bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using ROPScore and CHOP ROP for early prediction of retinopathy of prematurity in a Chinese population
Authors: Sun Huiqing , Dong Yubin , Liu Yanxia , Chen Qingqin , Wang Yanxi , Cheng Bin , Qin Shaobo , Meng Liping , Li Shanxiu , Zhang Yanlun , Zhang Aiguo , Yan Weiling , Dong Yuhong , Cheng Shuyi , Li Mingchao , Yu Zengyuan 
Published: February 2021

Abstract
Purpose
Retinopathy of prematurity (ROP) is a disease that causes vision loss, vision impairment, and blindness, most frequently manifesting among preterm infants. ROPScore and CHOP ROP (Children’s Hospital of Philadelphia ROP) are similar scoring models to predict ROP using risk factors such as postnatal weight gain, birth weight (BW), and gestation age (GA). The purpose of this study was to compare the accuracy and difference between using ROPScore and CHOP ROP for the early prediction of ROP.

Methods
A retrospective study was conducted from January 2009 to December 2019 in China. Patients eligible for enrollment included infants admitted to NICU at ≤32 weeks GA or those with ≤1500 g BW. The sensitivity and specificity of ROPScore and CHOP ROP were analyzed, as well as its suitability as an independent predictor of ROP.

Results
Severe ROP was found in 5.0% of preterm infants. The sensitivity and specificity of the ROPScore test at any stage of ROP was 55.8 and 77.8%, respectively. For severe ROP, the sensitivity and specificity was 50 and 87.0%, respectively. The area under the receiver operating characteristic curve for the ROPScore for predicting severe ROP was 0.76. This value was significantly higher than the values for birth weight (0.60), gestational age (0.73), and duration of ventilation (0.63), when each was category measured separately. For the CHOP ROP, it correctly predicted infants who developed type 1 ROP (sensitivity, 100%, specificity, 21.4%).

Conclusions
The CHOP ROP model predicted infants who developed type 1 ROP at a sensitivity of 100% whereas ROPScore had a sensitivity of 55.8%. Therefore, the CHOP ROP model is more suitable for Chinese populations than the ROPScore test.

Clinical registration number and STROBE guidelines
This article was a retrospective cohort study and reported the results of the ROPScore and CHOP ROP algorithms. No results pertaining to interventions on human participants were reported. Thus, registration was not required and this study followed STROBE guidelines.
Markers of endothelial and epithelial pulmonary injury in mechanically ventilated COVID-19 ICU patients
Authors: Spadaro Savino , Fogagnolo Alberto , Campo Gianluca , Zucchetti Ottavio , Verri Marco , Ottaviani Irene , Tunstall Tanushree , Grasso Salvatore , Scaramuzzo Valentina , Murgolo Francesco , Marangoni Elisabetta , Vieceli Dalla Sega Francesco , Fortini Francesca , Pavasini Rita , Rizzo Paola , Ferrari Roberto , Papi Alberto , Volta Carlo Alberto , Contoli Marco 
Published: February 2021

AbstractBackgroundBiomarkers can be used to detect the presence of endothelial and/or alveolar epithelial injuries in case of ARDS. Angiopoietin-2 (Ang-2), soluble intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion protein-1 (VCAM-1), P-selectin and E-selectin are biomarkers of endothelial injury, whereas the receptor for advanced glycation end-products (RAGE) reflects alveolar epithelial injury. The aims of this study were to evaluate whether the plasma concentration of the above-mentioned biomarkers was different 1) in survivors and non-survivors of COVID-19-related ARDS and 2) in COVID-19-related and classical ARDS.MethodsThis prospective study was performed in two COVID-19-dedicated Intensive Care Units (ICU) and one non-COVID-19 ICU at Ferrara University Hospital. A cohort of 31 mechanically ventilated patients with COVID-19 ARDS and a cohort of 11 patients with classical ARDS were enrolled. Ang-2, ICAM-1, VCAM-1, P-selectin, E-selectin and RAGE were determined with a bead-based multiplex immunoassay at three time points: inclusion in the study (T1), after 7 ± 2 days (T2) and 14 ± 2 days (T3). The primary outcome was to evaluate the plasma trend of the biomarker levels in survivors and non-survivors. The secondary outcome was to evaluate the differences in respiratory mechanics variables and gas exchanges between survivors and non-survivors. Furthermore, we compared the plasma levels of the biomarkers at T1 in patients with COVID-19-related ARDS and classical ARDS.ResultsIn COVID-19-related ARDS, the plasma levels of Ang-2 and ICAM-1 at T1 were statistically higher in non-survivors than survivors, (p = 0.04 and p = 0.03, respectively), whereas those of P-selectin, E-selectin and RAGE did not differ. Ang-2 and ICAM-1 at T1 were predictors of mortality (AUROC 0.650 and 0.717, respectively). At T1, RAGE and P-selectin levels were higher in classical ARDS than in COVID-19-related ARDS. Ang-2, ICAM-1 and E-selectin were lower in classical ARDS than in COVID-19-related ARDS (all p < 0.001).ConclusionsCOVID-19 ARDS is characterized by an early pulmonary endothelial injury, as detected by Ang-2 and ICAM-1. COVID-19 ARDS and classical ARDS exhibited a different expression of biomarkers, suggesting different pathological pathways.Trial registrationNCT04343053, Date of registration:April 13, 2020
Regulatory T lymphocyte infiltration in metastatic breast cancer—an independent prognostic factor that changes with tumor progression
Authors: Stenström Jenny , Hedenfalk Ingrid , Hagerling Catharina 
Published: February 2021

Abstract
Background
Patients diagnosed with metastatic breast cancer have poor outcome with a median survival of approximately 2 years. While novel therapeutic options are urgently needed, the great majority of breast cancer research has focused on the primary tumor and less is known about metastatic breast cancer and the prognostic impact of the metastatic tumor microenvironment. Here we investigate the immune landscape in unique clinical material. We explore how the immune landscape changes with metastatic progression and elucidate the prognostic role of immune cells infiltrating primary tumors and corresponding lymph node and more importantly distant metastases.

Methods
Immunohistochemical staining was performed on human breast cancer tissue microarrays from primary tumors (n = 231), lymph node metastases (n = 129), and distant metastases (n = 43). Infiltration levels of T lymphocytes (CD3+), regulatory T lymphocytes (Tregs, FOXP3+), macrophages (CD68+), and neutrophils (NE+) were assessed in primary tumors. T lymphocytes and Tregs were further investigated in lymph node and distant metastases.

Results
T lymphocyte and Treg infiltration were the most clinically important immune cell populations in primary tumors. Infiltration of T lymphocytes and Tregs in primary tumors correlated with proliferation (P = 0.007, P = 0.000) and estrogen receptor negativity (P = 0.046, P = 0.026). While both T lymphocyte and Treg infiltration had a negative correlation to luminal A subtype (P = 0.031, P = 0.000), only Treg infiltration correlated to luminal B (P = 0.034) and triple-negative subtype (P = 0.019). In primary tumors, infiltration of T lymphocytes was an independent prognostic factor for recurrence-free survival (HR = 1.77, CI = 1.01–3.13, P = 0.048), while Treg infiltration was an independent prognostic factor for breast cancer-specific survival (HR = 1.72, CI = 1.14–2.59, P = 0.01). Moreover, breast cancer patients with Treg infiltration in their distant metastases had poor post-recurrence survival (P = 0.039). Treg infiltration levels changed with metastatic tumor progression in 50% of the patients, but there was no significant trend toward neither lower nor higher infiltration.

Conclusion
Treg infiltration could have clinical applicability as a prognostic biomarker, deciphering metastatic breast cancer patients with worse prognosis, and accordingly, could be a suitable immunotherapeutic target for patients with metastatic breast cancer. Importantly, half of the patients had changes in Treg infiltration during the course of metastatic progression emphasizing the need to characterize the metastatic immune landscape.
ReSeq simulates realistic Illumina high-throughput sequencing data
Authors: Schmeing Stephan , Robinson Mark D. 
Published: February 2021

AbstractIn high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions at each step of a project. Simulations are a critical part of method comparisons, but for standard Illumina sequencing of genomic DNA, they are often oversimplified, which leads to optimistic results for most tools. ReSeq improves the authenticity of synthetic data by extracting and reproducing key components from real data. Major advancements are the inclusion of systematic errors, a fragment-based coverage model and sampling-matrix estimates based on two-dimensional margins. These improvements lead to more faithful performance evaluations. ReSeq is available athttps://github.com/schmeing/ReSeq.
iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
Authors: Wang Dongfang , Hou Siyu , Zhang Lei , Wang Xiliang , Liu Baolin , Zhang Zemin 
Published: February 2021

AbstractThe integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and interactions in complex biological systems. We present a novel unsupervised batch effect removal framework, called iMAP, based on both deep autoencoders and generative adversarial networks. Compared with current methods, iMAP shows superior, robust, and scalable performance in terms of both reliably detecting the batch-specific cells and effectively mixing distributions of the batch-shared cell types. Applying iMAP to tumor microenvironment datasets from two platforms, Smart-seq2 and 10x Genomics, we find that iMAP can leverage the powers of both platforms to discover novel cell-cell interactions.
Anatomical study of the proximal tibiofibular ligaments using ultrasound
Authors: Scarciolla Laura , Herteleer Matthias , Turquet Edouard , Badr Sammy , Demondion Xavier , Jacques Thibaut , Cotten Anne 
Published: February 2021

Abstract
Objectives
No description of the proximal tibiofibular (PTF) ligaments by means of high ultrasound has yet been reported in the literature. The purpose of this study was to assess whether ultrasound may allow the assessment of these ligaments.

Methods
This study was initially undertaken in three cadaveric knees, followed by an ultrasound study performed by two musculoskeletal radiologists working in consensus of 52 patients without history of trauma or surgery of the knee, and without lateral knee pain. The visibility, echogenicity, length and thickness of the PTF ligaments were assessed.

Results
Regarding the anterior PTF ligament, the superior bundle and the upper and lower middle bundles were clearly seen in 42.3%, 100% and 75% of the knees, respectively. Regarding the posterior PTF ligament, the superior and middle bundles were clearly seen in 88.4% and 51.9% of the knees, respectively. The echo-anatomy of these ligaments and the probe positioning allowing their best depiction were described in this study.

Conclusion
Most of the PTF ligaments can be visualized by means of ultrasound. This possible assessment may have clinical applications, particularly in patients with lateral knee pain.
Dual-energy CT angiography reveals high prevalence of perfusion defects unrelated to pulmonary embolism in COVID-19 lesions
Authors: Le Berre Alice , Boeken Tom , Caramella Caroline , Afonso Daniel , Nhy Caroline , Saccenti Laetitia , Tardivel Anne-Marie , Gerber Sophie , Frison Roche Adrien , Emmerich Joseph , Marini Valeria , Zins Marc , Toledano Sarah 
Published: February 2021

Abstract
Background
Lung perfusion defects (PDs) have been described in COVID-19 using dual-energy computed tomography pulmonary angiography (DE-CTPA). We assessed the prevalence and characteristics of PDs in COVID-19 patients with suspected pulmonary embolism (PE) and negative CTPA.

Methods
This retrospective study included COVID-19 and non-COVID-19 pneumonia groups of patients with DE-CTPA negative for PE. Two radiologists rated the presence of PD within the lung opacities and analyzed the type of lung opacities and PD pattern (i.e. homogeneous or heterogeneous). The clinical, biological, radiological characteristics including time from first symptoms and admission to DE-CTPA, oxygen requirements, CRP, D-dimer levels, duration of hospital admission and death were compared within the COVID-19 group between patients with (PD +) or without PD (PD-).

Results
67 COVID-19 and 79 non-COVID-19 patients were included. PDs were more frequent in the COVID-19 than in the non-COVID-19 group (59.7% and 26.6% respectively, p < 0.001). Patterns of PDs were different, with COVID-19 patients exhibiting heterogenous PDs (38/40, 95%) whereas non-COVID-19 patients showed mostly homogeneous perfusion defects (7/21 heterogeneous PDs, 33%), p < 0.001. In COVID-19 patients, most consolidations (9/10, 90%) exhibited PDs while less than a third of consolidations (19/67, 28%) had PDs in non-COVID-19 patients. D-dimer, oxygen levels and outcome were similar between COVID-19 PD + and PD- patients; however, time between admission and DE-CTPA was longer in PD + patients (median [IQR], 1 [0–7] and 0 [0–2]; p = 0.045).

Conclusion
Unlike in bacterial pneumonia, heterogeneous PDs within lung opacities are a frequent feature of COVID-19 pneumonia in PE-suspected patients.
Maternal and fetal effects of COVID-19 virus on a complicated triplet pregnancy: a case report
Authors: Rabiei Maryam , Soori Tahereh , Abiri Amene , Farsi Zohreh , Shizarpour Arshia , Pirjani Reihaneh 
Published: February 2021

Abstract
Background
Coronavirus disease 2019 (COVID-19), the global pandemic that has spread throughout the world, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Given the limited scientific evidence on the manifestations and potential impact of this virus on pregnancy, we decided to report this case.

Case presentation
The patient was a 38 year-old Iranian woman with a triplet pregnancy and a history of primary infertility, as well as hypothyroidism and gestational diabetes. She was hospitalized at 29 weeks and 2 days gestational age due to elevated liver enzymes, and finally, based on a probable diagnosis of gestational cholestasis, she was treated with ursodeoxycholic acid. On the first day of hospitalization, sonography was performed, which showed that biophysical scores and amniotic fluid were normal in all three fetuses, with normal Doppler findings in two fetuses and increased umbilical artery resistance (pulsatility index [PI] > 95%) in one fetus. On day 4 of hospitalization, she developed fever, cough and myalgia, and her COVID-19 test was positive. Despite mild maternal symptoms, exacerbated placental insufficiency occurred in two of the fetuses leading to the rapid development of absent umbilical artery end-diastolic flow. Finally, 6 days later, the patient underwent cesarean section due to rapid exacerbation of placental insufficiency and declining biophysical score in two of the fetuses. Nasopharyngeal swab COVID-19 tests were negative for the first and third babies and positive for the second baby. The first and third babies died 3 and 13 days after birth, respectively, due to collapsed white lung and sepsis. The second baby was discharged in good general condition. The mother was discharged 3 days after cesarean section. She had no fever at the time of discharge and was also in good general condition.

Conclusions
This was a complicated triplet pregnancy, in which, after maternal infection with COVID-19, despite mild maternal symptoms, exacerbated placental insufficiency occurred in two of the fetuses, and the third fetus had a positive COVID-19 test after birth. Therefore, in cases of pregnancy with COVID-19 infection, in addition to managing the mother, it seems that physicians would be wise to also give special attention to the possibility of acute placental insufficiency and subsequent fetal hypoxia, and also the probability of vertical transmission.
Actionable lessons for the US COVID vaccine program
Authors: Freed Gary L. 
Published: February 2021

AbstractWhen attempting to provide lessons for other countries from the successful Israeli COVID-19 vaccine experience, it is important to distinguish between the modifiable and non-modifiable components identified in the article by Rosen, et al. Two specific modifiable components included in the Israeli program from which the US can learn are (a) a national (not individual state-based) strategy for vaccine distribution and administration and (b) a functioning public health infrastructure. As a federal government, the US maintains an often complex web of state and national authorities and responsibilities. The federal government assumed responsibility for the ordering, payment and procurement of COVID vaccine from manufacturers. In designing the subsequent steps in their COVID-19 vaccine distribution and administration plan, the Trump administration decided to rely on the states themselves to determine how best to implement guidance provided by the Centers for Disease Control and Prevention (CDC). This strategy resulted in 50 different plans and 50 different systems for the dissemination of vaccine doses, all at the level of each individual state. State health departments were neither financed, experienced nor uniformly possessed the expertise to develop and implement such plans. A national strategy for the distribution, and the workforce for the provision, of vaccine beyond the state level, similar to that which occurred in Israel, would have provided for greater efficiency and coordination across the country. The US public health infrastructure was ill-prepared and ill-staffed to take on the responsibility to deliver > 450 million doses of vaccine in an expeditious fashion, even if supply of vaccine was available. The failure to adequately invest in public health has been ubiquitous across the nation at all levels of government. Since the 2008 recession, state and local health departments have lost > 38,000 jobs and spending for state public health departments has dropped by 16% per capita and spending for local health departments has fallen by 18%. Hopefully, COVID-19 will be a wakeup call to the US with regard to the need for both a national strategy to address public health emergencies and the well-maintained infrastructure to make it happen.
Effect of family-centered care interventions on motor and neurobehavior development of very preterm infants: a protocol for systematic review
Authors: Raghupathy Manasa Kolibylu , Rao Bhamini Krishna , Nayak Shubha R. , Spittle Alicia J. , Parsekar Shradha S. 
Published: February 2021

Abstract
Background
Globally, very preterm birth is a health concern leading to various developmental difficulties such as poor motor and/or cognitive function. For infants born very preterm, family-centered care (FCC) might promote developmental skills over the time in an appropriate enriched environment. The purpose of this study is to systematically review and assess the evidence of FCC interventions on the motor and neurobehavioral development in very preterm infants. Additionally, this review aims to determine the factors that might affect infant development.

Methods
Systematic review will be carried out by including (a) quasi-randomized controlled trials and randomized controlled trials (b) of very preterm born infants (born < 32 weeks of gestation), and their primary caregivers will be included in the review (c) who received FCC-based interventions such as collaborative interaction between a healthcare professional and a parent, home program, home visits, and parent education, and (d) measure motor and neurobehavioral function. Electronic databases such as Scopus, PubMed, Embase, Cochrane Library, Web of Science, CINAHL, and PsycINFO will be searched using database-specific terms. Additionally, searches will be carried out in ProQuest, and references of included studies will be searched. Two review authors, independently, will conduct the screening, data extraction, and critical appraisal of included studies. If possible, a meta-analysis will be undertaken to assess the effect of the FCC on the motor and neurobehavior of premature infants.

Conclusion
The review will provide insights regarding the effect of the FCC on preterm infants. This systematic review will guide the clinicians on the feasibility of practicing FCC that might support and promote the integration of parents into various rehabilitation settings.

Systematic review registration
Protocol has been registered in PROSPERO on August 26, 2020.
Inertial KM-type extragradient scheme for solving a variational inequality and a hierarchical fixed point problems
Authors: AlNemer Ghada , Ali Rehan , Kazmi K. R. 
Published: February 2021

AbstractWe propose an inertial KM-type extragradient scheme to approximate a common solution of a variational inequality problem and a hierarchical fixed point problem for nonexpansive mappings. This scheme generalizes and unifies a number of known iterative schemes. Furthermore, we discuss the weak convergence for the proposed scheme. We also discuss an example to illustrate the main theorem.
A new candidate vaccine for human brucellosis based on influenza viral vectors: a preliminary investigation for the development of an immunization schedule in a guinea pig model
Authors: Bugybayeva Dina , Kydyrbayev Zhailaubay , Zinina Nadezhda , Assanzhanova Nurika , Yespembetov Bolat , Kozhamkulov Yerken , Zakarya Kunsulu , Ryskeldinova Sholpan , Tabynov Kaissar 
Published: February 2021

Abstract
Background
A new candidate vector vaccine against human brucellosis based on recombinant influenza viral vectors (rIVV) subtypes H5N1 expressing Brucella outer membrane protein (Omp) 16, L7/L12, Omp19 or Cu–Zn SOD proteins has been developed. This paper presents the results of the study of protection of the vaccine using on guinea pigs, including various options of administering, dose and frequency. Provided data of the novel vaccine candidate will contribute to its further movement into the preclinical stage study.

Methods
General states of guinea pigs was assessed based on behavior and dynamics of a guinea pig weight-gain test. The effectiveness of the new anti-brucellosis vector vaccine was determined by studying its protective effect after conjunctival, intranasal and sublingual administration in doses 105 EID50, 106 EID50 and 107 EID50 during prime and boost vaccinations of animals, followed by challenge with a virulent strain of B. melitensis 16 M infection. For sake of comparison, the commercial B. melitensis Rev.1 vaccine was used as a control. The protective properties of vaccines were assessed by quantitation of Brucella colonization in organs and tissues of infected animals and compared to the control groups.

Results
It was observed a gradual increase in body weight of guinea pigs after prime and booster immunization with the vaccine using conjunctival, intranasal and sublingual routes of administration, as well as after using various doses of vaccine. The most optimal way of using the vaccine has been established: double intranasal immunization of guinea pigs at a dose of 106 EID50, which provides 80% protection of guinea pigs from B. melitensis 16 M infection (P < 0.05), which is comparable to the results of the effectiveness of the commercial B. melitensis Rev.1 vaccine.

Conclusions
We developed effective human vaccine candidate against brucellosis and developed its immunization protocol in guinea pig model. We believe that because of these studies, the proposed vaccine has achieved the best level of protection, which in turn provides a basis for its further promotion.