bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Electronic Medical Records with Self-report in Measuring Cancer Screening
Authors: Bhattacharyya Oindrila , Rawl Susan M. , Dickinson Stephanie L. , Haggstrom David A. 
Published: October 2022

Abstract
Background: Efficient measurement of the receipt of cancer screening has been attempted with electronic health records (EHRs), but EHRs are commonly implemented within a single health care setting. However, health information exchange (HIE) includes EHR data from multiple health care systems and settings, thereby providing a more population-based measurement approach. In this study, we set out to understand the value of statewide HIE data in comparison to survey self-report (SR) to measure population-based cancer screening.
Methods: A statewide survey was conducted among residents in Indiana who had been seen at an ambulatory or inpatient clinical setting in the past year. Measured cancer screening tests included Colonoscopy, Fecal Immunochemical Test (FIT) for colorectal cancer, Human Papilloma Virus (HPV) and Pap tests for cervical cancer, and Mammogram for breast cancer. For each screening test, the self-reported response for receipt of the screening (yes/no) and ‘time since last screening’ were compared with the corresponding information from patient HIE to evaluate the association between the two measures.
Results: Percent agreement of HIE and self-report of screening receipt ranged from 59% to 81%, with the Gwet’s AC ranging from 0.24-0.76, indicating a fair to substantial concordance. For the time since receipt of last screening test, Percent agreement ranged from 71% to 93% along with the Gwet’s AC ranging from 0.47-0.91. In comparison with SR data, HIE data provided relatively more additional information about laboratory-based tests: FIT (15% HIE alone vs. 4% SR alone) and HPV tests (24% HIE alone vs. 12% SR alone) and less additional information about procedures: Colonoscopy (7% HIE alone vs. 34% SR alone), Pap test (10% HIE alone vs. 27% SR alone), or Mammography (8% HIE alone vs. 20% SR alone).
Conclusion: Studies that use a single data source should consider the type of cancer screening test to choose the optimal data collection method. HIE and self-report both provided unique information in measuring cancer screening, and the most robust measurement approach involves collecting screening information from both HIE and patient self-report.
The effect of biomechanical foot-based interventions on patellofemoral joint loads during gait in adults with and without patellofemoral pain or osteoarthritis: a systematic review protocol.
Authors: Paterson Kade , Kayll Samual , Hinman Rana , Bennell Kim , Bryant Adam , Rowe Patrick 
Published: October 2022

Abstract
Background
Patellofemoral pain is highly prevalent across the lifespan, and a significant proportion of people report unfavourable outcomes years after diagnosis. Previous research has implicated patellofemoral joint loading during gait in patellofemoral pain and its sequelae, patellofemoral osteoarthritis. Biomechanical foot-based interventions (e.g., footwear, insoles, orthotics, taping or bracing) can alter patellofemoral joint loads, making them a promising treatment option. This systematic review will summarise the evidence about the effect of biomechanical foot-based interventions on patellofemoral joint loads during gait in adults with and without patellofemoral pain and osteoarthritis.
Methods
MEDLINE (Ovid), the Cumulative Index to Nursing and Allied Health Literature CINAHL, The Cochrane Central Register of Controlled Trials (CENTRAL), SPORTdiscus (EBSCO) and Embase (Ovid) will be searched. Our search strategy will include terms related to ‘patellofemoral joint’, ‘loads’ and ‘biomechanical foot-based interventions’. We will include studies published in the English language that assess the effect of biomechanical foot-based interventions on patellofemoral joint loads, quantified by patellofemoral joint pressure, patellofemoral joint reaction force and/or knee flexion moment. Two reviewers will independently screen titles and abstracts, complete full-text reviews, and extract data from included studies. Two reviewers will assess study quality using the Revised Cochrane Risk of Bias (RoB 2) tool or the Cochrane Risk Of Bias In Non-Randomized Studies – of Interventions (ROBINS-I) tool. We will provide a synthesis of the included studies’ characteristics and results. If three or more studies are sufficiently similar in population and intervention, we will pool the data to conduct a meta-analysis and report findings as standardised mean differences with 95% confidence intervals. If a meta-analysis cannot be performed, we will conduct a narrative synthesis of the results and produce forest plots for individual studies.
Discussion
This protocol outlines the methods of a systematic review that will determine the effect of biomechanical foot-based interventions on patellofemoral joint loads. Our findings will inform clinical practice by identifying biomechanical foot-based interventions that reduce or increase patellofemoral joint loads, which may aid the treatment of adults with patellofemoral pain and osteoarthritis.
Systematic review registry
Registered with PROSPERO on the 4th of May 2022 (CRD42022315207).
Management of severity lesions of hypomineralized molars (MIH) with different treatment alternatives: 9-months results of a clinical trial.
Authors: Özsoy Mine , Güngör Özge Erken 
Published: October 2022

AbstractObjectives:The aim of our study is to determine the most effective procedure by comparing the materials and imethods used in the treatment of MIH.Materials and Methods:189 first molars with MIH were restored with 4 different materials/methods. Equia Forte HT (GC, Tokyo, Japan) was used in Group 1; In Group 2, G-eanial composite (GC, Tokyo, Japan) was used with a Fuji IX (GC, Tokyo, Japan) base; In Group 3 and Group 4, EverX Posterior (GC, Tokyo, Japan) base and G-eanial composite (GC, Tokyo, Japan) were used. In group 4, deproteinization was performed with Papacarie Duo gel (F&A, Sao Paulo, Brazil). The clinical success of restorations at three/six/nine month periods was evaluated using Modified USPHS criteria.Results:When the marginal adaptation is evaluated; there was no statistically significant difference for the four groups at the 3rd month controls (p>0,05). Group 2 at the 6th and 9th month controls; it was found to be significantly different from Groups 3 and 4 (p<0,05). When the surface roungness is evaluated; Group 1 was statistically different from all other groups in all control months (p<0,05). There was no significant difference between the groups in terms of retention, color match, marginal discoloration and secondary caries in all control months (p>0,05).Conclusion:Restoration of MIH with Equia Forte HT is almost as successful as composites. The use of dentin replacement materials instead of glass ionomer cements as a base in composite restorations shows better results. Papacarie deproteinization showed similar success with other composite groups.Clinical Relevance:This study was the first clinical study in which Papacarie was used for deproteinization in teeth with MIH and will thus contribute to the literature.Trial registration number:ae5473c8-2c44-402c-bb62-706d27355c3b
Microbial signatures and continuum in endometrial cancer and benign patients
Authors: Semertzidou Anita , Whelan Eilbhe , Smith Ann , Ng Sherrianne , Brosens Jan , Marchesi Julian , Bennett Phillip , MacIntyre David , Kyrgiou Maria 
Published: October 2022

Abstract

Endometrial cancer is a multifactorial disease with inflammatory, metabolic and potentially microbial cues involved in disease pathogenesis. Here we sampled different regions of the reproductive tract (vagina, cervix, endometrium, fallopian tubes and ovaries) of 61 patients and showed that the upper genital tract of a subset of women with and without endometrial cancer harbour microbiota quantitatively and compositionally distinguishable from background contaminants. A microbial continuum, defined by detection of common bacterial species along the genital tract, was noted in most women without cancer while the continuum was less cohesive in endometrial cancer patients. Vaginal microbiota were poorly correlated with rectal microbiota in the studied cohorts. Endometrial cancer was associated with reduced cervicovaginal and rectal bacterial load together with depletion of Lactobacillus species relative abundance, including L. crispatus, increased bacterial diversity and enrichment of Porphyromonas, Prevotella, Peptoniphilus and Anaerococcus in the lower genital tract and endometrium. Treatment of benign and malignant endometrial organoids with L. crispatus conditioned media had minimal impact on cytokine and chemokine profiles. Our findings provide evidence that the upper female reproductive tract of some women contains detectable levels of bacteria, the composition of which is associated with endometrial cancer. Whether this is a cause or consequence of cancer pathophysiology remains to be elucidated.
Construction of a cuproptosis-related lncRNA signature as a novel prognostic model for pancreatic adenocarcinoma
Authors: Tong Li , Zheng Xiaofei , Gu Wang , Zhang Chong , Zhang Chao 
Published: October 2022

Abstract
Background
Pancreatic adenocarcinoma (PAAD) is one of the common malignant tumors, with high mortality and poor prognosis. Long non-coding RNA (lncRNA) plays a vital role in the progression of tumors. Cuproptosis, a newly identified form of programmed cell death, is thought to play a role in tumorigenesis. However, the role and prognostic value of cuproptosis-related lncRNA in PAAD remains unknown. Therefore, our study is to construct the role of cuproptosis-related lncRNA signature for predicting the prognosis of PAAD patients.
Material and methods
The mRNAs and lncRNAs expression profiles and clinical data of PAAD were obtained from The Cancer Genome Atlas (TCGA) databases. The prognosis signature was constructed by least absolute shrinkage and selection operator (LASSO) regression and Cox regression analysis. Patients were separated into high and low risk groups according to the median score. Using Kaplan-Meier, Concordance index (C-index), area under the receiver operating characteristic (ROC) curves to assess prognostic ability of the signature. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes Enrichment (KEGG), immune-related functions, and tumor mutation burden (TMB) were analyzed based on the signature. The likelihood of an immunotherapy response was estimated using tumor immune dysfunction and exclusion (TIDE) algorithms. PRRophetic package was used to identify its sensitivity toward potential drugs for PAAD.
Results
In total, we obtained 4 cuproptosis-related lncRNAs and constructed a prognostic signature. High-risk patients were correlated with worse overall survival (OS) and progression-free survival (PFS) and higher mortality. Multivariate Cox regression was performed to identify independent risk factor poor prognosis of high risk scores. ROC, C-index, and nomogram also showed the signature can accurately predict the prognosis of patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the biological functions of lncRNAs are associated with tumor development, especially immune response. Tumor Mutation Burden (TMB) and Tumor Immune Dysfunction and Exclusion (TIDE) scores were significantly different between high- and low-risk groups. The three drugs, including Paclitaxel, Gefitinib, and 17-AAG, were more sensitive in the high-risk group.
Conclusion
The 4 cuproptosis-related lncRNAs signature accurately predicted the prognosis of PAAD and led to better prognosis and treatment options for patients.
Quantification of cartilage and subchondral bone cysts on knee specimens based on a spectral photon-counting computed tomography
Authors: Garcelon Célestin , Abascal Juan , Olivier Cecile , Uk Stéphanie , Si-Mohamed Salim , Ea Hang-Korng , Douek Philippe , Peyrin Francoise , Chappard Christine 
Published: October 2022

Abstract
Spectral Photon-Counting Computed Tomography (SPCCT) is a new technique with the capability to provide mono-energetic (monoE) images with high signal to noise ratio. We demonstrate the feasibility of SPCCT to characterize at the same time cartilage and subchondral bone cysts (SBCs) without contrast agent in osteoarthritis (OA). To achieve this goal, 5 human knee specimens (3 normal and 2 with OA) were imaged with a clinical prototype SPCCT. The monoE images at 60 keV with isotropic voxels of 250x250x250 µm3 were compared with monoE synchrotron radiation CT (SR CT) images at 55 keV with isotropic voxels of 45x45x45 µm3 used as benchmark for cartilage segmentation. The volume and density of SBCs were evaluated in the two OA knees in SPCCT images. In 25 compartments (tibial lateral, tibial medial, femoral lateral, femoral medial and patella), the mean bias between SPCCT and SR CT analyses were 106 ± 196mm3 for cartilage volume and − 0.006mm ± 0.06 for mean cartilage thickness. The 2 OA knees displayed different SBCs profiles in terms of volume, density, and distribution according to size and location. SPCCT with fast acquisitions is able to characterize cartilage morphology and SBCs. SPCCT can be used potentially as a new tool in clinical studies in OA.
Reconsolidation of Traumatic Memories Protocol compared to Trauma Focussed Cognitive Behaviour Therapy for posttraumatic stress disorder in UK military veterans: a randomised controlled feasibility trial
Authors: Sturt Jackie , Rogers Rebecca , Armour Cherie , Cameron David , de Rijk Lisa , Fiorentino Francesca , Forbes Tricia , Glen Callum , Grealish Annmarie , Kreft Josh , de Souza Ida Meye , Spikol Eric , Tzouvara Vasiliki , Greenberg Neil 
Published: October 2022

Abstract
Background: Posttraumatic stress disorder (PTSD) occurs more commonly in military veterans than the general population. Whilst current therapies are effective, up to half of veterans commencing treatment don’t complete it. Reconsolidation of Traumatic Memories (RTM) protocol is a novel, easy to train, talking therapy with promising US findings. We examine the feasibility of undertaking an efficacy trial of RTM in UK veterans.
Methods: A parallel group, single-centre randomised controlled feasibility trial with a post-completion qualitative interview study. Sixty UK military veterans were randomised 2:1 to RTM (n=35) or Trauma Focussed CBT (n=25). We aimed to determine the rate of recruitment and retention, understand reasons for attrition, determine data quality and size of efficacy signal. We explored veterans’ perceptions of experiences of joining the trial, the research procedures and therapy, and design improvements for future veteran studies. UK military veterans with a diagnosis of PTSD or complex PTSD, and clinically significant symptoms, were recruited between January 2020 and June 2021. Primary outcome was feasibility using pre-determined progression criteria alongside PTSD symptoms, with depression, recovery and rehabilitation as secondary outcomes. Data were collected at baseline, 6, 12 and 20 weeks. Interviews (n=15) were conducted after 20 weeks. Both therapies were delivered by trained charity sector provider therapists.
Results: Participants’ mean age was 53yrs, the mean baseline PTSD symptoms score assessed by PCL-5 was 57. Fifty had complex PTSD and 39 had experienced ≥4 traumas. Data were analysed at 20 weeks for feasibility outcomes (n=60) and mental health outcomes (n=45). Seven of eight progression criteria were met. The RTM group experienced a mean 18-point reduction on the PCL-5. TFCBT group participants experienced a mean reduction of 8 points. 48% of the RTM group no longer met diagnostic criteria for PTSD compared to 16% in the TFCBT group. All veterans reported largely positive experiences of the therapy and research procedures and ways to improve them.
Conclusion: RTM therapy remains a promising psychological intervention for the treatment of PTSD, including complex PTSD, in military veterans. With specific strengthening, the research protocol is fit for purpose in delivering an efficacy trial.
Trial registration: ISRCTN registration no 10314773 on 01.10.2019
Human Salivary Concentrations of Brain Derived Neurotrophic Factor Correlates With Subjective Pain Intensity Associated With Initial Orthodontic Therapy.
Authors: Bhat Sagar S , Revankar Ameet Vaman , Naik Roopak D 
Published: October 2022

Abstract
Current study aimed to evaluate presence & concentration of salivary molecular pain biomarkers Calcitonin Gene Related Peptide(CGRP) and Brain-Derived Neurotrophic Factor(BDNF) during initial stages of orthodontic treatment and correlation with subjective pain scales, Numerical Rating Scale (NRS), Visual Analogue Scale (VAS), Verbal Rating Scale (VRS) and McGill Pain Questionnaire (MPQ). Consented, healthy-pain free patients(n=40) undergoing orthodontic therapy, having moderate crowding with pre-molar extraction were recruited. Unstimulated whole saliva was collected and stored at -80oC in cryotubes. Levels of CGRP & BDNF in salivary samples was assessed by enzyme–linked immunosorbent assay. Samples were collected under stipulated 5 time periods using saliva collection tube by passive drooling method: immediately after bonding but before wire placement(T0-baseline), after 24 hours(T1), 48 hours(T2), 72 hours(T3) & 168 hours(T4) after wire placement. Consolidated subjective pain scales were administered concurrently. Regression value(R2>0.9) confirmed BDNF & CGRP in saliva. Significant change was observed from baseline to 168 hrs in all subjective parameters(p<0.05). CGRP did not correlate with subjective pain scales statistically(p>0.05). BDNF levels correlated with all the subjective pain scales, NRS(T3-p=0.0092&T4-p=0.0064), VRS(T3-p=0.0112&T4-p=0.0500), VAS(T3-p=0.0092 &T4-p=0.0064) &MPQ (T1-p=0.0255). Mean BDNF & median subjective pain scale graphs were similar. BDNF correlated with all the subjective pain scales warranting further investigation.
Trial registration: Clinical Trial Registry - India (CTRI) Reg No: CTRI/2018/12/016571; Registered 10th December, 2018 (10/12/2018) prospectively; http://ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=29640&EncHid=&userName=Dr%20Sagar%20S%20Bhat
RNA-seq reveals novel mechanistic targets of Livin in bladder cancer
Authors: Li Xianwen , Fu Chunhua , Li Guofeng , He Haolin 
Published: October 2022

Abstract
Background
Bladder cancer is a very common malignancy with a high recurrence rate. The survival of patients with muscle-invasive bladder cancer is poor, and new therapies are needed. Livin has been reported to be upregulated in bladder cancer and influence the proliferation of cancer cells.
Materials & Methods
The Livin gene in human bladder cancer cell line T24 was knocked out, and the differentially expressed genes were identified by RNA-seq and qPCR.
Results
Livin knockdown affects gene expression and has strong negative effects on some cancer-promoting pathways. Furthermore, combined with bladder cancer clinical sample data downloaded from TCGA and GEO, 2 co-up-regulated genes and 28 co-down-regulated genes were identified and validated, which were associated with cancer proliferation and invasion.
Conclusion
All these results suggest that Livin plays an important role in bladder cancer and could be a potential anticancer target in clinical therapy.
An Adaptive 6-Dimensional Floating-Search Multi-Station Seismic-Event Detector (A6-DFMSD) and its Application to Low Frequency Earthquakes in the East Eifel Volcanic Field, Germany
Authors: Koushesh Mohsen , Ritter Joachim R. R. 
Published: October 2022

Abstract

We introduce a new seismic event detector that applies signal analysis in the frequency domain while searching matches coincidences at neighbouring recording stations. Unlike for the template matching based methods and the supervised and some unsupervised machine learning based methods, no a priori waveform information is needed for our Adaptive 6-Dimensional Floating-search Multi-station Seismic-event Detector (A6-DFMSD). As a challenging test example, the new detector is applied to a dataset with 5 months of micro-earthquake (ML < 2) recordings in the East Eifel Volcanic Field (EEVF), Germany. There both, magmatic and tectonic, earthquakes occur in a depth range between 3 km and 43 km. In summary, we detect 401 micro-earthquakes in this period without missing any of the 87 events listed in the existing catalogues of the region. This means that overall A6-DFMSD detected 4.6 times as many events were already known. After a manual location and classification of the events, we show that A6-DFMSD finds events of different origins (tectonic, magmatic, atmospheric, and anthropogenic). In particular, low-frequency earthquakes of magmatic origin with a complicated coda are very well identified. We suggest that seismological networks monitoring local seismicity with similar target zones should benefit from the use of A6-DFMSD to allow the detection of a wide range of seismic signals.
Pathological response of breast cancer of patients treated by neoadjuvant chemotherapy and correlation with survival. A perspective of real-world pathology
Authors: Brito Érika de Abreu Costa , Brito Hugo Leite de Farias , Marques Adriane Dórea , Moura Alex Rodrigues , Hora Evânia Curvelo , Lima Marcela Sampaio , Siqueira Hianga Fayssa Fernandes , Barreto Íkaro Daniel de Carvalho , Oliveira Leonardo Souto , Lima Carlos Anselmo 
Published: October 2022

Abstract
The main objective of this study is to evaluate the correlation of pathological parameters related to NACT and subsequent outcomes. The secondary objective is to correlate classical parameters and survival. We analyzed a retrospective cohort of 142 female patients treated with NACT, with primary breast cancer diagnosed between January 2011 and December 2017. Slides were reviewed by two independent pathologists. Treatment-related parameters were the average percentage of tumor cellularity, size of largest axillary metastasis, and regression pattern in lymph nodes. For statistical analysis, Kaplan–Meier method was applied to estimate the survival probability of the sample and overall survival (OS) and cancer-specific survival (SS). The Gehan-Breslow test was applied to evaluate the hypothesis of no difference in survival curves for different groups. In univariate regression analysis of parameters related to the treatment effect, macroscopic pattern, median of cellularity, cellularity pooled in 3 groups, and median of largest lymph node metastasis had independent prognostic values for overall survival (OS) and cancer-specific survival (SS). Classical parameters such as nuclear and histologic grade, mitotic index, grouped ypTNM stage, and lymphovascular invasion were also correlated to survival. In multivariate regression analysis, cellularity group ≥ 40% had a higher chance of death compared to 0–5% cellularity group for both OS (Hazard Ratio: 6.59; 95% Confidence Interval = 2.30–18.9; p < 0.001; adjusted Hazard Ratio: 3.40; 95% Confidence Interval = 1.12, 10.4; p = 0.031). and SS (Hazard Ratio: 3.9; 95% Confidence Interval = 1.58–9.72; p = 0.003; adjusted Hazard Ratio: 4.21; 95% Confidence Interval = 1.69–10.5; p = 0.002). Also, macroscopic pattern correlated to survival in multivariate analysis. The ypN1 + 2 + 3 stage group was the classical parameter with strongest correlation to worse prognosis for both OS (Hazard Ratio: 10.5; 95% Confidence Interval = 2.45–44.6; p = 0.002; adjusted Hazard Ratio: 6.78; 95% Confidence Interval = 1.50–30.6; p = 0.013) and SS (Hazard Ratio: 3.56; 95% Confidence Interval = 1.51–8.38; p = 0.004; adjusted Hazard Ratio: 2.65; 95% Confidence Interval = 1.09–6.48; p = 0.032). Other classical parameters such as triple-negative molecular subtype, lymphovascular invasion and nuclear grade 3 correlated to worse survival. Our findings support the incorporation of the percentage of tumor cellularity in the pathological reports of surgical specimens as an independent prognostic factor for patients treated with NACT.