bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Profiling Reveals The Developmental Regulation of NaCl-Treated Forcipomyia Taiwana Eggs
Authors: Chen Mu-En , Tsai Mong-Hsun , Huang Hsiang-Ting , Tsai Ching-Chu , Chen Mei-Ju , Yang Da-Syuan , Wang John , Huang Rong-Nan 
Published: February 2021

Abstract
Background: The biting midge, Forcipomyia taiwana, is one of the most annoying blood-sucking pests in Taiwan. Current chemical control only targets the adult, not the immature stages (egg to pupa) of F. taiwana. Discovering new or alternative tactics to enhance or replace existing methods are urgently needed to improve the effectiveness of F. taiwana control. The egg is the least understood life stage in this pest species but may offer a novel point of control as addition of NaCl to the egg environment inhibits development. Thus, the objective of this study was to use RNA profiling to better understand the developmental differences of wild-type melanized and NaCl-induced un-melanized and infertile F. taiwana eggs. Results: After de novo assembly with Trinity, 112,959 non-redundant transcripts (Ft-nr) with an N50 of 1,044 were obtained. Of these, 28,455 (24.8%) transcripts were predicted to have long open reading frames (ORFs, defined here as ≥300 nt) and 17,791 (15.8%) transcripts have at least one predicted functional domain. A comparison between the melanized (control) and un-melanized eggs revealed 15,996 differentially expressed genes (DEGs; 56.2% of the transcripts with long ORFs) with ≥2-fold difference. Of these, 8,865 were annotated to a Gene Ontology biological process and along with gene expression patterns can be separated into 5 clusters. KEGG pathway analysis revealed that 6,888 transcripts could be assigned to 102 significantly enriched pathways in 3 main categories (metabolism, genetic information processing, environmental information processing). As expected, most (78.24%) of these DEGs were down-regulated in un-melanized eggs. Surprisingly, the majority of genes associated with the pigmentation GO term were up-regulated in the pink egg samples; however, two key terminal genes, laccase2 and DCE/Yellow, were significantly down-regulated, and further verified by qPCR. Conclusion: We have assembled and annotated the first egg transcriptome for F. taiwana, a biting midge. We found that down-regulation of laccase2 and DCE/Yellow genes might be the mechanism responsible for the NaCl-induced inhibition of melanization of F. taiwana eggs.
Traceless enzymatic protein synthesis without ligation sites constraint
Authors: Li Ruifeng , Schmidt Marcel , Zhu Tong , Yang Xinyu , Feng Jing , Yue Tian , Cui Yinglu , Nuijens Timo , Wu Bian 
Published: February 2021

Abstract
Protein synthesis and semisynthesis offer immense promise for life science and have impacted pharmaceutical innovation. Nevertheless, the absence of a generally applicable method for traceless peptide conjugation with flexible choices of junction sites remains a bottleneck to accessing many important synthetic targets. Here we introduce the protein activation and ligation with multiple enzymes (PALME) platform designed for the sequence-unconstrained synthesis and modification of biomacromolecules. The upstream activating modules accept and process easily accessible synthetic peptides and recombinant proteins, avoiding the challenges associated with the preparation and manipulation of activated peptide substrates. Cooperatively, the downstream coupling module provides comprehensive solutions for sequential peptide condensation, cyclization, and protein N/C-terminal or internal functionalization. This methodology’s practical utility was showcased by synthesizing a series of bioactive targets, ranging from pharmaceutical ingredient to synthetically challenging protein. Together, the modular PALME platform exhibits unprecedented broad accessibility for the traceless protein synthesis and functionalization and holds enormous potential to extent the scope of protein chemistry and synthetic biology.
Analysis of viral load change in Case of HIV/AIDS Patients under ART Follow-up in Arba Minch General Hospital
Authors: Erango Markos , Gergiso Kabtamu , Hebo Sultan 
Published: February 2021

Abstract
Background: Monitoring human immunodeficiency virus plasma viral load over time is critical to identify virologic treatment failure in patients taking antiretroviral therapy. The aim of this study was to determine whether the overtime viral load changes depends on patient characteristic measured at baseline of human immunodeficiency virus patients at Arba Minch General Hospital.Methods: This prospective follow up study was conducted using data obtained from medical records, patient interviews, and laboratory workup for six months. The study was employed among 152 adult patients that were selected by systematic random sampling. Longitudinal data analysis that accounts for the correlated nature of the data handled through linear mixed effect models were used to fit the data set in this study.Result: The mean viral load declines over time for each of the adherence level groups. The estimates of linear (p = 0.0006) and quadratic visit time (p=0.0256) effects and the baseline characteristics sex, age, adherence level, and Isoniazid preventive therapy had significant effects on change of viral load of patients over time. Conclusion: In order to improve the status of the patient’s viral load over time, considering the patients’ differences in adherence to antiretroviral therapy, sex, age, and Isoniazid preventive therapy are important.
The Risk Factors of the Progression of Rhegmatogenous Retinal Detachment on Patients with the Fourteen-day Quarantine in the Early Period of COVID-19 Outbreak
Authors: Zhao Meng , Li Jipeng , She Haicheng , Liu Ningpu 
Published: February 2021

Abstract
Backgrounds: The COVID-19 pandemic has great impact on hospitals and patients. The fourteen-day quarantine caused surgery of RRD postponed. To explore the risk factors of rhegmatogenous retinal detachment (RRD) progression in a group of patients whose surgery was postponed during the top-level emergency response of COVID-19.Methods: Retrospective case series study. The information on RRD patients who received surgeries in Beijing Tongren Hospital's retina service from February 16, 2020, to April 30, 2020 has been collected retrospectively. The history, manifestation on presentation and admission, and progression of RRD were recorded. RRD progression was defined as the presence of either choroidal detachment (CD) or proliferative vitreoretinopathy (PVR) progression during the quarantine period. Risk factors were analyzed using the Cox proportional hazards model, survival analysis, and logistic regression.Results: There were 79 cases enrolled in this study. The median time from the patients' presentation at the clinic to admission for surgery was 14 days (3–61 days). There were 70 cases (88.6%) who did not present to the hospital within one week of the onset of visual symptoms. There were 69 (87.3%) macular-off cases at the presentation. There were 27 (34.2%) cases combined with choroidal detachment. There were 49 (62.0%) cases with PVR B, 22 (27.8%) cases with PVR C, 4 (5.1%) cases with PVR D, and 4 (5.1%) cases with PVR A. After the 14-day quarantine, 21 (26.6%) cases showed RRD progression, and 9 cases showed RD regression at the time of surgery. Neither the time of onset of the visual symptom (p=0.46) nor the time between presentation and admission (p=0.31) was significantly different between the patients with RRD progression and patients without RRD progression. The combination of CD (3.61, 1.86-6.99, p=0.001) and retinal breaks located posterior to the equator (3.78, 1.25-11.45, p=0.02) were factors related to the progression of RRD. Conclusions: In the cases enrolled in our study during the COVID-19 outbreak period, the RRD progression risk factors included a combination of CD and retinal breaks posterior to the equator. Ophthalmologists should schedule the surgeries for RRD patients with these signs as soon as possible.
Efficacy of Systemic Oncological Treatments in Patients With Advanced Esophageal or Gastric Cancers at High Risk of Dying in the Middle and Short Term: An Overview of Systematic Reviews
Authors: Santero Marilina , Pérez-Bracchiglione Javier , Acosta-Dighero Roberto , Meade Adriana Gabriela , Martín Alba Antequera , Auladell-Rispau Ariadna , Quintana Maria Jesús , Requeijo Carolina , Rodríguez-Grijalva Gerardo , Dorantes-Romadía Rosario , Salazar Josefina , Solà Ivan , Gerard Urrútia , Bonfill-Cosp Xavier , Salas-Gama Karla 
Published: February 2021

Abstract
Background

Esophageal and gastric cancers are a significant public health problem worldwide, with most patients presenting with advanced-stage disease and, consequently, poor prognosis. Systemic oncological treatments (SOT) have been widely used over more conservative approaches, such as supportive care. Nevertheless, its effectiveness in this scenario is not sufficiently clear. This paper provides an overview of systematic reviews that assessed the effectiveness of SOT compared with the best supportive care (BSC) or placebo in patients with advanced esophageal or gastric cancers in an end-of-life context.
Methods

We searched MEDLINE, EMBASE, The Cochrane Library, Epistemonikos, and PROSPERO for eligible systematic reviews (SRs) published from 2008 onwards. The primary outcomes were overall survival (OS), progression-free survival (PFS), functional status, and toxicity. Two authors assessed eligibility and extracted data independently. We evaluated the methodological quality of included SRs using the AMSTAR-2 tool and the overlap of primary studies (corrected covered area, CCA). Also, we performed a de novo meta-analysis with data reported for each primary study when it was possible. We assessed the certainty of evidence using the GRADE approach.
Results

We identified 16 SRs (19 included trials) for inclusion within this overview. Most reviews had a critically low methodological quality, and there was a very high overlap of primary studies. It is uncertain whether SOT improves OS and PFS over more conservative approaches due to the very low certainty of evidence.
Conclusions

The evidence is very uncertain about the effectiveness of SOT for advanced esophageal or gastric cancers. High-quality SRs and further randomized clinical trials that include a thorough assessment of patient-centered outcomes are needed.
Registration:
Open Science Framework, DOI 10.17605/OSF.IO/7CHX6.
Antioxidant and Anti-Inflammatory Activities of Aralia Cachemirica Decne.: A Comparative Study
Authors: Majid Neelofar , Nissar Saduf , Raja Weekar Younus , Nawchoo Irshad A. , Bhat Zulfikar Ali , Rashid Sufiya 
Published: February 2021

Abstract
Background: Aralia cachemirica Decne. is an important medicinal plant species of Kashmir Himalaya. Regardless of having enormous medicinal importance little information exists on the biological activities of the species. For this reason, present work was carried out for providing comprehensive details on the antioxidant and anti-inflammatory activities of different parts of A. cachemirica.Methods: In this connection, different parts (leaves, stem and root) of the plant were examined following standard methodologies. Antioxidant potential of the plant was determined by three different standard methodologies viz. DPPH radical scavenging activity, reducing power activity and metal chelating activity. For anti-inflammatory activities two different standard methods viz. human RBC membrane stabilization method and protein denaturation method were followed.Results: The extracts exhibited concentration dependent antioxidant and anti-inflammatory activities but were weaker than the standards. Also, the highest activities were recorded in the root and least in the leaves. Also, the highest activities were recorded in the leaves and least in the stem.Conclusion: This is the first study providing information regarding antioxidant and anti-inflammatory potential of different parts of the species. The antioxidant activity of the extract could have great importance as therapeutic agents in preventing or slowing the progress of aging and age associated, oxidative stress related degenerative diseases. Plant derived anti-inflammatory agents are competent cure for inflammation caused by a range of agents, which shows the way to their soaring requirement. Exploitation of these agents requires to be regulated in order, to be sustainable and keep up with demands.
A Route Pruning Algorithm for an Automated Geographic Location Graph Construction
Authors: Schweimer Christoph , Geiger Bernhard C. , Wang Meizhu , Gogolenko Sergiy , Mahmood Imran , Jahani Alireza , Suleimenova Diana , Groen Derek 
Published: February 2021

Abstract
Automated construction of location graphs is instrumental but challenging, particularly in logistics optimisation problems and agent-based movement simulations. Hence, we propose an algorithm for automated construction of location graphs, in which vertices correspond to geographic locations of interest and edges to direct travelling routes between them. Our approach involves two steps. In the first step, we use a routing service to compute distances between all pairs of L locations, resulting in a complete graph. In the second step, we prune this graph by removing edges corresponding to indirect routes, identified using the triangle inequality. The computational complexity of this second step is σ(L3), which outperforms the complexity of σ(L4 log L) to enable computation of location graphs for all towns and cities on the road network of an entire continent. To illustrate the utility of our algorithm in an application, we constructed location graphs for four regions of different size and road infrastructures and compared them to manually created ground truths. Our algorithm simultaneously achieved precision and recall values around 0.9 for a wide range of the single hyperparameter, suggesting that it is a valid approach to create large location graphs for which a manual creation is infeasible.
Performance of a Score to Characterize Adequate Contact among the Social Network of Persons with Tuberculosis
Authors: Castellanos Maria Eugenia , Zalwango Sarah , Quach Trang , Kakaire Robert , Martínez Leonardo , Ebell Mark H. , Dobbin Kevin K. , Kiwanuka Noah , Whalen Christopher C. 
Published: February 2021

Abstract
Background. Exposure to an individual with tuberculosis is necessary for transmission to occur. Previously, we developed a score that measures contact between tuberculosis cases and their social networks in an African urban context. This score was built using exploratory factor analysis and identified contact as the conjunction of two domains – setting and relationship. Now, our aim is to determine whether this score covaries with the presence of tuberculous infection among social contacts of tuberculosis cases.Methods. This was a large cross-sectional study conducted in Kampala, Uganda from 2012-2016. Tuberculous infection was assessed in social contacts of adult tuberculosis cases. We estimated the prevalence of tuberculous infection in this population, overall and according to the setting and relationship domains. We calculated the prevalence ratio (PR) for the association between increasing scores in the setting and relationship domains and tuberculous infection, adjusted by other covariates, using modified Poisson regression models. Results. We enrolled 955 household and community contacts from 119 tuberculosis cases. The overall prevalence of tuberculous infection in the social networks was 52% (95% confidence interval [CI], 48-55). The prevalence of tuberculous infection in very low, low, medium, and high setting-contact quartiles was 44%, 40%, 53%, and 70% respectively (Ptrend<.0001). By the relationship score, the prevalence of tuberculous infection in very low, low, moderate and high-contact groups was 41%, 47%, 53% and 66% respectively (Ptrend<.0001). The effect of the setting score in the prevalence of tuberculous infection was higher among children between 5-14 years (PR=1.26; 95% CI 1.15-1.39) whereas the relationship score was associated with tuberculous infection in children of 0-4 years (PR=1.42; 95% CI 1.10-1.82)Conclusion. In this large observational study from an urban African setting, participants, especially children, with higher setting and relationship scores were more likely infected with Mycobacterium tuberculosis among contacts of a tuberculosis case.
Pre-cART&nbsp;Inflammation, Microbial Translocation and Long-Term Probability of Clinical Progression in People Living With HIV&nbsp;
Authors: Merlini Esther , Cozzi-Lepri Alessandro , Castagna Antonella , Costantini Andrea , Caputo Sergio Lo , Carrara Stefania , Roldan Eugenia Quiros , Ursitti Maria A , Antinori Andrea , Monforte Antonella d'Arminio , Marchetti Giulia C 
Published: February 2021

Abstract
Background. We aimed to investigate the role of pre-cART inflammation and microbial translocation (MT) as predictors of clinical progression in HIV+ patients enrolled in the Icona Foundation Study Cohort.Methods. We included Icona patients with plasma stored within 6 months before cART initiation and at least one CD4 count after therapy available. Circulating biomarker: LPS, sCD14, EndoCab, hs-CRP. Kaplan-Meier curves and Cox regression models were used. We defined the endpoint of clinical progression as the occurrence of a new AIDS-defining condition, severe non-AIDS condition (SNAEs) or death whichever occurred first. Follow-up accrued from the data of starting cART and was censored at the time of last available clinical visit. Biomarkers were evaluated as both binary (above/below median) and continuous variables (logescale).Results. We studied 486 patients with 125 clinical events:10.8 (0.77-14.8)/1000 PYFU new AIDS, 18.3 (14.2-23.3)/1000 PYFU SNAEs, and 5.56 (3.40-8.57)/1000 PYFU deaths. Among morbidity events, the incidence of infectious-related events was 19.4 (15.2-24.5)/1000 PYFU. Hs-CRP seemed to be the only biomarker retaining some association with the endpoint of clinical progression (i.e. AIDS/SNAEs/death p=.056).Conclusions. Circulating pre-cART hs-CRP but not MT seems associated with the risk of disease progression after cART initiation, suggesting that pre-therapy HIV-driven pro-inflammatory milieu might overweight MT and its downstream immune-activation. This result should help guiding the design of interventional studies.
Multi-reference Poly-conformational Computational Methods for De-novo Design, Optimization, and Repositioning of Pharmaceutical Compounds.
Authors: Alexandrov Vadim , Kirpich Alexander , Gankin Yuriy 
Published: February 2021

Abstract
The COVID-19 epidemic, SARS-CoV-2, that began in December of 2019 has drastically altered the aspects of daily life across the global society. Time-effective treatment of those infected has since become a major goal with multiple treatment strategies having been designed to prevent the progression of the disease into severe pneumonia. To date, no drug has been found to be 100% effective against SARS-COV-2, possibly because each candidate drug was targeting only one particular mechanism of action (MoA). Neither proposed up-to-date anti-SARS-COV-2 vaccine are 100% effective. To contribute to the process of finding a more robust small-molecule solution, utilizing several anti-SARS-COV-2 MoAs, a novel framework is presented; where the in silico generated set of virtual library compounds is compared to six known reference drugs: Chloroquine, Favipiravir, Remdesivir, JQ1, Apicidine, and Haloperidol which have been already used for SARS-CoV-2 treatment. The aims were: a) to present a universal search framework for potential candidate compounds based on the comparison of multiple similarities between compounds’ conformers and b) to identify candidate compounds that are simultaneously “close” to each of the six known reference compounds that counteract SARS-CoV-2 via different mechanisms of action.
Optimized Design for Illusion Device by Genetic Algorithm
Authors: yu zhenzhong , Yang Zhong , Wang yizhi , Hu Xingliu , Tian Xiaomin , Zhang Yan 
Published: February 2021

Abstract
The optimized design for the illusion device is studied based on the genetic algorithm. For an electrically small target, a core-shell illusion device by optimizing the material and geometrical parameters of the covering shell can achieve the equivalent scattering, in which the monopolar and dipolar modes are dominant. With the increase of the device size, more scattering terms become obvious, and the ability of the single-layered shell to manipulate the scattering is very limited. For a target with dimension compared with the wavelength, we construct a concentric multi-layered device made of isotropic and homogeneous materials. The full-wave simulations are carried out to demonstrate the illusion performance of the optimized multilayer. The physical explanation is given that all scattering modes of the multi-layered illusion device after optimization approach to that of the target.
Prognostic Factors of Restrictive Myopathy in Thyroid Eye Disease
Authors: Choi Jae Hwan , Noh Hoon , Kim Yoon-Duck , Woo Kyung In 
Published: February 2021

Abstract
To investigate the prognostic factors of extraocular muscle restriction in patients with thyroid eye disease (TED), sixty-five patients with TED and restrictive myopathy were evaluated. Demographics, clinical activity score (CAS), smoking status, thyroid disease status, thyroid hormone status, thyroid autoantibody status, orbital computed tomography (CT) scan at initial presentation, and treatment regimens were assessed. The movements of the most severely affected extraocular muscles were categorized into five grades. The patients were divided into the improved and the not-improved group based on the improvement in the limitation of the extraocular muscle excursion (LOM) throughout the follow-up, and the groups were compared using clinical factors. The mean LOM significantly improved from 2.3 ± 1.1 to 1.7 ± 1.2 after 1 year of follow-up. The excursion of the most restricted muscle improved in 32 patients but not in 33 patients during the follow-up. The initial concentration of the thyroid-stimulating antibody (TSAb) was significantly lower in the improved than in the not-improved group. Age, sex, smoking status, CAS, thyroid status, and muscle thickness on the CT scan did not significantly differ in the groups. This study showed that the initial concentration of TSAb is a factor affecting the recovery of restrictive myopathy.
High Biodiversity in a Limited Mountain Area Revealed in The Traditional Production of Historic Rebel Cheese By An Integrated Microbiota-Lipidomic Approach.
Authors: Turri Federica , Cremonesi Paola , Battelli Giovanna , Severgnini Marco , Gandini Gustavo , Pizzi Flavia 
Published: February 2021

Abstract
Historic Rebel (HR) cheese is an Italian heritage cheese, produced from raw milk during the summer grazing period in the Alps. The aim of this work was i) to characterize the cheese microbiota, by 16S rRNA gene amplicons sequencing and the volatile and non-volatile lipophilic fraction, by Gas Chromatography and Dynamic Headspace - Extraction Gas Chromatography- Mass Spectrometry, and ii) to evaluate their respective associations. HR cheese was dominated by Firmicutes phylum (99% of the entire abundance), with members of the Streptococcus, Lactobacillus, Lactococcus, Leuconostoc and Pediococcus together representing 87.2% - 99.6% of the total abundance. The polyunsaturated fatty acids composition showed a high PUFA n-3, PUFA n-6 and CLA content, two fold higher than typical plain cheeses. A complex volatilome was detected, dominated in terms of abundance by ketones, fatty acids and alcohols. The main terpenes compounds were α-pinene, camphene and β-pinene.The HR cheese showed a great diversity (P<0.05) of bacterial species and lipophilic fractions among producers, despite they belonging to a small alpine area, revealing a scarce cheese standardization and a chemical fingerprint of a typical mountain cheese produced during the grazing period. A deeper knowledge of the variability of HR cheese will be appreciated in particular by elite consumers looking for niche products, adding economic value to farming in these alpine areas.