bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved cytometric analysis of untouched lung leukocytes by enzymatic liquefaction of sputum samples
Authors: Santopolo Giulia , Clemente Antonio , Rojo-Molinero Estrella , Fernández Sara , Álvarez María Concepción , Oliver Antonio , de la Rica Roberto 
Published: November 2022

Abstract
Background
Phenotyping sputum-resident leukocytes and evaluating their functional status are essential analyses for exploring the cellular basis of pathological processes in the lungs, and flow cytometry is widely recognized as the gold-standard technique to address them. However, sputum-resident leukocytes are found in respiratory samples which need to be liquefied prior to cytometric analysis. Traditional liquefying procedures involve the use of a reducing agent such as dithiothreitol (DTT) in temperature-controlled conditions, which does not homogenize respiratory samples efficiently and impairs cell viability and functionality.

Methods
Here we propose an enzymatic method that rapidly liquefies samples by means of generating O2 bubbles with endogenous catalase. Sputum specimens from patients with suspected pulmonary infection were treated with DTT, the enzymatic method or PBS. We used turbidimetry to compare the liquefaction degree and cell counts were determined using a hemocytometer. Finally, we conducted a comparative flow cytometry study for evaluating frequencies of sputum-resident neutrophils, eosinophils and lymphocytes and their activation status after liquefaction.

Results
Enzymatically treated samples were better liquefied than those treated with DTT or PBS, which resulted in a more accurate cytometric analysis. Frequencies of all cell subsets analyzed within liquefied samples were comparable between liquefaction methods. However, the gentle cell handling rendered by the enzymatic method improves cell viability and retains in vivo functional characteristics of sputum-resident leukocytes (with regard to HLA-DR, CD63 and CD11b expression).

Conclusion
In conclusion, the proposed enzymatic liquefaction method improves the cytometric analysis of respiratory samples and leaves the cells widely untouched for properly addressing functional analysis of lung leukocytes.
Semantic interoperability: ontological unpacking of a viral conceptual model
Authors: Bernasconi Anna , Guizzardi Giancarlo , Pastor Oscar , Storey Veda C. 
Published: November 2022

AbstractBackgroundGenomics and virology are unquestionably important, but complex, domains being investigated by a large number of scientists. The need to facilitate and support work within these domains requires sharing of databases, although it is often difficult to do so because of the different ways in which data is represented across the databases. To foster semantic interoperability, models are needed that provide a deep understanding and interpretation of the concepts in a domain, so that the data can be consistently interpreted among researchers.ResultsIn this research, we propose the use of conceptual models to support semantic interoperability among databases and assess their ontological clarity to support their effective use. This modeling effort is illustrated by its application to the Viral Conceptual Model (VCM) that captures and represents the sequencing of viruses, inspired by the need to understand the genomic aspects of the virus responsible for COVID-19. For achieving semantic clarity on the VCM, we leverage the “ontological unpacking” method, a process of ontological analysis that reveals the ontological foundation of the information that is represented in a conceptual model. This is accomplished by applying the stereotypes of the OntoUML ontology-driven conceptual modeling language.As a result, we propose a new OntoVCM, an ontologically grounded model, based on the initial VCM, but with guaranteed interoperability among the data sources that employ it.ConclusionsWe propose and illustrate how the unpacking of the Viral Conceptual Model resolves several issues related to semantic interoperability, the importance of which is recognized by the “I” in FAIR principles. The research addresses conceptual uncertainty within the domain of SARS-CoV-2 data and knowledge.The method employed provides the basis for further analyses of complex models currently used in life science applications, but lacking ontological grounding, subsequently hindering the interoperability needed for scientists to progress their research.
Off-pump versus on-pump coronary artery bypass graft surgery outcomes in patients with severe left ventricle dysfunction: inverse probability weighted study
Authors: Sheikhy Ali , Fallahzadeh Aida , Forouzannia Khalil , Pashang Mina , Tajdini Masih , Momtahen Shahram , Mansourian Soheil , Shirzad Mahmoud , Sadeghian Saeed , Hosseini Kaveh 
Published: November 2022

Abstract
Objective
In this study we aimed to compare on-pump and off-pump coronary artery bypass grafting (CABG) outcomes in patients presented with low left ventricular ejection fraction (EF) as a high-risk group of patients.

Methods
In this registry-based study from 2014 and 2016, all patients with severe left ventricular dysfunction (EF less than 35%) were included and followed until 2020. The median follow-up period was 47.83 [38.41, 55.19] months. Off pump CABG (OPCABG) was compared with on-pump CABG (ONCABG) in terms of mid-term non-fatal cardiovascular events (CVEs) and all-cause mortality. Propensity score method (with inverse probability weighting technique) was used to compare these two groups.

Results
From 14,237 patients who underwent isolated CABG, 2055 patients with EF ≤ 35% were included; 1705 in ONCABG and 350 patients in OPCABG groups. Although OPCABG was associated with lower risk of 30-days mortality (Odds Ratio [OR]: 0.021; Confidence Interval [CI] 95% [0.01, 0.05], P < 0.001); there was no significant difference between OPCABG and ONCABG in term of mid-term mortality and non-fatal CVEs ((Hazard ratio [HR]: 0.822; 95%CI [0.605, 1.112], p = 0.208) and (HR: 1.246; 95%CI [0.805, 1.929], p = 0.324), respectively). Patients with more than three traditional coronary artery disease risk factors, had more favorable outcomes (in terms of mid-term mortality) if underwent OPCABG (HR: 0.420; 95%CI [0.178, 0.992], p = 0.048).

Conclusion
OPCABG was associated with lower risk of 30-days mortality; however, mid-term outcomes were comparable in both OPCABG and ONCABG techniques.
Borrelia multiplex: a bead-based multiplex assay for the simultaneous detection of Borrelia specific IgG/IgM class antibodies
Authors: Häring Julia , Hassenstein Max J. , Becker Matthias , Ortmann Julia , Junker Daniel , Karch André , Berger Klaus , Tchitchagua Tatia , Leschnik Olaf , Harries Manuela , Gornyk Daniela , Hernández Pilar , Lange Berit , Castell Stefanie , Krause Gérard , Dulovic Alex , Strengert Monika , Schneiderhan-Marra Nicole 
Published: November 2022

Abstract
Background
Lyme borreliosis (LB) is the most common tick-borne infectious disease in the northern hemisphere. The diagnosis of LB is usually made by clinical symptoms and subsequently supported by serology. In Europe, a two-step testing consisting of an enzyme-linked immunosorbent assay (ELISA) and an immunoblot is recommended. However, due to the low sensitivity of the currently available tests, antibody detection is sometimes inaccurate, especially in the early phase of infection, leading to underdiagnoses.

Methods
To improve upon Borrelia diagnostics, we developed a multiplex Borrelia immunoassay (Borrelia multiplex), which utilizes the new INTELLIFLEX platform, enabling the simultaneous dual detection of IgG and IgM antibodies, saving further time and reducing the biosample material requirement. In order to enable correct classification, the Borrelia multiplex contains eight antigens from the five human pathogenic Borrelia species known in Europe. Six antigens are known to mainly induce an IgG response and two antigens are predominant for an IgM response.

Results
To validate the assay, we compared the Borrelia multiplex to a commercial bead-based immunoassay resulting in an overall assay sensitivity of 93.7% (95% CI 84.8–97.5%) and a specificity of 96.5% (95%CI 93.5–98.1%). To confirm the calculated sensitivity and specificity, a comparison with a conventional 2-step diagnostics was performed. With this comparison, we obtained a sensitivity of 95.2% (95% CI 84.2–99.2%) and a specificity of 93.0% (95% CI 90.6–94.7%).

Conclusion
Borrelia multiplex is a highly reproducible cost- and time-effective assay that enables the profiling of antibodies against several individual antigens simultaneously.
Vessel wall imaging features of Moyamoya disease in a North American population: patterns of negative remodelling, contrast enhancement, wall thickening, and stenosis
Authors: Larson Anthony S. , Klaas James P. , Johnson Matthew P. , Benson John C. , Shlapak Darya , Lanzino Giuseppe , Savastano Luis E. , Lehman Vance T. 
Published: November 2022

Abstract
Background
This study characterized vessel wall imaging (VWI) features of Moyamoya disease (MMD) in a predominantly adult population at a North American center.

Methods
Consecutive patients with VWI were included. Twelve arterial segments were analyzed for wall thickening, degree and pattern of contrast enhancement, and remodeling.

Results
Overall, 286 segments were evaluated in 24 patients (mean age = 36.0 years [range = 1–58]). Of 172 affected segments, 163 (95%) demonstrated negative remodeling. Complete vessel wall obliteration was most frequent in the proximal M1 (17/48, 35%). Affected segments enhanced in 72/172 (42%) (n = 15 for grade II; n = 54 for concentric and n = 18 for eccentric); 20 of 24 (83%) patients had at least one enhancing segment. Both enhancing and non-enhancing segments were present in 19/20 (95%) patients. Vessel wall enhancement was most common in the proximal segments and correlated to the degree of stenosis (p < 0.001), and outer wall diameter (p < 0.001), but not disease duration (p = 0.922) or Suzuki score (p = 0.477). Wall thickening was present in 82/172 (48%) affected segments and was associated with contrast enhancement (p < 0.001), degree of stenosis (p < 0.001), and smaller outer wall diameter (p = 0.004).

Conclusion
This study presents VWI findings in North American patients with MMD. Negative remodeling was the most common finding. Most patients had both enhancing and non-enhancing abnormal segments. Vessel wall enhancement was most common in proximal segments, variable in pattern or degree and was correlated to the degree of stenosis and smaller outer wall diameter.
Fentanyl for labour pain management: a scoping review
Authors: Show Kyaw Lwin , Ngamjarus Chetta , Kongwattanakul Kiattisak , Rattanakanokchai Siwanon , Duangkum Chatuporn , Bohren Meghan A. , Betrán Ana Pilar , Somjit Monsicha , Win Wint Ye Hla , Lumbiganon Pisake 
Published: November 2022

AbstractBackgroundLabour pain has been identified as an important reason for women to prefer caesarean section (CS). Fentanyl is one of the short acting opioids recommended by World Health Organization for pain relief during labour. This study aimed to identify and describe the available evidence on the use of fentanyl (monotherapy) for labour pain management by any routes of administration or regime.MethodsWe included the records published until 31 December 2021 which reported administration of fentanyl to women with normal labour for labour pain relief. Data were extracted by one reviewer and checked by another reviewer using a standardised agreement form. We mapped and presented data descriptively in figure and tabular format.ResultsWe included 51 records from 49 studies in our scoping review. The studies were conducted in 12 countries, mostly high-income countries. The study designs of the 51 included records were varied as follows: 38 (74.5%) experimental studies (35 randomised controlled trials and three quasi-experimental studies), and 12 (23.5%) observational studies (five retrospective cohort studies, four prospective cohort studies, two retrospective descriptive studies, and one descriptive study) and one qualitative study. Of the included records, six used intranasal fentanyl, five used subcutaneous fentanyl, 18 (35.3%) used intravenous fentanyl, 18 (35.3%) used intrathecal fentanyl, and nine used epidural fentanyl. Many records compared fentanyl with another analgesic agent while five records (9.8%) had no comparison group and seven records (13.7%) compared with no analgesia group. The doses of fentanyl varied by routes, study and the requirement depended on the women. Pain assessment was the most frequent outcome measure presented in the records (78.4%). Only nine records (17.6%) investigated women’s satisfaction about labour pain relief using fentanyl and seven records (13.7%) reported the effect of fentanyl on breastfeeding. The most common reported neonatal outcomes were foetal heart rate (33 records, 64.7%) and Apgar score (32 records, 62.7%).ConclusionThere is limited primary evidence especially randomised controlled trials to evaluate the effectiveness and harms of different routes of fentanyl in low- or middle-income countries. There is a need for high-quality research to establish the most effective route of fentanyl and associated effects for evidence-based international guidelines.
Antenatal care utilization and compliance with national and WHO guidelines in rural Ethiopia: a cohort study
Authors: Roro Meselech , Deressa Wakgari , Lindtjørn Bernt 
Published: November 2022

Abstract
Background
Antenatal health care utilization has the potential to influence maternal and new-born health. In this study, we assessed compliance of antenatal care utilization with national and World Health Organization (WHO) guidelines. We also examined association of antenatal care utilization with adverse pregnancy outcomes as secondary outcome.

Methods
This was a community-based cross sectional study conducted from July 2016 to November 2017 in rural south-central Ethiopia. We described antenatal care received by pregnant women, whom we followed at three prescheduled visits during pregnancy and collected birth data at time of delivery. Extent of antenatal care content received, timing of antenatal care, place of antenatal care and place and mode of delivery were obtained and computed in accordance with national and WHO guidelines. For adverse pregnancy outcomes, computed as sum of low birth weight, preterm birth, intrauterine foetal death, and stillbirth, the exposure variable used was antenatal care utilization.

Results
Seven hundred and four (704) women participated in the study, and 536 (76.1%) had attended at least one antenatal care visit. Among women who attended antenatal care visit, majority, 421 (79.3%), had done so at health centres and hospitals, while 110 (20.7%) attended at health post. Average number of antenatal care visits was 2.5, which is less than that recommended in national and WHO guidelines. Only 18 (2.6%) women had attended antenatal care in their first trimester, which is low in contrast to the expected 100% specified in the guidelines. Less than half (47%) of the women delivered in a health facility. This is in contrast to the 100% expected health institution deliveries. Low birth weight was 7.9% (n = 48), and preterm birth was 4.9% (n = 31). There were 12 twin pregnancies, three stillbirths, 11 spontaneous abortions, and two intrauterine foetal deaths. We did not find significant association between adverse pregnancy outcomes and antenatal care utilization (COR = 1.07, 95% CI 0.62, 1.86).

Conclusion
This study showed that antenatal care service utilization in the study area was markedly low compared to that recommended in national and WHO guidelines. The obtained antenatal health care utilization was not associated with the registered adverse pregnancy outcomes.
Prognostic value of preoperative C-reactive protein to albumin ratio in patients with thymic epithelial tumors: a retrospective study
Authors: Huang Yang-Yu , Liu Xuan , Liang Shen-Hua , Hu Yu , Ma Guo-Wei 
Published: November 2022

Abstract
Background
The C-reactive protein to albumin ratio (CAR) is associated with poor prognosis in various cancers. However, its value in thymic epithelial tumors remains to be elucidated, we aimed to evaluate the prognostic significance of preoperative CAR in patients with surgically resected thymic epithelial tumors (TETs).

Methods
We retrospectively collected data from 125 patients with TETs who underwent thymoma resection at our center. The best cutoff values ​​for the continuous variable, CAR, were obtained using X-tile software. Univariate and multivariate Cox regression analyses were used to evaluate CAR as an independent predictor of overall survival (OS) and recurrence-free survival (RFS). Kaplan–Meier analysis and log-rank tests were used to present risk stratification of patients based on CAR and the Glasgow-prognostic-score (GPS). The prognostic effect of CAR was assessed using a receiver operating characteristic curve.

Results
Patients were categorized into high (≥ 0.17) and low (< 0.17) CAR groups according to the optimal cutoff value of 0.17. Univariate and multivariate analyses showed that CAR was an independent predictor of prognosis. World health organization stage, CAR level, GPS score, and drinking history were important independent prognostic factors for OS (p < 0.05). T stage, CAR level, and drinking history were important independent prognostic factors for RFS (p < 0.05). The area under the curve value of CAR to predict prognosis was 0.734 for OS and 0.680 for RFS.

Conclusions
Elevated preoperative CAR was independently associated with poor OS and RFS after thymectomy. Therefore, CAR may be a valuable biomarker for the postoperative prognosis of TETs.
Broad-spectrum antibiotics associated gut microbiome disturbance impairs T cell immunity and promotes lung cancer metastasis: a retrospective study
Authors: Xu Ke , Cai Jixu , Xing Jun , Li Xu , Wu Beishou , Zhu Zhuxian , Zhang Ziqiang 
Published: November 2022

Abstract
Background
Gut microbiome has been linked to a regulatory role in cancer progression. However, whether broad-spectrum antibiotics (ATB) associated gut microbiome dysbiosis contributes to an impaired T cell immune function, and ultimately promotes lung cancer metastasis is not well known.

Methods
In this study, a retrospective analysis was performed in a cohort of 263 patients initially diagnosed with non-small cell lung cancer (NSCLC) patients, including the ATB group (patients with broad-spectrum antibiotics treatment) (n = 124), and non-ATB group (n = 139) as control. ATB patients were prescribed ATB for over 5 days within 30 days prior to the collection of blood and fecal specimens and followed surgical treatment or first-line therapy. T cell immune function and metastasis-free survival (MFS) were evaluated between the two groups. Gut microbiota was evaluated by 16S rDNA sequencing. The predictive value of T cell immunity for MFS was evaluated by ROC analysis and Cox regression analysis.

Results
Our results suggest that broad-spectrum antibiotics (ATB) impair T cell immune function in patients with either early-stage or advanced NSCLC, which likely contribute to the promotion of lung cancer metastasis. Results of the survival analysis show that metastasis-free survival (MFS) is significantly shorter in the ATB patients than that in the non-ATB patients with stage III NSCLC. The 16S rDNA sequencing shows that ATB administration contributes to a significant dysbiosis of the composition and diversity of gut microbiota. Moreover, ROC analysis results of CD4 (AUC 0.642, p = 0.011), CD8 (AUC was 0.729, p < 0.001), CD16 + 56 + (AUC 0.643, p = 0.003), and the combination of CD4, CD8 and CD16 + 56+ (AUC 0.810, p < 0.001), or Cox regression analysis results of CD4 (HR 0.206, p < 0.001), CD8 (HR 0.555, p = 0.009), which is likely regulated by ATB administration, have significantly predictive values for MFS.

Conclusion
These results provide evidence of gut microbiome disturbance due to ATB administration is involved in the regulation of T cell immunity, and their predictive value for the tumor metastasis in lung cancer patients. Thus, gut microbiota may serve as a therapeutic target for lung cancer. Consequently, caution should be exercised before the long-term administration of broad-spectrum antibiotics in cancer patients.
Gastrointestinal bleeding due to idiopathic early onset of vitamin K deficiency bleeding in a girl baby 50 min after birth: a rare case
Authors: Ringoringo Harapan Parlindungan , Tambunan Katherine Richel , Ananda Fajar Khalis , Nawati Felynawati , Permana Yanuar Nusca 
Published: November 2022

Abstract
Background
The incidence of early-onset vitamin K deficiency bleeding (VKDB) in at-risk neonates who did not receive vitamin K supplementation varied from 6 to 12%. This case report aims to show that VKDB can occur abruptly after birth despite vitamin K1 1 mg IM being given immediately after birth.

Case presentation
A term female baby was born through vaginal delivery of a 28 years old mother, G1P0A0, 39–40 weeks gestation with normal APGAR score, and birth weight was 3445 g, birth length was 52 cm. During pregnancy, the mother did not take any drugs except vitamins. There are no abnormalities on the baby’s physical examination. The anus is patent. Immediately after birth, the baby received a vitamin K1 1 mg intramuscularly. Abruptly, 50 min after delivery, there was meconium with lots of fresh blood. Laboratory results showed hemoglobin, 19.6 g/dL; leukocytes, 25,010/uL; platelets, 390,000/uL, with increased PT and aPTT. A peripheral blood smear showed a normal blood morphology. When 7 h old, the baby had much hematochezia. Laboratory results showed decreased hemoglobin to 17.5 g/dL and increased PT, aPTT, and INR. No abnormalities were found on the babygram and abdominal ultrasound. The working diagnosis was gastrointestinal bleeding due to idiopathic early-onset VKDB. The baby received vitamin K1 2 mg IM, Fresh Frozen Plasma, and a Packed Red Cells transfusion. The patient returned home in good clinical condition.

Conclusion
Vitamin K1 1 mg IM prophylaxis should be given immediately after birth to prevent early-onset VKDB. In addition, pregnant women who receive drugs that interfere with vitamin K metabolism (anti-epileptic drugs, anti-tuberculosis drugs, vitamin K antagonist drugs) should be given prophylactic vitamin K1, 20 mg/d orally, for at least two weeks before the expected time of delivery.