bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aggressive squamous cell carcinoma of the cranium of a dog
Authors: Łojszczyk Anna , Łopuszyński Wojciech , Szadkowski Mateusz , Orzelski Maciej , Twardowski Piotr 
Published: April 2021

AbstractBackgroundThe authors report a case of keratinized squamous cell carcinoma (SCC) in a 14-year-old dog with extensive cranial bone invasion. To our knowledge, this is the first description of such a case of cranial keratinized SCC with aggressive generalized osteolysis described in a dog.Case presentationThe 14-year-old dog was referred for radiological examination with suspicion of head trauma with clinical signs of head deformation, exophthalmos and nasal discharge. The skull radiographs showed a large osteolytic defect of the frontal bone and parietal bone in the region of the external sagittal crest. Findings from the skull CT scan included generalized osteolysis in the region of parietal bone, frontal bones, maxilla on the right side and the nasal bone including the dorsal nasal concha. In the area of bone loss, new soft tissue formation with multifocal foci of mineralization was visible. The ultrasound examination revealed hypoechogenic changes with hyperechoic foci consistent with mineralization and poor vascularization. The brain and ocular structures were without visible changes. Fine needle aspiration cytology (FNAC) was performed, and squamous cell carcinoma was suspected. After 3 months, the re-presented to the clinic. The dog became progressively listless, his appetite was decreased, and he became acutely blind. Follow-up skull CT scan revealed significant osteolysis, which affected a significant aspect of the cranium. All bone defects had been replaced by new 3.5 cm-thick soft tissue formations with multifocal small 1–2 mm areas of mineralization. There was no evidence of metastasis. Histological examination confirmed the suspicion of squamous cell carcinoma.ConclusionsThis paper is the first report of cranial SCC in a dog causing extensive bone osteolysis. The lesions in this dog originated from the frontal and parietal bones including frontal sinuses.There are variants of tumors that arise from squamous epithelium or resemble SCC in the skull. These examples include adenosquamous carcinoma and proliferating trichilemmal tumours. In addition, there is possible malignant transformation caused by papilloma viruses. In the veterinary literature, there is only one similar description of adenosquamous carcinoma in a cat with similar clinical manifestations. It is justified to suspect a process of neoplastic epithelial origin in all cases of aggressive and extensive skull bone lysis. This issue should be subject to further investigation.
Ugandan stakeholder hopes and concerns about gene drive mosquitoes for malaria control: new directions for gene drive risk governance
Authors: Hartley Sarah , Smith Robert D. J. , Kokotovich Adam , Opesen Chris , Habtewold Tibebu , Ledingham Katie , Raymond Ben , Rwabukwali Charles B. 
Published: April 2021

Abstract
Background
The African Union’s High-Level Panel on Emerging Technologies identified gene drive mosquitoes as a priority technology for malaria elimination. The first field trials are expected in 5–10 years in Uganda, Mali or Burkina Faso. In preparation, regional and international actors are developing risk governance guidelines which will delineate the framework for identifying and evaluating risks. Scientists and bioethicists have called for African stakeholder involvement in these developments, arguing the knowledge and perspectives of those people living in malaria-afflicted countries is currently missing. However, few African stakeholders have been involved to date, leaving a knowledge gap about the local social-cultural as well as ecological context in which gene drive mosquitoes will be tested and deployed. This study investigates and analyses Ugandan stakeholders’ hopes and concerns about gene drive mosquitoes for malaria control and explores the new directions needed for risk governance.

Methods
This qualitative study draws on 19 in-depth semi-structured interviews with Ugandan stakeholders in 2019. It explores their hopes for the technology and the risks they believed pertinent. Coding began at a workshop and continued through thematic analysis.

Results
Participants’ hopes and concerns for gene drive mosquitoes to address malaria fell into three themes: (1) ability of gene drive mosquitoes to prevent malaria infection; (2) impacts of gene drive testing and deployment; and, (3) governance. Stakeholder hopes fell almost exclusively into the first theme while concerns were spread across all three. The study demonstrates that local stakeholders are able and willing to contribute relevant and important knowledge to the development of risk frameworks.

Conclusions
International processes can provide high-level guidelines, but risk decision-making must be grounded in the local context if it is to be robust, meaningful and legitimate. Decisions about whether or not to release gene drive mosquitoes as part of a malaria control programme will need to consider the assessment of both the risks and the benefits of gene drive mosquitoes within a particular social, political, ecological, and technological context. Just as with risks, benefits—and importantly, the conditions that are necessary to realize them—must be identified and debated in Uganda and its neighbouring countries.
Predicting plaque vulnerability change using intravascular ultrasound + optical coherence tomography image-based fluid–structure interaction models and machine learning methods with patient follow-up data: a feasibility study
Authors: Guo Xiaoya , Maehara Akiko , Matsumura Mitsuaki , Wang Liang , Zheng Jie , Samady Habib , Mintz Gary S. , Giddens Don P. , Tang Dalin 
Published: April 2021

Abstract
Background
Coronary plaque vulnerability prediction is difficult because plaque vulnerability is non-trivial to quantify, clinically available medical image modality is not enough to quantify thin cap thickness, prediction methods with high accuracies still need to be developed, and gold-standard data to validate vulnerability prediction are often not available. Patient follow-up intravascular ultrasound (IVUS), optical coherence tomography (OCT) and angiography data were acquired to construct 3D fluid–structure interaction (FSI) coronary models and four machine-learning methods were compared to identify optimal method to predict future plaque vulnerability.

Methods
Baseline and 10-month follow-up in vivo IVUS and OCT coronary plaque data were acquired from two arteries of one patient using IRB approved protocols with informed consent obtained. IVUS and OCT-based FSI models were constructed to obtain plaque wall stress/strain and wall shear stress. Forty-five slices were selected as machine learning sample database for vulnerability prediction study. Thirteen key morphological factors from IVUS and OCT images and biomechanical factors from FSI model were extracted from 45 slices at baseline for analysis. Lipid percentage index (LPI), cap thickness index (CTI) and morphological plaque vulnerability index (MPVI) were quantified to measure plaque vulnerability. Four machine learning methods (least square support vector machine, discriminant analysis, random forest and ensemble learning) were employed to predict the changes of three indices using all combinations of 13 factors. A standard fivefold cross-validation procedure was used to evaluate prediction results.

Results
For LPI change prediction using support vector machine, wall thickness was the optimal single-factor predictor with area under curve (AUC) 0.883 and the AUC of optimal combinational-factor predictor achieved 0.963. For CTI change prediction using discriminant analysis, minimum cap thickness was the optimal single-factor predictor with AUC 0.818 while optimal combinational-factor predictor achieved an AUC 0.836. Using random forest for predicting MPVI change, minimum cap thickness was the optimal single-factor predictor with AUC 0.785 and the AUC of optimal combinational-factor predictor achieved 0.847.

Conclusion
This feasibility study demonstrated that machine learning methods could be used to accurately predict plaque vulnerability change based on morphological and biomechanical factors from multi-modality image-based FSI models. Large-scale studies are needed to verify our findings.
The financing need of equitable provision of paid maternal leave in the informal sector in Indonesia: a comparison of estimation methods
Authors: Siregar Adiatma Y. M. , Pitriyan Pipit , Hardiawan Donny , Zambrano Paul , Mathisen Roger 
Published: April 2021

Abstract
Background
Providing an enabling environment for breastfeeding is hampered by the inequitable implementation of paid maternity leave, primarily due to perceived or actual financial costs. To estimate the real cost of paid maternity leave requires using reliable methods. We compared methods utilized in two recent studies in Indonesia. Study A estimated the financial need of providing paid maternity leave in the formal sector with a 10-year forecast at 21% coverage of eligible mothers, while study B estimated similar costs for the informal sector at 100% coverage annually. Results are critical for guiding future application of either method to inform paid maternity leave policies.

Methods
We compared number of covered mothers working informally, total annual cost, and cost per mother. We modified some parameters used in study A (method A) to be similar to study B (method B) for comparison, namely the period of estimate (annual), coverage (100%), estimate of women potentially breastfeeding, exchange rate, female labor force participation rate, the percentage of women working in the informal sector, and adding administration cost.

Results
The methods differ in determining the number of mothers working in the informal sector who gave birth, the minimum wage as unit cost, and administrative cost. Both studies estimated the cost at various lengths of leave period. Method A requires more macro (e.g. national/regional) level data, while method B involves (e.g. individual) micro level data. We compared the results of method A with method B, respectively: 1) number of covered mothers working informally were 1,425,589 vs. 1,147,204; 2) total annual costs including administrative costs were US$650,230,167 vs. US$633,942,726, and; 3) cost/mother was US$456 vs US$553.

Conclusion
Certain flexibilities can be applied to both methods, namely using parameters specific to respective regions (e.g. provincial level parameters), flexible period of analysis, and the use of administrative cost. In a setting where micro data is scarce and not easily accessible, method A provides a feasible approach, while method B will be most appropriate if suitable micro data is available. Future comparison studies in other settings are needed to provide further evidence on the strengths and weaknesses of both methods.
Diagnostic performance of Oncuria™, a urinalysis test for bladder cancer
Authors: Hirasawa Yosuke , Pagano Ian , Chen Runpu , Sun Yijun , Dai Yunfeng , Gupta Amit , Tikhonenkov Sergei , Goodison Steve , Rosser Charles J. , Furuya Hideki 
Published: April 2021

AbstractBackgroundDue to insufficient accuracy, urine-based assays currently have a limited role in the management of patients with bladder cancer. The identification of multiplex molecular signatures associated with disease has the potential to address this deficiency and to assist with accurate, non-invasive diagnosis and monitoring.MethodsTo evaluate the performance of Oncuria™, a multiplex immunoassay for bladder detection in voided urine samples. The test was evaluated in a multi-institutional cohort of 362 prospectively collected subjects presenting for bladder cancer evaluation. The parallel measurement of 10 biomarkers (A1AT, APOE, ANG, CA9, IL8, MMP9, MMP10, PAI1, SDC1 and VEGFA) was performed in an independent clinical laboratory. The ability of the test to identify patients harboring bladder cancer was assessed. Bladder cancer status was confirmed by cystoscopy and tissue biopsy. The association of biomarkers and demographic factors was evaluated using linear discriminant analysis (LDA) and predictive models were derived using supervised learning and cross-validation analyses. Diagnostic performance was assessed using ROC curves.ResultsThe combination of the 10 biomarkers provided an AUROC 0.93 [95% CI 0.87–0.98], outperforming any single biomarker. The addition of demographic data (age, sex, and race) into a hybrid signature improved the diagnostic performance AUROC 0.95 [95% CI 0.90–1.00]. The hybrid signature achieved an overall sensitivity of 0.93, specificity of 0.93, PPV of 0.65 and NPV of 0.99 for bladder cancer classification. Sensitivity values of the diagnostic panel for high-grade bladder cancer, low-grade bladder cancer, MIBC and NMIBC were 0.94, 0.89, 0.97 and 0.93, respectively.ConclusionsUrinary levels of a biomarker panel enabled the accurate discrimination of bladder cancer patients and controls. The multiplex Oncuria™ test can achieve the efficient and accurate detection and monitoring of bladder cancer in a non-invasive patient setting.
Biologically consistent dose accumulation using daily patient imaging
Authors: Niebuhr Nina I. , Splinter Mona , Bostel Tilman , Seco Joao , Hentschke Clemens M. , Floca Ralf O. , Hörner-Rieber Juliane , Alber Markus , Huber Peter , Nicolay Nils H. , Pfaffenberger Asja 
Published: April 2021

Abstract
Background
This work addresses a basic inconsistency in the way dose is accumulated in radiotherapy when predicting the biological effect based on the linear quadratic model (LQM). To overcome this inconsistency, we introduce and evaluate the concept of the total biological dose, bEQDd.

Methods
Daily computed tomography imaging of nine patients treated for prostate carcinoma with intensity-modulated radiotherapy was used to compute the delivered deformed dose on the basis of deformable image registration (DIR). We compared conventional dose accumulation (DA) with the newly introduced bEQDd, a new method of accumulating biological dose that considers each fraction dose and tissue radiobiology. We investigated the impact of the applied fractionation scheme (conventional/hypofractionated), uncertainties induced by the DIR and by the assigned α/β-value.

Results
bEQDd was systematically higher than the conventionally accumulated dose with difference hot spots of 3.3–4.9 Gy detected in six out of nine patients in regions of high dose gradient in the bladder and rectum. For hypofractionation, differences are up to 8.4 Gy. The difference amplitude was found to be in a similar range to worst-case uncertainties induced by DIR and was higher than that induced by α/β.

Conclusion
Using bEQDd for dose accumulation overcomes a potential systematic inaccuracy in biological effect prediction based on accumulated dose. Highest impact is found for serial-type late responding organs at risk in dose gradient regions and for hypofractionation. Although hot spot differences are in the order of several Gray, in dose-volume parameters there is little difference compared with using conventional or biological DA. However, when local dose information is used, e.g. dose surface maps, difference hot spots can potentially change outcomes of dose-response modelling and adaptive treatment strategies.
Unusual complications following left ventricular assisted device implantation: case series
Authors: Shalabi Amjad , Kachel Erez , Kassif Yigal , Faqeeh Muin , Sergey Preisman , Sternik Leonid , Grosman-Rimon Liza , Kinany Wadi , Amir Offer , Ram Eilon , Lavee Jacob , Grupper Avishay 
Published: April 2021

Abstract
Background
While left ventricular assisted devices (LVAD) have revolutionized the treatment of advanced heart failure, they are associated with a wide range of complications, including bleeding and infection which are the most common complications reported in the literature. Our case series report four unusual complications not related to gastrointestinal bleeding and infections and their management.

Case presentation
A 61 year old female after LVAD implantation with late onset of severe symptomatic aortic regurgitation treated by transfemoral transcatheter valve implantation (TAVI) with good long term results.
A 75 year old male patient with acute pump failure secondary to cable damage, who underwent urgent pump replacement. A 49 year old female patient with a history of myoma who developed massive uterine bleeding which was treated with emergent open hysterectomy after failed gonadotropin-releasing hormone therapy replacement. A 57 year old male patient with device display failure 1 month after LVAD implantation without the ability to monitor speed, power consumption and blood flow.

Conclusions
LVAD patients can be presented with a great variety of complications. Physicians should be aware of their manifestations and the management options.
TREM2/PLCγ2 signalling in immune cells: function, structural insight, and potential therapeutic modulation
Authors: Magno Lorenza , Bunney Tom D. , Mead Emma , Svensson Fredrik , Bictash Magda N. 
Published: April 2021

AbstractThe central role of the resident innate immune cells of the brain (microglia) in neurodegeneration has become clear over the past few years largely through genome-wide association studies (GWAS), and has rapidly become an active area of research. However, a mechanistic understanding (gene to function) has lagged behind. That is now beginning to change, as exemplified by a number of recent exciting and important reports that provide insight into the function of two key gene products – TREM2 (Triggering Receptor Expressed On Myeloid Cells 2) and PLCγ2 (Phospholipase C gamma2) – in microglia, and their role in neurodegenerative disorders. In this review we explore and discuss these recent advances and the opportunities that they may provide for the development of new therapies.
Chemotherapy-elicited exosomal miR-378a-3p and miR-378d promote breast cancer stemness and chemoresistance via the activation of EZH2/STAT3 signaling
Authors: Yang Qianxi , Zhao Shaorong , Shi Zhendong , Cao Lixia , Liu Jingjing , Pan Teng , Zhou Dongdong , Zhang Jin 
Published: April 2021

Abstract
Background
Not all breast cancer (BC) patients who receive neoadjuvant chemotherapy achieve a pathologic complete response (pCR), but the reasons for this are unknown. Previous studies have shown that exosomes produced in the tumor microenvironment in response to chemotherapy promote a chemotherapy-resistant phenotype in tumors. However, the role of BC chemotherapy-elicited exosomes in regulating chemoresistance is poorly understood.

Methods
Using commercial kits, serum exosomes were extracted from patients before neoadjuvant chemotherapy, after one cycle of chemotherapy and after four cycles of chemotherapy consisting of doxorubicin (DOX) and paclitaxel (PTX). Their miRNAs were sequenced, and the correlation between the sequencing results and chemotherapy effects was further verified by RT-qPCR using patient serum exosomes. Cell Counting Kit-8 (CCK-8) was used to detect chemosensitivity. Stemness was assessed by CD44+/CD24- population analysis and mammosphere formation assays. Chromatin immunoprecipitation (ChIP) experiments were performed to verify the binding of signal transducer and activator of transcription 3 (STAT3) to the promoter of miRNAs.

Results
Here, we provide clinical evidence that chemotherapy-elicited exosomal miR-378a-3p and miR-378d are closely related to the chemotherapy response and that exosomes produced by BC cells after stimulation with DOX or PTX deliver miR-378a-3p and miR-378d to neighboring cells to activate WNT and NOTCH stemness pathways and induce drug resistance by targeting Dickkopf 3 (DKK3) and NUMB. In addition, STAT3, which is enhanced by zeste homolog 2 (EZH2), bound to the promoter regions of miR-378a-3p and miR-378d, thereby increasing their expression in exosomes. More importantly, chemotherapeutic agents combined with the EZH2 inhibitor tazemetostat reversed chemotherapy-elicited exosome-induced drug resistance in a nude mouse tumor xenograft model.

Conclusion
This study revealed a novel mechanism of acquired chemoresistance whereby chemotherapy activates the EZH2/STAT3 axis in BC cells, which then secrete chemotherapy-elicited exosomes enriched in miR-378a-3p and miR-378d. These exosomes are absorbed by chemotherapy-surviving BC cells, leading to activation of the WNT and NOTCH stem cell pathways via the targeting of DKK3 and NUMB and subsequently resulting in drug resistance. Therefore, blocking this adaptive mechanism during chemotherapy may reduce the development of chemotherapy resistance and maximize the therapeutic effect.
Falls in ED patients: do elderly patients on direct oral anticoagulants bleed less than those on vitamin K antagonists?
Authors: Müller Martin , Chanias Ioannis , Nagler Michael , Exadaktylos Aristomenis K. , Sauter Thomas C. 
Published: April 2021

Abstract
Background
Falls from standing are common in the elderly and are associated with a significant risk of bleeding. We have compared the proportional incidence of bleeding complications in patients on either direct oral anticoagulants (DOAC) or vitamin K antagonists (VKA).

Methods
Our retrospective cohort study compared elderly patients (≥65 years) on DOAC or VKA oral anticoagulation who presented at the study site – a Swiss university emergency department (ED) – between 01.06.2012 and 01.07.2017 after a fall. The outcomes were the proportional incidence of any bleeding complication and its components (e.g. intracranial haemorrhage), as well as procedural and clinical parameters (length of hospital stay, admission to intensive care unit, in-hospital-mortality). Uni- and multivariable analyses were used to compare the studied outcomes.

Results
In total, 1447 anticoagulated patients were included – on either VKA (n = 1021) or DOAC (n = 426). There were relatively more bleeding complications in the VKA group (n = 237, 23.2%) than in the DOAC group (n = 69, 16.2%, p = 0.003). The difference persisted in multivariable analysis with 0.7-fold (95% CI: 0.5–0.9, p = 0.014) lower odds for patients under DOAC than under VKA for presenting with any bleeding complications, and 0.6-fold (95% 0.4–0.9, p = 0.013) lower odds for presenting with intracranial haemorrhage. There were no significant differences in the other studied outcomes.

Conclusions
Among elderly, anticoagulated patients who had fallen from standing, those under DOACs had a lower proportional incidence of bleeding complications in general and an even lower incidence of intracranial haemorrhage than in patients under VKAs.
Simplitigs as an efficient and scalable representation of de Bruijn graphs
Authors: Břinda Karel , Baym Michael , Kucherov Gregory 
Published: April 2021

Abstractde Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and demonstrate that simplitigs provide a substantial improvement in the cumulative sequence length and their number. When combined with the commonly used Burrows-Wheeler Transform index, simplitigs reduce memory, and index loading and query times, as demonstrated with large-scale examples of GenBank bacterial pan-genomes.