bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of interstitial lung diseases and their progressive-fibrosing behaviour in six European countries
Authors: Hilberg Ole , Hoffmann-Vold Anna-Maria , Smith Vanessa , Bouros Demosthenes , Kilpeläinen Maritta , Guiot Julien , Morais Antonio , Clemente Susana , Daniil Zoe , Papakosta Despina , Fretheim Havard , Neves Sofia , Alfaro Tiago M. , Antoniou Katerina M. , Valveny Neus , Asijee Guus , Soulard Stéphane , Wuyts Wim ,   the PERSEIDS study group, Brusselle Guy , Tzilas Vassilios , Tzouvelekis Argyris , Bouros Evangelos , Perkonoja Katariina , Henket Monique , Cunin Marie-Pierre , Rosa Raquel , Martín Teresa , Branco Joana , Alvarenga Maria , Dimeas Ilias , Simopoulou Theodora , Fouka Evangelia , Tsiouprou Ioanna , Zaharias Athanasios , Campainha Sergio , Nogueira Carla , Freitas Sara , Fernandes Vânia , Cabo Carolina , Vasarmidi Irini 
Published: December 2021

The PERSEIDS study aimed to estimate incidence/prevalence of interstitial lung diseases (ILDs), fibrosing interstitial lung diseases (F-ILDs), idiopathic pulmonary fibrosis (IPF), systemic sclerosis-associated ILD (SSc-ILD), other non-IPF F-ILDs and their progressive-fibrosing (PF) forms in six European countries, as current data are scarce.This retrospective, two-phase study used aggregate data (2014–2018). In Phase 1, incident/prevalent cases of ILDs above were identified from clinical databases through an algorithm based on codes/keywords, and incidence/prevalence was estimated. For non-IPF F-ILDs, the relative percentage of subtypes was also determined. In Phase 2, a subset of non-IPF F-ILD cases was manually reviewed to determine the percentage of PF behaviour and usual interstitial pneumonia-like (UIP-like) pattern. A weighted mean percentage of progression was calculated for each country and used to extrapolate incidence/prevalence of progressive-fibrosing ILDs (PF-ILDs).In 2018, incidence/105person-years ranged between 9.4 and 83.6 (ILDs), 7.7 and 76.2 (F-ILDs), 0.4 and 10.3 (IPF), 6.6 and 71.7 (non-IPF F-ILDs), and 0.3 and 1.5 (SSc-ILD); and prevalence/105persons ranged between 33.6 and 247.4 (ILDs), 26.7 and 236.8 (F-ILDs), 2.8 and 31.0 (IPF), 22.3 and 205.8 (non-IPF F-ILDs), and 1.4 and 10.1 (SSc-ILD). Among non-IPF F-ILDs, sarcoidosis was the most frequent subtype. PF behaviour and UIP-like pattern were present in a third of non-IPF F-ILD cases each and hypersensitivity pneumonitis showed the highest percentage of progressive behaviour. Incidence of PF-ILDs ranged between 2.1 and 14.5/105person-years, and prevalence between 6.9 and 78.0/105persons.To our knowledge, PERSEIDS is the first study assessing incidence, prevalence and rate of progression of ILDs across several European countries. Still below the threshold for orphan diseases, the estimates obtained were higher and more variable than reported in previous studies, but differences in study design/population must be considered.
Variation characteristics of ocean sediment Fe levels and their relationship with grain sizes in culture areas over a long period
Authors: Zhang Baoyi , Li Manyi , An Maoguo , Zhi Chenglong , Li Qingcai , Zhang Yingmei , Han Shuangyuan , Zheng Haitao , Li Jun , Chen Huaixin , Chen Qiao 
Published: December 2021

AbstractIron (Fe) is an essential component for marine ecosystems, and it is related to the growth of phytoplankton communities and environmental evolution in coastal area. However, the effect of aquaculture activities on sediment Fe levels is not well studied. Fe levels and grain sizes are determined in two cores (respectively Core C in the culture area and Core A in the control area) in Sishili Bay to reveal the influence of cultivation on sediment Fe levels over an extended period. The sediment Fe levels are distinguished in the upper sections (culture period) but equal in the lower sections (non-culture period) of the two cores. The core C has the same Fe levels as Core A before 1950s (non-culture period). However, the sediment Fe levels of Core C increased during 1950s–1970s (the algae culture period) and decreased after the 1970s (shellfish culture period) compared with Core A, indicating the algae and shellfish culture impose opposite effects on sediment Fe levels. Similarly, sediment grain sizes are observed to be finer during the algae culture period but coarser during the shellfish culture period, and the variation of sediment grain sizes because of culture activities is the important factor affecting sediment Fe levels. The slowing down of ocean current due to algae culture causes finer particles and higher Fe levels in sediment. However, during the shellfish culture period, bio-deposition and re-suspension play major roles in coarsening sediment particles and decreasing sediment Fe levels.
Is there a relationship between serum vitamin D and semen parameters? A cross-sectional sample of the Iranian infertile men
Authors: Hajianfar Hossein , Karimi Elham , Mollaghasemi Negar , Rezaei Sheyda , Arab Arman 
Published: December 2021

Abstract
Background
Recent studies suggest that serum vitamin D may be associated with semen parameters. In the present cross-sectional study, we attempted to investigate the association between serum vitamin D levels and semen parameters among Iranian sub-fertile men.

Results
A total of 350 infertile men recruited for this cross-sectional study using a simple random sampling method with a mean age of 34.77 years old, body mass index of 26.67 kg/m2, serum vitamin D of 20.17 ng/ml, semen volume of 3.82 mL, sperm count of 44.48 (106/mL), sperm total motility of 38.10 %, and morphologically normal sperm of 7.0 %. After controlling for potential confounders, serum vitamin D was positively associated with semen volume (β = 0.63, 95 % CI: 0.06, 1.20), sperm count (β = 14.40, 95 % CI: 4.56, 24.25), sperm total motility (β = 18.12, 95 % CI: 12.37, 23.86), and sperm normal morphology (β = 1.95, 95 % CI: 1.07, 2.83).

Conclusions
The present findings suggest that higher serum vitamin D levels are positively associated with higher semen volume, sperm count, sperm total motility, and normal morphology rate. These findings, however, do not specify a cause-and-effect relationship, and there is a need for further research in this area to understand whether vitamin D supplementation can improve semen parameters.
A Metabolomics approach for the diagnosis Of SecondAry InfeCtions in COVID-19 (MOSAIC): a study protocol
Authors: McCreath Gordan , Whitfield Phillip D. , Roe Andrew J. , Watson Malcolm J. , Sim Malcolm A. B. 
Published: December 2021

Abstract
Background
Critically ill patients with COVID-19 are at an increased risk of developing secondary bacterial infections. These are both difficult to diagnose and are associated with an increased mortality. Metabolomics may aid clinicians in diagnosing secondary bacterial infections in COVID-19 through identification and quantification of disease specific biomarkers, with the aim of identifying underlying causative microorganisms and directing antimicrobial therapy.

Methods
This is a multi-centre prospective diagnostic observational study. Patients with COVID-19 will be recruited from critical care units in three Scottish hospitals. Three serial blood samples will be taken from patients, and an additional sample taken if a patient shows clinical or microbiological evidence of secondary infection. Samples will be analysed using LC–MS and subjected to bioinformatic processing and statistical analysis to explore the metabolite changes associated with bacterial infections in COVID-19 patients. Comparisons of the data sets will be made with standard microbiological and biochemical methods of diagnosing infection.

Discussion
Metabolomics analyses may provide additional strategies for identifying secondary infections, which might permit faster initiation of specific tailored antimicrobial therapy to critically ill patients with COVID-19.
Avelumab as neoadjuvant therapy in patients with urothelial non-metastatic muscle invasive bladder cancer: a multicenter, randomized, non-comparative, phase II study (Oncodistinct 004 - AURA trial)
Authors: Martinez Chanza Nieves , Soukane Louisa , Barthelemy Philippe , Carnot Aurélien , Gil Thierry , Casert Vinciane , Vanhaudenarde Vincent , Sautois Brieuc , Staudacher Lionel , Van den Brande Jan , Culine Stephane , Seront Emmanuel , Gizzi Marco , Albisinni Simone , Tricard Thibault , Fantoni Jean Christophe , Paesmans Marianne , Caparica Rafael , Roumeguere Thierry , Awada Ahmad 
Published: December 2021

Abstract
Introduction
Cisplatin-based neoadjuvant chemotherapy (NAC) followed by surgery is the standard treatment for patients with non-metastatic muscle invasive bladder cancer (MIBC). Unfortunately, many patients are not candidates to receive cisplatin due to renal impairment. Additionally, no predictive biomarkers for pathological complete response (pCR) are currently validated in clinical practice. Studies evaluating immune checkpoint inhibitors in the peri-operative setting are emerging with promising results. Clinical trials are clearly required in the neoadjuvant setting in order to improve therapeutic strategies.

Methods and analysis
Oncodistinct 004 – AURA is an ongoing multicenter phase II randomized trial assessing the efficacy and safety of avelumab single-agent or combined to different NAC regimens in patients with non-metastatic MIBC. Patients are enrolled in two distinct cohorts according to their eligibility to receive cisplatin-based NAC. In the cisplatin eligible cohort, patients are randomized in a 1:1 fashion to receive avelumab combined with cisplatin-gemcitabine or with dose-dense methotrexate-vinblastine-doxorubicin-cisplatin. In the cisplatin ineligible cohort, patients are randomized at a 1:1 ratio to paclitaxel-gemcitabine associated to avelumab or avelumab alone. Primary endpoint is pCR. Secondary endpoints are pathological response and safety.

Ethics and dissemination
The study is approved by ethics committee from all participating centers. All participants provide informed consent prior inclusion to the study. Once completed, results will be published in peer-reviewed journals.

Trial registration number
ClinicalTrials.gov (NCT03674424).
Exosomal microRNA-107 reverses chemotherapeutic drug resistance of gastric cancer cells through HMGA2/mTOR/P-gp pathway
Authors: Jiang Lu , Zhang Yan , Guo Linghui , Liu Chaoyang , Wang Pan , Ren Weihong 
Published: December 2021

Abstract
Background
RNA cargo in exosomes, especially microRNAs (miRNAs), play an important role in the chemotherapy drug resistance of human cancers. However, the role and mechanism of exosomal miR-107 on multidrug resistance of gastric cancer cells was still not clear. In this study, we sought to explore whether exosomal miR-107 could reverse the resistance of gastric cancer cells to the chemotherapy drugs.

Methods
We extracted exosomes from sensitive (SGC-7901, MGC-803) and resistant (SGC-7901/5-FU) gastric cancer cells by ultracentrifugation and the isolated exosomes were identified using transmission electron microscopy (TEM) and dynamic light scattering analysis (DLS). The expression of miR-107 and high mobility group A2 (HMGA2) were detected by real-time quantitative PCR (RT-qPCR). MTT assay was used to investigate the effect of exosomes on gastric cancer cells growth in vitro. The uptake of exosomes by recipient cells were observed using a fluorescence microscope. The predicted target relationship between miR-107 and HMGA2 was verified by gauss-luciferase reporter assay. The expression of HMGA2, p-mTOR/mTOR, P-gp and other exosomal indicated marker proteins was detected by western blot.

Results
Our results indicated that the isolated exosomes were typically cup-like lipid bilayer membranes structure. SGC-7901/5-FU cells were cross-resistant to chemotherapy drug cisplatin (CDDP), and the sensitive cells-secreted exosomes drastically reversed the resistance of the resistant GC cells to the chemotherapeutic drugs, which was verified by exosomal inhibitor GW4896. Mechanistically, the reversal effect was mainly mediated by exosome-secreted miR-107 through downregulating the expression of target molecular HMGA2 and inhibiting HMGA2/mTOR/P-gp pathway, which were supported by results from luciferase reporter assay and rescue assay.

Conclusions
These findings demonstrated that exosome-transmitted miR-107 significantly enhanced the sensitivity of resistant gastric cancer cells to chemotherapeutic agents by mediating the HMGA2/mTOR/P-gp axis and exosomal miR-107 may be a novel target in gastric cancers treatment.
Nutritional status and associated factors among children with congenital heart disease in selected governmental hospitals and cardiac center,Addis Ababa Ethiopia
Authors: Woldesenbet Rediet , Murugan Rajalakshmi , Mulugeta Feven , Moges Tamirat 
Published: December 2021

Abstract
Background
Children with congenital heart disease are at risk for poor growth and under-nutrition compared with healthy children. The aim of this study was to assess the nutritional status of children with congenital heart disease and associated factors in selected governmental hospitals and cardiac center Addis Ababa, Ethiopia.

Method
Institutional based cross sectional study among 373 children aged under15 years was conducted from February to March; 2021G.c. Data was collected using structured questionnaire and chart review. Z-scores based on WHO reference ranges were used. Anthropometric z-scores based on WHO 2007 reference ranges were generated for each child. Weight-for-age z-scores for children 0–10 years and height-for-age and BMI-for-age z-scores for all children. Binary logistic regression was used for associated factors.

Result
A total of 373 children were participated in this study. The prevalence of wasting and stunting was 144(38.6%) and 134(35.9%) respectively. The prevalence of underweight and malnutrition in children under 10 years was 143(43.1%). Most of the children were diagnosed with VSD (36.7%). Children age group of 13 months-5 years were associated with wasting and underweight [AOR = 0.434, 95%CI: (0.231, 0.816)] and [AOR = 0.360, 95%CI: (0.183, 0.711)] respectively. Children diagnosed with PAH were 1.885 times more likely to be underweight [AOR = 1.885, 95%CI: (1.094, 3.246)]. When the hemoglobin level increases by every unit per g/dl the chance to be wasting and underweight decreases by 13.1 and 18.6%[AOR = 0.869, 95%CI: (0.792, 0.955)] and [AOR = 0.869, 95%CI: (0.792, 0.955)] respectively. The level of SPO2 is associated with stunting and underweight [AOR = 0.970, 95%CI: (0.943, 0.998)] and [AOR = 0.970, 95%CI: (0.943, 0.998)] respectively.

Conclusion
The prevalence of malnutrition in children with CHD is pretty high. Decreased level of hemoglobin and SPO2 was found to be associated factors for malnutrition in this case. There need to be a new strategy about including different health professional while care giving.
Novel screening model of obstructive sleep apnea for snorers with suspected NAFLD undergoing liver sonography
Authors: Lu Yang-Bor , Weng Yu-Chieh , Huang Yung-Ning , Huang Hsiung-Ying , Cheng Pei-Ting , Hsieh Hui-Shan , Tsai Ming-Shao 
Published: December 2021

Abstract
Background/aims
Given the increased incidence of obstructive sleep apnea (OSA) among patients with nonalcoholic fatty liver disease (NAFLD), noninvasive screening methods are urgently needed to screen for OSA risk in these patients when conducting an office-based assessment of hepatic steatosis. Therefore, we investigated the controlled attenuation parameter (CAP) and hepatic steatosis index (HSI) in patients with and without OSA and developed screening models to detect OSA.

Methods
We retrospectively reviewed the medical records of all adult snorers with suspected NAFLD undergoing liver sonography between June 2017 and June 2020. Records encompassed CAP and HSI data as well as data collected during in-hospital full-night polysomnography. The multivariate logistic regression models were constructed to explore the predictors of OSA risk. Furthermore, model validation was performed based on the medical records corresponding to the July 2020–June 2021 period.

Results
A total of 59 patients were included: 81.4% (48/59) were men, and the mean body mass index (BMI) was 26.4 kg/m2. Among the patients, 62.7% (37/59) and 74.6% (44/59) (detected by the HSI and CAP, respectively) had NAFLD, and 78% (46/59) were diagnosed with OSA on the basis of polysomnography. Three screening models based on multivariate analysis were established. The model combining male sex, a BMI of > 24.8, and an HSI of > 38.3 screened for OSA risk the most accurately, with an area under the receiver operating characteristic curve of 0.81 (sensitivity: 78%; specificity: 85%; and positive and negative predictive values: 95% and 52%, respectively) in the modeling cohort. An accuracy of 70.0% was achieved in the validation group.

Conclusions
The combination screening models proposed herein provide a convenient, noninvasive, and rapid screening tool for OSA risk and can be employed while patients receive routine hepatic check-ups. These models can assist physicians in identifying at-risk OSA patients and thus facilitate earlier detection and timely treatment initiation.
Risk factor analysis of intravesical recurrence after retroperitoneoscopic nephroureterectomy for upper tract urothelial carcinoma
Authors: Yanagi Masato , Hamasaki Tsutomu , Akatsuka Jun , Endo Yuki , Takeda Hayato , Kondo Yukihiro 
Published: December 2021

Abstract
Background
One of the major concerns of patients with upper tract urothelial carcinoma (UTUC) treated with nephroureterectomy is intravesical recurrence (IVR). The purpose of the present study was to investigate the predictive risk factors for IVR after retroperitoneoscopic nephroureterectomy (RNU) for UTUC.

Methods
Clinicopathological and surgical information were collected from the medical records of 73 patients treated with RNU for non-metastatic UTUC, without a history of or concomitant bladder cancer. The association between IVR after RNU and clinicopathological and surgery-related factors, including preoperative urine cytology and pneumoretroperitoneum time, was analyzed using the Fisher exact test.

Results
During the median follow-up time of 39.1 months, 18 (24.7%) patients had subsequent IVR after RNU. The 1- and 3-year IVR-free survival rates were 85.9% and 76.5%, respectively. The Fisher exact test revealed that prolonged pneumoretroperitoneum time of ≥ 210 min was a risk factor for IVR in 1 year after RNU (p = 0.0358) and positive urine cytology was a risk factor for IVR in 3 years after RNU (p = 0.0352).

Conclusions
In UTUC, the occurrences of IVR in 1 and 3 years after RNU are highly probable when the pneumoretroperitoneum time is prolonged (≥ 210 min) and in patients with positive urine cytology, respectively. Strict follow-up after RNU is more probable recommended for these patients.
Teaching the technical performance of bronchoscopy to residents in a step-wise simulated approach: factors supporting learning and impacts on clinical work – a qualitative analysis
Authors: Eickelmann Anne Kathrin , Waldner Noemi Jelena , Huwendiek Sören 
Published: December 2021

Abstract
Background
The ability to perform a bronchoscopy is a valuable clinical skill for many medical specialities. Learning this skill is demanding for residents, due to the high cognitive load. Lessons learned from cognitive load theory might provide a way to facilitate this learning. The aim of this study was to investigate residents’ perception of factors that support and hinder learning, as well as outcome and acceptance of a workshop on flexible bronchoscopy.

Methods
Three half-day workshops were designed to teach 12 residents the basics of handling a flexible bronchoscope. They consisted of four phases that alternated between short theoretical aspects and longer practical situations. The practical phases focussed initially on manoeuvring a bronchoscope through holes in panels inside a box, and then on examination and practice using a three-dimensional printed model of the bronchial tree. Afterwards, three audio- and video-recorded focus groups were conducted, transcribed and coded, and underwent reflexive thematic analysis.

Results
Analysis of the focus groups defined two themes: (1) factors that supported a safe and positive learning environment were optimised for intrinsic load, simulated setting, absence of pressure, dyad practice (working in pairs), small group sizes and playful learning; and (2) impacts on clinical work were perceived as high levels of learning and improved patient safety. The residents did not report factors that hindered their learning. Some suggestions were made to improve the set-up of the wooden box.

Conclusions
The half-day workshop was designed according to several factors, including cognitive load theory in a simulated setting, and creation of a safe and positive learning environment. The residents perceived this as supporting learning and patient safety. Further studies can be designed to confirm these results in a quantitative setting.

Trial registration
This study was not interventional, therefore was not registered.
A nomogram model for predicting prognosis of obstructive colorectal cancer
Authors: Lv Jian , Liu Yuan yuan , Jia Yi tao , He Jing li , Dai Guang yao , Guo Peng , Zhao Zhao long , Zhang Yan ni , Li Zhong xin 
Published: December 2021

Abstract
Background
The prognosis of obstructive colorectal cancer (oCRC) is worse than that of nonobstructive colorectal cancer. However, no previous study has established an individualized prediction model for the prognosis of patients with oCRC. We aimed to screen the factors that affect the prognosis of oCRC and to use these findings to establish a nomogram model that predicts the individual prognosis of patients with oCRC.

Methods
This retrospective study collected data of 181 patients with oCRC from three medical hospitals between February 2012 and December 2017. Among them, 129 patients from one hospital were used as the training cohort. Univariate and multivariate analyses were used in this training cohort to select independent risk factors that affect the prognosis of oCRC, and a nomogram model was established. The other 52 patients from two additional hospitals were used as the validation cohort to verify the model.

Results
Multivariate analysis showed that carcinoembryonic antigen level (p = 0.037, hazard ratio [HR] = 2.872 [1.065–7.740]), N stage (N1 vs. N0, p = 0.028, HR = 3.187 [1.137–8.938]; N2 vs. N0, p = 0.010, HR = 4.098 [1.393–12.051]), and surgical procedures (p = 0.002, HR = 0.299 [0.139–0.643]) were independent prognostic factors of overall survival in patients with oCRC. These factors were used to construct the nomogram model, which showed good concordance and accuracy.

Conclusion
Carcinoembryonic antigen, N stage, and surgical method are independent prognostic factors for overall survival in patients with oCRC, and the nomogram model can visually display these results.
Therapeutic implications of cancer gene amplifications without mRNA overexpression: silence may not be golden
Authors: Boichard Amélie , Lippman Scott M. , Kurzrock Razelle 
Published: December 2021

AbstractAmplifications of oncogenic genes are often considered actionable. However, not all patients respond. Questions have therefore arisen regarding the degree to which amplifications, especially non-focal ones, mediate overexpression. We found that a subset of high-level gene amplifications (≥ 6 copies) (from The Cancer Genome Atlas database) was not over-expressed at the RNA level. Unexpectedly, focal amplifications were more frequently silenced than non-focal amplifications. Most non-focal amplifications were not silenced; therefore, non-focal amplifications, if over-expressed, may be therapeutically tractable. Furthermore, specific silencing of high-level focal or non-focal gene amplifications may explain resistance to drugs that target the relevant gene product.