a longer incubation period led to a longer epidemic period. If the comprehensive quarantine measures were reduced by 10%, then the nucleic acid testing would need to increase by 20% or more to minimize the cumulative number of cases.

Conclusions
Incubation period was longer than serial interval suggested that more secondary transmission may occur before symptoms onset. The long incubation period made it necessary to extend the isolation period to control the outbreak. Timely contact tracing and implementation of a centralized quarantine quickly contained this epidemic in Shijiazhuang. Large-scale nucleic acid testing also helped to identify cases and reduce virus transmission.
Identification of new candidate biomarkers to support doxorubicin treatments in canine cancer patients
Authors: Walters Kristine , Stornetta Alessia , Jacobs Foster , Villalta Peter W. , Razzoli Maria , Grant Marianne , Zordoky Beshay , Bartolomucci Alessandro , Borgatti Antonella , Balbo Silvia 
Published: December 2021

Abstract
Background
Both human and veterinary cancer chemotherapy are undergoing a paradigm shift from a “one size fits all” approach to more personalized, patient-oriented treatment strategies. Personalized chemotherapy is dependent on the identification and validation of biomarkers that can predict treatment outcome and/or risk of toxicity. Many cytotoxic chemotherapy agents, including doxorubicin, base their mechanism of action by interaction with DNA and disruption of normal cellular processes. We developed a high-resolution/accurate-mass liquid chromatography-mass spectrometry DNA screening approach for monitoring doxorubicin-induced DNA modifications (adducts) in vitro and in vivo. We used, for the first time, a new strategy involving the use of isotope-labeled DNA, which greatly facilitates adduct discovery. The overall goal of this work was to identify doxorubicin-DNA adducts to be used as biomarkers to predict drug efficacy for use in veterinary oncology.

Results
We used our novel mass spectrometry approach to screen for adducts in purified DNA exposed to doxorubicin. This initial in vitro screening identified nine potential doxorubicin-DNA adduct masses, as well as an intense signal corresponding to DNA-intercalated doxorubicin. Two of the adduct masses, together with doxorubicin and its metabolite doxorubicinol, were subsequently detected in vivo in liver DNA extracted from mice exposed to doxorubicin. Finally, the presence of these adducts and analytes was explored in the DNA isolated from dogs undergoing treatment with doxorubicin. The previously identified nine DOX-DNA adducts were not detected in these preliminary three samples collected seven days post-treatment, however intercalated doxorubicin and doxorubicinol were detected.

Conclusions
This work sets the stage for future evaluation of doxorubicin-DNA adducts and doxorubicin-related molecules as candidate biomarkers to personalize chemotherapy protocols for canine cancer patients. It demonstrates our ability to combine in one method the analysis of DNA adducts and DNA-intercalated doxorubicin and doxorubicinol. The last two analytes interestingly, were persistent in samples from canine patients undergoing doxorubicin chemotherapy seven days after treatment. The presence of doxorubicin in all samples suggests a role for it as a promising biomarker for use in veterinary chemotherapy. Future studies will involve the analysis of more samples from canine cancer patients to elucidate optimal timepoints for monitoring intercalated doxorubicin and doxorubicin-DNA adducts and the correlation of these markers with therapy outcome.