bluuebunny/crossref_metadata_2025_split huggingface dataset:
METROID: an automated method for robust quantification of subcellular fluorescence events at low SNR
Authors: Zoccoler Marcelo , de Oliveira Pedro X. 
Published: July 2020

Abstract
Background
In cell biology, increasing focus has been directed to fast events at subcellular space with the advent of fluorescent probes. As an example, voltage sensitive dyes (VSD) have been used to measure membrane potentials. Yet, even the most recently developed genetically encoded voltage sensors have demanded exhausting signal averaging through repeated experiments to quantify action potentials (AP). This analysis may be further hampered in subcellular signals defined by small regions of interest (ROI), where signal-to-noise ratio (SNR) may fall substantially. Signal processing techniques like blind source separation (BSS) are designed to separate a multichannel mixture of signals into uncorrelated or independent sources, whose potential to separate ROI signal from noise has been poorly explored. Our aims are to develop a method capable of retrieving subcellular events with minimal a priori information from noisy cell fluorescence images and to provide it as a computational tool to be readily employed by the scientific community.

Results
In this paper, we have developed METROID (Morphological Extraction of Transmembrane potential from Regions Of Interest Device), a new computational tool to filter fluorescence signals from multiple ROIs, whose code and graphical interface are freely available. In this tool, we developed a new ROI definition procedure to automatically generate similar-area ROIs that follow cell shape. In addition, simulations and real data analysis were performed to recover AP and electroporation signals contaminated by noise by means of four types of BSS: Principal Component Analysis (PCA), Independent Component Analysis (ICA), and two versions with discrete wavelet transform (DWT). All these strategies allowed for signal extraction at low SNR (− 10 dB) without apparent signal distortion.

Conclusions
We demonstrate the great capability of our method to filter subcellular signals from noisy fluorescence images in a single trial, avoiding repeated experiments. We provide this novel biomedical application with a graphical user interface at 10.6084/m9.figshare.11344046.v1, and its code and datasets are available in GitHub at https://github.com/zoccoler/metroid.
Do-not-resuscitate orders in patients with community-acquired pneumonia: a retrospective study
Authors: Egelund Gertrud Baunbæk , Jensen Andreas Vestergaard , Petersen Pelle Trier , Andersen Stine Bang , Lindhardt Bjarne Ørskov , Rohde Gernot , Ravn Pernille , von Plessen Christian 
Published: July 2020

Abstract
Background
To investigate the use of do-not-resuscitate (DNR) orders in patients hospitalized with community-acquired pneumonia (CAP) and the association with mortality.

Methods
We assembled a cohort of 1317 adults hospitalized with radiographically confirmed CAP in three Danish hospitals. Patients were grouped into no DNR order, early DNR order (≤48 h after admission), and late DNR order (> 48 h after admission). We tested for associations between a DNR order and mortality using a cox proportional hazard model adjusted for patient and disease related factors.

Results
Among 1317 patients 177 (13%) patients received a DNR order: 107 (8%) early and 70 (5%) late, during admission. Patients with a DNR order were older (82 years vs. 70 years, p < 0.001), more frequently nursing home residents (41% vs. 6%, p < 0.001) and had more comorbidities (one or more comorbidities: 73% vs. 59%, p < 0.001). The 30-day mortality was 62% and 4% in patients with and without a DNR order, respectively. DNR orders were associated with increased risk of 30-day mortality after adjustment for age, nursing home residency and comorbidities. The association was modified by the CURB-65 score Hazard ratio (HR) 39.3 (95% CI 13.9–110.6), HR 24.0 (95% CI 11.9–48,3) and HR 9.4 (95% CI: 4.7–18.6) for CURB-65 score 0–1, 2 and 3–5, respectively.

Conclusion
In this representative Danish cohort, 13% of patients hospitalized with CAP received a DNR order. DNR orders were associated with higher mortality after adjustment for clinical risk factors. Thus, we encourage researcher to take DNR orders into account as potential confounder when reporting CAP associated mortality.
Effects of delayed hip replacement on postoperative hip function and quality of life in elderly patients with femoral neck fracture
Authors: Song Jidong , Zhang Gensheng , Liang Jialin , Bai Chuanyi , Dang Xiaoqian , Wang Kunzheng , He Caiyou , Liu Ruiyu 
Published: July 2020

Abstract
Background
For various reasons, some elderly patients with femoral neck fracture undergo delayed surgical treatment. There is little information about the effect of delayed treatment on postoperative hip function and quality of life. The aim of this study was to investigate the effect of delayed hip arthroplasty on hip function, quality of life, and satisfaction in patients with femoral neck fractures.

Methods
Forty-seven patients with femoral neck fracture and hip replacement delayed over 21 days served as the delayed group (D group). Patients with femoral neck fracture, matched 1:1 for age and sex, and hip replacement within 7 days served as the control group (C group). The Harris hip score (HHS) and health-related quality of life (HRQoL) were assessed before surgery and 3 months, 6 months and 1 year postoperatively. The satisfaction questionnaires were completed by the patients themselves at the last follow-up.

Results
The HHS in the C group was lower than that in the D group (32.64 ± 9.11 vs. 46.32 ± 9.88, P < 0.05) before surgery but recovered faster after surgery. The HHS in the D group was lower than that in the C group 1 year postoperatively (85.2 ± 3.80 vs. 89.8 ± 3.33, P < 0.05). The patients’ quality of life changed similarly to their HHS. The HHS 1 year after surgery was related to the preoperative HHS in group D (rs = 0.521, P < 0.01). Patients in the D group showed significantly higher satisfaction scores than those in the C group (P < 0.05).

Conclusions
Hip function in patients with femoral neck fracture surgery delayed over 21 days recovered more slowly than that in those who underwent surgery within 7 days. However, they were more satisfied with the surgery. Moderate hip movement to ameliorate the lower limb muscle atrophy was recommended for patients facing a temporary inability to undergo surgery.
Reclassification of tumor size for solitary HBV-related hepatocellular carcinoma by minimum p value method: a large retrospective study
Authors: Liu Hongzhi , Yang Yuan , Chen Chuanchun , Wang Lei , Huang Qizhen , Zeng Jianxing , Lin Kongying , Zeng Yongyi , Guo Pengfei , Zhou Weiping , Liu Jingfeng 
Published: July 2020

Abstract
Background and objectives
Tumor size is one of the most important issues for hepatocellular carcinoma (HCC) treatment and prognosis, but the classification of it is still controversial. The aim of this study was to screen appropriate cutoffs for size of solitary hepatitis B virus (HBV)-related HCC.

Methods
A cohort of 1760 patients with solitary HBV-related HCC undergoing curative liver resection was divided into 11 groups based on tumor size in 1-cm interval. The minimum p value method was used to screen the appropriate size cutoff according to overall survival (OS). If multiple cutoffs meet the above standard, a univariate analysis will be performed by using the Cox proportional hazards regression model, and hazard ratio (HR) will be considered as a criterion to assess the difference in survival.

Results
There are 8 dichotomy, 8 trichotomy, and no inquartation cutoffs that were screened when classifying tumor sizes in accordance with OS. The HR values of tumor size at these trichotomy cutoffs for OS were compared, and the highest HR value is 2.79 when size cutoff is 3/9 cm. Then, we reclassified patients into three new classifications: ≤ 3 cm (n = 422), > 3 and ≤ 9 cm (n = 1072), and > 9 cm (n = 266). The comparison of clinicopathologic characteristics among these three classifications showed that the increase of tumor size was associated with the increase of α-fetoprotein (AFP), microvascular invasion (MVI), tumor differentiation, and liver cirrhosis. And the comparison of the OS among three classifications showed statistical differences.

Conclusions
This study suggested that size criteria of 3 cm and 9 cm in solitary HBV-related HCC patients were appropriate based on biological characteristics and prognostic significance.
Understanding transmission and control of the pork tapeworm with CystiAgent: a spatially explicit agent-based model
Authors: Pray Ian W. , Wakeland Wayne , Pan William , Lambert William E. , Garcia Hector H. , Gonzalez Armando E. , O’Neal Seth E. ,   for the Cysticercosis Working Group in Peru
Published: July 2020

Abstract
Background
The pork tapeworm, Taenia solium, is a serious public health problem in rural low-resource areas of Latin America, Africa and Asia, where the associated conditions of nuerocysticercosis (NCC) and porcine cysticercosis cause substantial health and economic harms. An accurate and validated transmission model for T. solium would serve as an important new tool for control and elimination, as it would allow for comparison of available intervention strategies, and prioritization of the most effective strategies for control and elimination efforts.

Methods
We developed a spatially-explicit agent-based model (ABM) for T. solium (“CystiAgent”) that differs from prior T. solium models by including a spatial framework and behavioral parameters such as pig roaming, open human defecation, and human travel. In this article, we introduce the structure and function of the model, describe the data sources used to parameterize the model, and apply sensitivity analyses (Latin hypercube sampling-partial rank correlation coefficient (LHS-PRCC)) to evaluate model parameters.

Results
LHS-PRCC analysis of CystiAgent found that the parameters with the greatest impact on model uncertainty were the roaming range of pigs, the infectious duration of human taeniasis, use of latrines, and the set of “tuning” parameters defining the probabilities of infection in humans and pigs given exposure to T. solium.

Conclusions
CystiAgent is a novel ABM that has the ability to model spatial and behavioral features of T. solium transmission not available in other models. There is a small set of impactful model parameters that contribute uncertainty to the model and may impact the accuracy of model projections. Field and laboratory studies to better understand these key components of transmission may help reduce uncertainty, while current applications of CystiAgent may consider calibration of these parameters to improve model performance. These results will ultimately allow for improved interpretation of model validation results, and usage of the model to compare available control and elimination strategies for T. solium.
Loss of Tdp-43 disrupts the axonal transcriptome of motoneurons accompanied by impaired axonal translation and mitochondria function
Authors: Briese Michael , Saal-Bauernschubert Lena , Lüningschrör Patrick , Moradi Mehri , Dombert Benjamin , Surrey Verena , Appenzeller Silke , Deng Chunchu , Jablonka Sibylle , Sendtner Michael 
Published: July 2020

AbstractProtein inclusions containing the RNA-binding protein TDP-43 are a pathological hallmark of amyotrophic lateral sclerosis and other neurodegenerative disorders. The loss of TDP-43 function that is associated with these inclusions affects post-transcriptional processing of RNAs in multiple ways including pre-mRNA splicing, nucleocytoplasmic transport, modulation of mRNA stability and translation. In contrast, less is known about the role of TDP-43 in axonal RNA metabolism in motoneurons. Here we show that depletion of Tdp-43 in primary motoneurons affects axon growth. This defect is accompanied by subcellular transcriptome alterations in the axonal and somatodendritic compartment. The axonal localization of transcripts encoding components of the cytoskeleton, the translational machinery and transcripts involved in mitochondrial energy metabolism were particularly affected by loss of Tdp-43. Accordingly, we observed reduced protein synthesis and disturbed mitochondrial functions in axons of Tdp-43-depleted motoneurons. Treatment with nicotinamide rescued the axon growth defect associated with loss of Tdp-43. These results show that Tdp-43 depletion in motoneurons affects several pathways integral to axon health indicating that loss of TDP-43 function could thus make a major contribution to axonal pathomechanisms in ALS.
Revealing unique inscriptions of a Nazi collaborator in Doodencel 601 of the Oranjehotel
Authors: Wempe Joost , van den Brink Rick , Mooldijk Esmée , Feirabend Nienke , Wiersma Ruben , Sietsma Jilt , Dik Joris 
Published: July 2020

Abstract
During the Second World War the German occupants of the Netherlands made ample use of the Scheveningen prison near The Hague, popularly nicknamed the Oranjehotel. One former death cell in this infamous prison (Doodencel 601) has been preserved in its original condition, showing wartime inscriptions on the cell walls. Interestingly, a small section of the wall has been given an additional plaster layer, presumably covering inscriptions. Here, we report on the visualization of this enigmatic text, which so far had escaped the reach of historians. Our visualization methodology was threefold. First, we determined the cell-wall stratigraphy and its composition based on a sample cross-section. Second, we prepared a physical model wall, mimicking the layering of the original cell wall. Third, we tested a combination of raking light photography and infrared thermography on the model wall. Applying this methodology on the original wall revealed the inscriptions, including the author’s name Daniël de Blocq van Scheltinga, a prominent Nazi collaborator, as well as a calendar and an important date of his post-war trial in the fall of 1945. Our visualizations flawlessly dovetail with archival findings. Together, they offer an intimate view of an early post-war inmate of the Scheveningen prison, whose message was covered up once the cell was transformed into a war monument in 1946.
How social capital can inform targeting formal social safety net interventions in vulnerable communities in eastern Ethiopia: an ethnographic case study
Authors: Endris Getachew Shambel , Kibwika Paul , Obaa Bernard B. , Hassan Jemal Yousuf 
Published: July 2020

AbstractSafety nets in Ethiopia are targeted and delivered in a context in which informal social capital practices also operate. But the role of social relations is largely overlooked in welfare programming. Understanding how social capital is mobilized and under which condition it enhances or constrains social safety net targeting may inform policy to design sustainable and inclusive welfare programs to improve household resilience. Using an ethnographic case study design, we studied the role of social capital in the implementation of a welfare intervention. Data were collected through observations and interviews with 30 households. Besides, data on household social network characteristics were collected using semi-structured interviews. The result suggested that greater access to social capital by a household enhances the efficiency of safety net targeting and delivery. Positioning the social transfer instruments within the broader sets of community social arrangements can optimize the allocation of scarce safety net resources and improves community relationships.
The use of 3D additive manufacturing technology in autogenous dental transplantation
Authors: Cahuana-Bartra Pau , Cahuana-Cárdenas Abel , Brunet-Llobet Lluís , Ayats-Soler Marta , Miranda-Rius Jaume , Rivera-Baró Alejandro 
Published: July 2020

Abstract
Background
In medicine and dentistry, 3D technology allows the virtual planning and printing of surgical replicas of anatomical structures that can facilitate certain transplant procedures. In dentistry, 3D technology is useful in autogenous tooth transplantation.

Case presentation
We present a clinical case of an ectopic mandibular second premolar, describing the preoperative planning with dental replicas and the autotransplantation surgery. 3D prints of the surgical replica of the tooth to be transplanted was made using an Objet30 Prime® Printer, PolyJet. Clinical controls performed at 3, 6 and 12 months indicated the satisfactory evolution of the transplanted tooth.

Conclusion
3D additive manufacturing technology allows the preparation of a new recipient socket with the aid of a surgical replica of the tooth to be transplanted, thus minimizing handling and extraoral time.
Quantification and correction of distortion in diffusion-weighted MRI at 1.5 and 3 T in a muscle-invasive bladder cancer phantom for radiotherapy planning
Authors: Rogers Jane , Sherwood Victoria , Wayte Sarah C. , Duffy Jonathan A. , Manolopoulos Spyros 
Published: July 2020

Objective:
Limited visibility of post-resection muscle-invasive bladder cancer (MIBC) on CT hinders radiotherapy dose escalation of the residual tumour. Diffusion-weighted MRI (DW-MRI) visualises areas of high tumour burden and is increasingly used within diagnosis and as a biomarker for cancer. DW-MRI could, therefore, facilitate dose escalation, potentially via dose-painting and/or accommodating response. However, the distortion inherent in DW-MRI could limit geometric accuracy. Therefore, this study aims to quantify DW-MRI distortion via imaging of a bladder phantom.

Methods:
A phantom was designed to mimic MIBC and imaged using CT, DW-MRI and T2W-MRI. Fiducial marker locations were compared across modalities and publicly available software was assessed for correction of magnetic susceptibility-related distortion.

Results:
Fiducial marker locations on CT and T2W-MRI agreed within 1.2 mm at 3 T and 1.8 mm at 1.5 T. The greatest discrepancy between CT and apparent diffusion coefficient (ADC) maps was 6.3 mm at 3 T, reducing to 1.8 mm when corrected for distortion. At 1.5 T, these values were 3.9 mm and 1.7 mm, respectively.

Conclusions:
Geometric distortion in DW-MRI of a model bladder was initially &gt;6 mm at 3 T and &gt;3 mm at 1.5 T; however, established correction methods reduced this to &lt;2 mm in both cases.

Advances in knowledge:
A phantom designed to mimic MIBC has been produced and used to show distortion in DW-MRI can be sufficiently mitigated for incorporation into the radiotherapy pathway. Further investigation is therefore warranted to enable individually adaptive image-guided radiotherapy of MIBC based upon DW-MRI.
Multiparametric MRI with diffusion-weighted imaging in predicting response to chemotherapy in cases of osteosarcoma and Ewing’s sarcoma
Authors: Saleh Mahmoud Mohamed , Abdelrahman Tamer Moustafa , Madney Youusef , Mohamed Ghada , Shokry Ahmed Mohammed , Moustafa Amr Farouk 
Published: July 2020

Objective: To evaluate the multiparametric MRI in predicting chemotherapy response in pathologically proven cases of osteosarcoma and Ewing’s sarcoma. Correlation between the tumor size changes and internal breakdown using RECIST 1.1, modified RECIST, quantitative apparent diffusion coefficient (ADC) and tumor volume as well as dynamic contrast-enhanced MRI (DCE-MRI). Methods: The study included 104 patients pathologically proved osteosarcoma (53) and Ewing`s sarcoma (51) underwent MRI examinations; before and after chemotherapy. All patients were assessed using the RECIST 1.1 criteria, m-RECIST, quantitative ADC, and tumor volume evaluation. 21 patients underwent DCE-MRI curve type with quantitative parameters. Correlation between the different evaluations was carried out. Results were correlated with the post-operative pathology in 42 patients who underwent surgery and for statistical evaluation, Those patients were classified into responders (≥90% necrosis) and non-responders (<90% necrosis). Results: The initial mean ADC of 104 patients of osteosarcoma and Ewing’s sarcoma (0.90 ± 0.29) and (0.71 ± 0.16) respectively, differed significantly from that after treatment (1.62 ± 0.46) and (1.6 ± 0.39) respectively with (p<0.001). ADC variations (ADC%) in the non-progressive group were higher than those of the progressive group (128.3 ± 63.49 vs 36.34 ± 78.7) % with (p<0.001). ADC values and ADC variations were inversely correlated with morphologic changes, regardless of the effectiveness of chemotherapy expressed as changes in tumor size based on (RECIST 1.1, RECIST, and 3D volume). Linear regression analysis revealed a Pearson correlation coefficient of r=-0.427, -0.498 and -0.408, respectively with (p<0.001). An increase in the ADC value was not always associated with a reduction in tumor volume. The disease control rate (defined as the percentage of CR+PR+SD patients) was 89.4% and 93.9% according to RECIST 1.1 and m-RECIST respectively. 42 out of the 104 patients had postsurgical histological evaluation as regards the chemotherapeutic response divided into two groups. ADC values showed a statistically significant difference between Group A and Group B being more evident with minimum ADC% (p<0.001). Conclusion: Quantitative diffusion-weighted imaging with ADC mapping and ADC % after chemotherapy allows a detailed analysis of the treatment response in osteosarcoma and Ewing’s sarcoma. The therapeutic response can be underestimated using RECIST 1.1, so the modified RECIST should be also considered. Advances in knowledge: Quantitative ADC especially ADC% provided an accurate non-invasive tool in the assessment of post-therapeutic cases of osteosarcoma and Ewing's sarcoma