bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma cell-free DNA (cfDNA) as a predictive and prognostic marker in patients with metastatic breast cancer
Authors: Fernandez-Garcia Daniel , Hills Allison , Page Karen , Hastings Robert K. , Toghill Bradley , Goddard Kate S. , Ion Charlotte , Ogle Olivia , Boydell Anna Rita , Gleason Kelly , Rutherford Mark , Lim Adrian , Guttery David S. , Coombes R. Charles , Shaw Jacqueline A. 
Published: December 2019

Abstract
Background
Breast cancer (BC) is the most common cancer in women, and despite the introduction of new screening programmes, therapies and monitoring technologies, there is still a need to develop more useful tests for monitoring treatment response and to inform clinical decision making.
The purpose of this study was to compare circulating cell-free DNA (cfDNA) and circulating tumour cells (CTCs) with conventional breast cancer blood biomarkers (CA15-3 and alkaline phosphatase (AP)) as predictors of response to treatment and prognosis in patients with metastatic breast cancer (MBC).

Methods
One hundred ninety-four female patients with radiologically confirmed MBC were recruited to the study. Total cfDNA levels were determined by qPCR and compared with CELLSEARCH® CTC counts and CA15-3 and alkaline phosphatase (AP) values. Blood biomarker data were compared with conventional tumour markers, treatment(s) and response as assessed by RECIST and survival.
Non-parametric statistical hypothesis tests were used to examine differences, correlation analysis and linear regression to determine correlation and to describe its effects, logistic regression and receiver operating characteristic curve (ROC curve) to estimate the strength of the relationship between biomarkers and clinical outcomes and value normalization against standard deviation to make biomarker values comparable. Kaplan–Meier estimator and Cox regression models were used to assess survival. Univariate and multivariate models were performed where appropriate.

Results
Multivariate analysis showed that both the amount of total cfDNA (p value = 0.024, HR = 1.199, CI = 1.024–1.405) and the number of CTCs (p value = 0.001, HR = 1.243, CI = 1.088–1.421) are predictors of overall survival (OS), whereas total cfDNA levels is the sole predictor for progression-free survival (PFS) (p value = 0.042, HR = 1.193, CI = 1.007–1.415) and disease response when comparing response to non-response to treatment (HR = 15.917, HR = 12.481 for univariate and multivariate analysis, respectively). Lastly, combined analysis of CTCs and cfDNA is more informative than the combination of two conventional biomarkers (CA15-3 and AP) for prediction of OS.

Conclusion
Measurement of total cfDNA levels, which is a simpler and less expensive biomarker than CTC counts, is associated with PFS, OS and response in MBC, suggesting potential clinical application of a cheap and simple blood-based test.
NEDD4 expression is associated with breast cancer progression and is predictive of a poor prognosis
Authors: Wan Lingfeng , Liu Tao , Hong Zhipeng , Pan You , Sizemore Steven T. , Zhang Junran , Ma Zhefu 
Published: December 2019

Abstract
Background
A role for neural precursor cell-expressed developmentally downregulated gene 4 (NEDD4) in tumorigenesis has been suggested. However, information is lacking on its role in breast tumor biology. The purpose of this study was to determine the role of NEDD4 in the promotion of the growth and progression of breast cancer (BC) and to evaluate the clinicopathologic and prognostic significance of NEDD4.

Methods
The impact of NEDD4 expression in BC cell growth was determined by Cell Counting Kit-8 and colony formation assays. Formalin-fixed paraffin-embedded specimens were collected from 133 adjacent normal tissues (ANTs), 445 BC cases composed of pre-invasive ductal carcinoma in situ (DCIS, n = 37), invasive ductal carcinomas (IDC, n = 408, 226 without and 182 with lymph node metastasis), and 116 invaded lymph nodes. The expression of NEDD4 was analyzed by immunohistochemistry. The association between NEDD4 expression and clinicopathological characteristics was analyzed by chi-square test. Survival was evaluated using the Kaplan–Meier method, and curves were compared using a log-rank test. Univariate and multivariate analyses were performed using the Cox regression method.

Results
NEDD4 promoted BC growth in vitro. In clinical retrospective studies, 16.5% of ANTs (22/133) demonstrated positive NEDD4 staining. Strikingly, the proportion of cases showing NEDD4-positive staining increased to 51.4% (19/37) in DCIS, 58.4% (132/226) in IDC without lymph node metastasis, and 73.1% (133/182) in BC with lymph node metastasis (BCLNM). In addition, NEDD4-positive staining was associated with clinical parameters, including tumor size (P = 0.030), nodal status (P = 0.001), estrogen receptor status (P = 0.035), and progesterone receptor status (P = 0.023). Moreover, subset analysis in BCLNM revealed that high NEDD4 expression correlated with an elevated risk of relapse (P = 0.0276). Further, NEDD4 expression was an independent prognostic predictor. Lastly, the rates for 10-year overall survival and disease-free survival were significantly lower in patients with positive NEDD4 staining than those in BC patients with negative NEDD4 staining BC (P = 0.0024 and P = 0.0011, respectively).

Conclusions
NEDD4 expression is elevated in BC and is associated with BC growth. NEDD4 correlated with clinicopathological parameters and predicts a poor prognosis. Thus, NEDD4 is a potential biomarker of poor prognosis and a potential therapeutic target for BC treatment.
The global forum on bioethics in research meeting, “ethics of alternative clinical trial designs and methods in low- and middle-income country research”: emerging themes and outputs
Authors: Hunt Adrienne , Saenz Carla , Littler Katherine 
Published: December 2019

AbstractAlternative clinical trial designs and methods are increasingly being used in place of the conventional individually randomised controlled trial (RCT) in high-income and in low-income and middle-income country (LMIC) research. These approaches - including adaptive, cluster-randomised and stepped-wedge designs and controlled human infection models - offer a number of potential advantages, including being more efficient and making the clinical trial process more socially acceptable. However, these designs and methods are generally not familiar to researchers, research ethics committees and regulators and their ethical implications have not received sufficient international attention from the bioethics, research, and policymaking communities working together. The ethics of alternative clinical trial designs and methods in LMIC research was chosen as a topic for the 2017 Global Forum on Bioethics in Research (GFBR). The meeting opened a global dialogue about this emerging issue in research ethics and gave voice to the LMIC perspective. It identified the need to take a multidisciplinary approach and to develop capacity amongst researchers and research ethics committees and regulators to propose, review and regulate these novel designs and methods. Building skills and infrastructure will empower researchers to choose from a broad range of designs and methods and adopt the most scientifically suitable, efficient, ethical and context-appropriate of these. The need for capacity development is most pressing from the LMIC perspective, where limited resources create an urgency to seek the most efficient trial design and method. The aim of this paper is to encourage broad debate about this complex area of research. By opening up this debate, GFBR aims to promote the appropriate and ethical use of novel designs and methods so their full potential to address the health needs in LMICs can be realised.
Ethics of alternative trial designs and methods in low-resource settings
Authors: van der Graaf Rieke , Cheah Phaik Yeong 
Published: December 2019

AbstractThis editorial introduces articles in this Special Issue, which are based on presentations given at the 2017 meeting of the Global Forum of Bioethics in Research meeting. The main themes presented at the meeting were the use of cluster randomized trials, stepped-wedge cluster randomized trials, and controlled human infection models in research conducted in low-resource settings. The editorial sets out which ethical issues may arise in the context of alternative trial designs and describes the articles in this issue that addresses some or more of the ethical issues, such as justification of the research design, risk-benefit evaluations and consent.
When could human challenge trials be deployed to combat emerging infectious diseases? Lessons from the case of a Zika virus human challenge trial
Authors: Palacios Ricardo , Shah Seema K. 
Published: December 2019

AbstractHuman challenge trials (HCTs) deliberately infect participants in order to test vaccines and treatments in a controlled setting, rather than enrolling individuals with natural exposure to a disease. HCTs are therefore potentially powerful tools to prepare for future outbreaks of emerging infectious diseases. Yet when an infectious disease is emerging, there is often substantial risk and uncertainty about its complications, and few available interventions, making an HCT ethically complex. In light of the need to consider ethical issues proactively as a part of epidemic preparedness, we use the case of a Zika virus HCT to explore whether and when HCTs might be ethically justified to combat emerging infectious diseases. We conclude that emerging infectious diseases could be appropriate candidates for HCTs and we identify relevant considerations and provide a case example to illustrate when they might be ethically acceptable.
Evaluation of antibody responses to the early transcribed membrane protein family in Plasmodium vivax
Authors: Lee Seong-Kyun , Han Jin-Hee , Park Ji-Hoon , Ha Kwon-Soo , Park Won Sun , Hong Seok-Ho , Na Sunghun , Cheng Yang , Han Eun-Taek 
Published: December 2019

Abstract
Background
Malaria parasites form intracellular membranes that separate the parasite from the internal space of erythrocytes, and membrane proteins from the parasites are exported to the host via the membrane. In our previous study, Plasmodium vivax early transcribed membrane protein (PvETRAMP) 11.2, an intracellular membrane protein that is highly expressed in blood-stage parasites, was characterized as a highly immunogenic protein in P. vivax malaria patients. However, the other PvETRAMP family proteins have not yet been investigated. In this study, PvETRAMPs were expressed and evaluated to determine their immunological profiles.

Methods
The protein structure and amino acid alignment were carried out using bioinformatics analysis software. A total of six PvETRAMP family proteins were successfully expressed and purified using a wheat germ cell free protein expression system and the purified proteins were used for protein microarray and immunization of mice. The localization of the protein was determined with serum against PvETRAMP4. IgG subclasses were assessed from the immunized mice.

Results
In silico analysis showed that P. vivax exhibits nine genes encoding the ETRAMP family. The ETRAMP family proteins are relatively small molecules with conserved structural features. A total of 6 recombinant ETRAMP proteins were successfully expressed and purified. The serum positivity of P. vivax malaria patients and healthy individuals was evaluated using a protein microarray method. Among the PvETRAMPs, ETRAMP4 showed the highest positivity rate of 62%, comparable to that of PvETRAMP11.2, which served as the positive control, and a typical export pattern of PvETRAMP4 was observed in the P. vivax parasite. The assessment of IgG subclasses in mice immunized with PvETRAMP4 showed high levels of IgG1 and IgG2b. PvETRAMP family proteins were identified and characterized as serological markers.

Conclusions
The relatively high antibody responses to PvETRAMP4 as well as the specific IgG subclasses observed in immunized mice suggest that the ETRAMP family is immunogenic in pathogens and can be used as a protein marker and for vaccine development.
Show us your ticks: a survey of ticks infesting dogs and cats across the USA
Authors: Saleh Meriam N. , Sundstrom Kellee D. , Duncan Kathryn T. , Ientile Michelle M. , Jordy Julia , Ghosh Parna , Little Susan E. 
Published: December 2019

AbstractBackgroundA variety of tick species infest dogs and cats in North America. Although most of these species also readily feed on people, national data regarding the species and abundance of ticks on dogs and cats are lacking. Here we report a large-scale study of ticks from dogs and cats in the USA over a 12-month period.MethodsTick submissions were invited from veterinary practices in all 50 states. Ticks were submitted with information about the pet and the attachment sites of each tick marked on a biopsy chart. Upon receipt, ticks were identified to species and stage using morphologic keys; when necessary, species identification was confirmed molecularly.ResultsFrom February 2018 through January 2019, 10,978 ticks were submitted from 1494 dogs and 336 cats in 49 states and ticks were collected in every month. Dog and cat infestation intensities ranged from 1 to 4765 and from 1 to 38 (median = 1, mean = 6.7 and 2.6), respectively. Dogs were primarily infested withDermacentor variabilis(532/1494; 35.6%),Ixodes scapularis(409/1494; 27.4%),Amblyomma americanum(345/1494; 23.1%) andRhipicephalus sanguineus(172/1494; 11.5%). Cats were primarily infested withI. scapularis(156/336; 46.4%),A. americanum(99/336; 29.5%) andD. variabilis(60/336; 17.9%). Other submitted ticks includedA. maculatum,Haemaphysalis longicornis,Otobius megnini, and less commonDermacentorspp. andIxodesspp. Co-infestations were documented in 93 dogs and 14 cats. Reported attachment sites of common tick species differed. In dogs,A. americanumwas most commonly attached to the abdomen, axillary, and inguinal regions;D. variabilisandI. scapularisto the head, neck, and back; andR. sanguineusto the head, neck, abdomen, legs, and feet. In cats,I. scapulariswas most commonly attached to the head andA. americanumwas most commonly attached to the tail and perianal region.ConclusionsThese data confirm that dogs and cats in the USA are at risk of tick infestation throughout the year and that tick species present in the region have apparent attachment site preferences.
High-throughput sequencing of CD4+ T cell repertoire reveals disease-specific signatures in IgG4-related disease
Authors: Wang Liwen , Zhang Panpan , Li Jieqiong , Lu Hui , Peng Linyi , Ling Jing , Zhang Xuan , Zeng Xiaofeng , Zhao Yan , Zhang Wen 
Published: December 2019

AbstractBackgroundCD4+T cells play critical roles in the pathogenesis of IgG4-related disease (IgG4-RD). The aim of this study was to investigate the TCR repertoire of peripheral blood CD4+T cells in IgG4-RD.MethodsThe peripheral blood was collected from six healthy controls and eight IgG4-RD patients. TCR β-chain libraries of CD4+T cells were constructed by 5′-rapid amplification of cDNA ends (5′-RACE) and sequenced by Illumina Miseq platform. The relative similarity of TCR repertoires between samples was evaluated according to the total frequencies of shared clonotypes (metric F), correlation of frequencies of shared clonotypes (metric R), and total number of shared clonotypes (metric D).ResultsThe clonal expansion and diversity of CD4+T cell repertoire were comparable between healthy controls and IgG4-RD patients, while the proportion of expanded and coding degenerated clones, as an indicator of antigen-driven clonal expansion, was significantly higher in IgG4-RD patients. There was no significant difference in TRBV and TRBJ gene usage between healthy controls and IgG4-RD patients. The complementarity determining region 3 (CDR3) length distribution was skewed towards longer fragments in IgG4-RD. Visualization of relative similarity of TCR repertoires by multi-dimensional scaling analysis showed that TCR repertoires of IgG4-RD patients were separated from that of healthy controls in F and D metrics. We identified 11 IgG4-RD-specific CDR3 amino acid sequences that were expanded in at least 2 IgG4-RD patients, while not detected in healthy controls. According to TCR clonotype networks constructed by connecting all the CDR3 sequences with a Levenshtein distance of 1, 3 IgG4-RD-specific clusters were identified. We annotated the TCR sequences with known antigen specificity according to McPAS-TCR database and found that the frequencies of TCR sequences associated with each disease or immune function were comparable between healthy controls and IgG4-RD patients.ConclusionAccording to our study of CD4+T cells from eight IgG4-RD patients, TCR repertoires of IgG4-RD patients were different from that of healthy controls in the proportion of expanded and coding degenerated clones and CDR3 length distribution. In addition, IgG4-RD-specific TCR sequences and clusters were identified in our study.
The effect of comorbidities for the prognosis of community-acquired pneumonia: an epidemiologic study using a hospital surveillance in Japan
Authors: Nguyen Mai Thi Ngoc , Saito Nobuyuki , Wagatsuma Yukiko 
Published: December 2019

Abstract
Objective
Pneumonia is a common but serious illness that continues to present significant morbidity and mortality. Although the effect of severity at admission on outcome has been well reported, the role of comorbidity is still not widely understood. The Charlson Comorbidity Index measures comorbidity with a well-established history of predicting long-term outcome but its utility in pneumonia prognosis is still limited. Here, we use the Charlson Comorbidity Index and hospital surveillance data to investigate associations between comorbidities and in-hospital mortality due to community-acquired pneumonia.

Results
Among the 535 eligible adult patients (69.0% male, median [IQR] age, 79 [70–84] years), 100 (18.7%) acquired severe to extremely severe pneumonia. The median [IQR] CCI was 1 [1–3]. Malignancy (129 of 535, 24.1%), chronic pulmonary diseases (113 of 535, 21.1%) and congestive heart failure (103 of 535, 19.3%) were frequent. Higher Charlson Comorbidity Index scores were associated with higher risk of in-hospital mortality (OR 1.28; 95% CI 1.07–1.53). These results support the inclusion of comorbid burden in predicting community-acquired pneumonia outcome.
Cross-sectional imaging of acute gynaecologic disorders: CT and MRI findings with differential diagnosis—part I: corpus luteum and haemorrhagic ovarian cysts, genital causes of haemoperitoneum and adnexal torsion
Authors: Tonolini Massimo , Foti Pietro Valerio , Costanzo Valeria , Mammino Luca , Palmucci Stefano , Cianci Antonio , Ettorre Giovanni Carlo , Basile Antonio 
Published: December 2019

AbstractAcute gynaecologic disorders are commonly encountered in daily clinical practice of emergency departments (ED) and predominantly occur in reproductive-age women. Since clinical presentation may be nonspecific and physical findings are often inconclusive, imaging is required for a timely and accurate diagnosis. Although ultrasound is the ideal non-invasive first-line technique, nowadays multidetector computed tomography (CT) is extensively used in the ED, particularly when a non-gynaecologic disorder is suspected and differential diagnosis from gastrointestinal and urologic diseases is needed. As a result, CT often provides the first diagnosis of female genital emergencies. If clinical conditions and scanner availability permit, magnetic resonance imaging (MRI) is superior to CT for further characterisation of gynaecologic abnormalities, due to the excellent soft-tissue contrast, intrinsic multiplanar capabilities and lack of ionising radiation.The purpose of this pictorial review is to provide radiologists with a thorough familiarity with gynaecologic emergencies by illustrating their cross-sectional imaging appearances. The present first section will review the CT and MRI findings of corpus luteum and haemorrhagic ovarian cysts, gynaecologic haemoperitoneum (from either ruptured corpus luteum or ectopic pregnancy) and adnexal torsion, with an emphasis on differential diagnosis. Additionally, comprehensive and time-efficient MRI acquisition protocols are provided.
Pre-aggregation of scalp progenitor dermal and epidermal stem cells activates the WNT pathway and promotes hair follicle formation in in vitro and in vivo systems
Authors: Su Yiqun , Wen Jie , Zhu Junrong , Xie Zhiwei , Liu Chang , Ma Chuan , Zhang Qun , Xu Xin , Wu Xunwei 
Published: December 2019

Abstract
Background
Billions of dollars are invested annually by pharmaceutical companies in search of new options for treating hair loss conditions; nevertheless, the challenge remains. One major limitation to hair follicle research is the lack of effective and efficient drug screening systems using human cells. Organoids, three-dimensional in vitro structures derived from stem cells, provide new opportunities for studying organ development, tissue regeneration, and disease pathogenesis. The present study focuses on the formation of human hair follicle organoids.

Methods
Scalp-derived dermal progenitor cells mixed with foreskin-derived epidermal stem cells at a 2:1 ratio aggregated in suspension to form hair follicle-like organoids, which were confirmed by immunostaining of hair follicle markers and by molecular dye labeling assays to analyze dermal and epidermal cell organization in those organoids. The hair-forming potential of organoids was examined using an in vivo transplantation assay.

Results
Pre-aggregation of dermal and epidermal cells enhanced hair follicle formation in vivo. In vitro pre-aggregation initiated the interactions of epidermal and dermal progenitor cells resulting in activation of the WNT pathway and the formation of pear-shape structures, named type I aggregates. Cell-tracing analysis showed that the dermal and epidermal cells self-assembled into distinct epidermal and dermal compartments. Histologically, the type I aggregates expressed early hair follicle markers, suggesting the hair peg-like phase of hair follicle morphogenesis. The addition of recombinant WNT3a protein to the medium enhanced the formation of these aggregates, and the Wnt effect could be blocked by the WNT inhibitor, IWP2.

Conclusions
In summary, our system supports the rapid formation of a large number of hair follicle organoids (type I aggregates). This system provides a platform for studying epithelial-mesenchymal interactions, for assessing inductive hair stem cells and for screening compounds that support hair follicle regeneration.
Drosophila Prominin-like, a homolog of CD133, interacts with ND20 to maintain mitochondrial function
Authors: Wang Xuexiang , Zheng Huimei , Jia Zexiao , Lei Zhaoying , Li Mengyao , Zhuang Qianqian , Zhou Hui , Qiu Yue , Fu Yong , Yang Xiaohang , Xi Yongmei , Yan Qingfeng 
Published: December 2019

Abstract
Background
Drosophila Prominin-like is a homolog of mammalian CD133, which is recognized as a biomarker for stem cells. The interacting proteins of CD133 and their biological functions remain elusive.

Results
In this study, we using yeast two-hybrid assays, GST pull-down assay and co-immunoprecipitation (Co-IP) methods found that Drosophila Prominin-like interacts with ND20, a subunit of mitochondrial respiratory complex I. Bioinformatics analysis suggests that Prominin-like is a six-transmembrane glycoprotein which localizes on cellular membranes. Immunostaining and mitochondrial fractionation indicate that Drosophila Prominin-like could localize in the mitochondria. The knockdown of prominin-like in S2 cells resulted in transient mitochondrial dysfunctions as evidenced by reduced ATP production, elevated ROS generation and an accompanied reduction in mitochondrial proteins. Mitochondrial dysfunctions were detected in aged prominin-like mutant flies.

Conclusion
Our data indicates that Prominin-like acts to maintain mitochondrial function through its interaction with ND20 which, itself, is active in the mitochondrial electron transport chain. Our study provides insights into a novel molecular mechanism of Drosophila prominin-like and suggests a similar function of CD133 in mammals.