bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bautype: Capsule and Lipopolysaccharide Serotype Prediction for Acinetobacter baumannii Genome
Authors: Hua Xiaoting , Liang Qian , Fang Li , He Jintao , Wang Meixia , Hong Wenjie , Leptihn Sebastian , Wang Hengliang , Yu Yunsong , Chen Huan 
Published: April 2020

Abstract

Acinetobacter baumannii has three clusters of genes for polysaccharide synthesis. Capsular polysaccharides and lipopolysaccharides are major virulence determinants in many Gram-negative bacteria, and play key roles in the overall fitness and virulence in A. baumannii, meanwhile poly-beta-1-6-N-acetylglucosamine was critical for biofilm formation. A variety of studies have been conducted which focused on the surveillance of antimicrobial resistance genes and clones in A. baumannii. However, a tool to perform serotype prediction in A. baumannii is still lacking. Here we present Bautype, a tool for whole genome sequencing-based K and O locus typing in A. baumannii. Using Bautype, users can upload and analyze the genome assembled in a web browser, with the results being displayed in a tabular or graphical format. We demonstrated the high accuracy of predicting K and O locus diversity using Bautype when analyzing more than 3000 A. baumannii genomes. Using our software, we were able to analyze K and O locus diversity among 593 genomes belonging to ST208 (3 K and 8 O). These diverse loci can serve as epidemiological markers for Multi-drug Resistance (MDR) strain subtyping. We also identified 45 novel O locus types. Our findings highlight the importance in monitoring the capsule type and LOS of A. baumannii strains for which Bautype is a tailored clinical software. Bautype is available at http://BauType.net.
Erosive Adenomatosis of the Nipple Masquerading as Paget's Disease: A Case Report
Authors: Guo Qin , Ji Jin , Tan Cheng , Zhang Qi , Feng Su-Ying 
Published: April 2020

Abstract

Introduction:
Erosive adenomatosis of the nipple is a rare benign lesion involving nipple which can be easily misdiagnosed as more ominous entities such as Pagets disease. Here we reported a case of erosive adenomatosis on the nipple masquerading as paget's disease.

Case presentation:
A 21-year-old woman presented with a 6-year history of breast erythema involving her left nipple with tenderness and mild itching. The nipple appeared rough and thickened with areas of erosion and fissuring. Physical examination of other areas of breast as well as imaging studies including ultrasound and mammography showed no abnormalities. The histological examination reveal adiagnosis of erosive adenomatosis of nipple (EAN). The patient was treated by a simple surgical excision without complications and recurrence during 9-month follow-up.

Discussion:
In the early stage, it can mimic eczema, but in the later stage, more serious diagnosis such as Pagets disease should be differential. It is diagnosed by histopathological examination. Surgical excision is an optimal choice for treament with or without plastic reconstruction.

Conclusion:
EAN should be considered in the diagnosis of erythema and erosion lesions involving nipple. The gold standard for diagnosis is histopathological examination. A prompt and correct diagnosis of EAN can avoid both unnecessary over treatment and patients emotional stress.
Bowen's Disease on the Left Fifth Finger Successfully Treated with Photodynamic Therapy: A Case Report
Authors: Wu Wei-Hong , Al-Muriesh Maher , Deng Xiao-Hong , Huang Chang-Zheng 
Published: April 2020

Abstract

Introduction:
Bowen's disease is a squamous cell carcinoma in situ. It is more common on the head and neck, less common on the nail units in which it usually involves the second to fourth fingers of both hands. Here, we report a case of Bowen's disease involving the left fifth finger of a 78-year-old Chinese woman.

Case presentation:
The patient was treated with nine sessions of topical 5-aminolevulinic acid-photodynamic therapy (5-ALA-PDT), with a one-week interval between sessions. The 5-ALA cream was applied to the lesion and the region surrounding its marginal diameter by 0.5cm. After 3-4hours, the lesion was irradiated with 635 ± 10nm red light at an intensity of 80mw/cm2 for 20minutes. An excellent result with a topical 5-ALA-PDT was reached.

Discussion:
PDT involves the application of a combination of a photosensitizing drug and light to cause selective damage to the target tissue. PDT is more appropriate than surgical excision for lesions located in sites with poor healing ability.

Conclusion:
PDT appears to be effective, safe and has a better cosmetic outcome in the treatment of Bowen's disease of the finger unit.
Lichen Striatus With Nail Involvement: Two Case Reports
Authors: Liu Zhen-Ru , Zhou Yuan , Liu Meng-Xi , Wang Xiao-Qing , Wang Da-Guang 
Published: April 2020

Abstract

Introduction:
Lichen striatus (LS) is a benign, self-limiting, linear inflammatory skin disease that was rarely reported. Here we report two cases of nail involvement in children with LS.

Case presentation:
Two children was referred to our hospital with asymptomatic linear eruption and nail dystrophy. Histopathological examination revealed epidermal hyperkeratosis, infiltration of inflammatory cells around the adnexal region, hyperpigmentation in the rete ridges, and focal liquefactive degeneration of the basal layer.

Discussion:
There is no specific treatment for nail LS. Without treatment, LS can resolve spontaneously over a period of time. Topical steroid treatment can improve symptoms and shorten the duration of the disease. It is important for clinicians to distinguish LS from other linear diseases, which may lead to unnecessary treatment and surgical intervention.

Conclusion:
The appearance of nail and skin lesions is importance of clinical features in making the diagnosis of nail LS, and also distinguish to other linear and nail diseases.
Chinese Experts Consensus on Biologic Therapy for Psoriasis#
Authors: Chen Ai-Jun , Gao Xing-Hua , Gu Heng , Gu Jun , Hao Fei , Jiang Xian , Jin Hong-Zhong , Kang Xiao-Jing , Li Cheng-Xin , Li Yu-Zhen , Liu Xiao-Ming , Shi Yu-Ling , Sun Qing , Wang Gang , Yang Bin , Zhang Jun-Ling , Zhang Xi-Bao , Zhang Xue-Jun , Zhao Yi , Zheng Min 
Published: April 2020

Abstract
Biologic drugs have been increasingly used in the treatment of psoriasis and are especially favorable for severe, recalcitrant, and special-type cases. Therefore, appropriate, effective, and safe use of biologic drugs has drawn attention from dermatologists. For this purpose, Chinese experts majoring in psoriasis analyzed domestic and international research data, summarized current clinical experiences, investigated features of Chinese patients with psoriasis, and finally formulated the present consensus, which provides detailed guidances to clinicians in terms of the principles and methods of the application of biologics, the efficacy and safety profile, patient screening and monitoring, main adverse events and corresponding solutions, and precautions for special patient populations.
Chinese Experts Consensus on Pre-examination and Triage in Dermatology Clinics during the COVID-19 Outbreak#
Authors: Ma Lin , Wang Gang , Mu Qi-Ri , Ran Yu-Ping , Liu Quan-Zhong , Xiao Sheng-Xiang , Zhang Xue-Jun , Zhang Jian-Zhong , Zhang Fu-Ren , He Li , Chen Ai-Jun , Chen Xiang , Zheng Jie , Yang Rong-Ya , Yao Zhi-Rong , Tu Ping , Li Yu-Zhen , Gao Xing-Hua , Xu Jin-Hua , Gu Heng , Cheng Bo , Lai Wei , Lu Qian-Jin 
Published: April 2020

Abstract
The SARS-CoV-2 infection has brought a great challenge in prevention and control of the national epidemic of coronavirus disease 2019 (COVID-19) in China. During the COVID-19 epidemic, properly carrying out pre-examination and triage for patients with skin lesions and fever has become a practical problem encountered in hospitals for skin diseases and dermatology clinics in general hospitals. Some of the carriers of the SARS-CoV-2 and patients with COVID-19 in the early stage may not present with any symptoms of COVID-19, while certain other skin diseases can also cause fever. Therefore, to properly deal with the patients presenting at dermatology clinics, the Chinese Society of Dermatology organized experts to formulate principles and procedures for the pre-examination and triage of patients at dermatology clinics during the COVID-19 epidemic.
The Immune Function of Keratinocytes in Anti-Pathogen Infection in the Skin
Authors: Wang Jia-Ning , Li Min 
Published: April 2020

Abstract
Keratinocytes, located in the outer part of human skin, are the main epidermal cell type and play an essential role in skins defense against infection. Besides creating a physical barrier between the environment and the internal body, keratinocytes exert powerful immune function in anti-pathogen infection in the skin. At the recognition stage, pattern recognition receptors (PRRs) expressed by keratinocytes sense pathogen-associated molecular patterns (PAMPs) existing in pathogens. Toll like receptors (TLRs) are the most important PRRs in keratinocytes. Other PRRs such as dectin-1 and nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are also found to participate in this process. Activated PRRs enhance the secretion of cytokines, chemokines and the production of antimicrobial peptides (AMPs). Proinflammatory cytokines tumor necrosis factor-α, interleukin (IL)-1α, IL-6, IL-1β and IL-18, chemokines (C-X-Cmotif) ligand (CXCL) 1, CXCL2, CCL20, CCL2 and IL-8, AMPs human β-defensin (HBD) 2, HBD3 and LL37 are the main molecules expressed in this procedure. Thymic stromal lymphopoietin (TSLP), IL-36γ, IL-17 family member IL-17C and anti-inflammatory cytokine IL-10 can also be secreted. Some molecules produced by keratinocytes such as ribonuclease 5 and 7, S100 proteins own antimicrobial properties. Keratinocytes defense responses can be regulated by internal and external factors. This review summarizes recent advances on the innate immune function of keratinocytes against infection, promoting the finding of a new direction for avoiding severe skin infection as well as the potential treatment of keratinocyte-associated inflammatory dermatosis.
The dynamics of Covid-19: weather, demographics and infection timeline
Authors: Pedrosa Renato H. L. 
Published: April 2020

AbstractWe study the effects of temperature, absolute humidity, population density and when country/U.S. state reached 100 cases on early pace of Covid-19 expansion, for all 50 U.S. states and 110 countries with enough data. For U.S. states, weather variables show opposite effects when compared to the case of countries: higher temperature or absolute humidity imply faster early outbreak. The higher the population density or the earlier the date when state reached 100th case, the faster the pace of outbreak. When all variables are considered, only population density and the timeline variable show statistical significance. Discounting the effect of the timeline variable, we obtain an estimate for the initial growth rate of Covid-19, which can be also used to estimate the basic reproduction number for a region, in terms of population density. This has policy implications regarding how to control the pace of Covid-10 outbreak in a particular area, and we discuss some of them. In the case of countries, for which we did not have demographic information, weather variables lose statistical significance once the timeline variable is added. Relaxing CI requirements, absolute humidity contributes mildly to the reduction of growth rate of cases for the countries studied. Our results suggest that population density should be employed as a control variable and that analysis should have a local character, for subregions and countries separately, in studies involving the dynamics of Covid-19 and similar infectious diseases.
In silicoIdentification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis CropCorchorus capsularis
Authors: Hasan Mahmudul , Ahmed Milad , Ahmed Foeaz , Ahmed Jamil , Nazneen Akhand Mst Rubaiat , Azim Kazi Faizul , Shukur Imran Md. Abdus , Hoque Syeda Farjana 
Published: April 2020

AbstractCorchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre and fibre based products alongside lower environmental threat. Nowadays, the study of lignin biosynthesis pathways with other molecular basis of fibres formation are being more focused for its economic perspective. Small noncoding ∼21 to 24 nt nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including specific gene targets involved in the crucial cellular process. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were 18 nucleotide length, within a range of -0.49 to -1.56 MFEI values and 55% to 61% of (A+U) content of their correspondence pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. The five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met–dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation which could play significant roles in the overall fibre biogenesis. The characterization of conserved miRNAs and their functional annotation of specific gene targets might enhance the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.
A national landscaping survey of critical care services in hospitals accredited for training in a lower-middle income country: Pakistan
Authors: Hashmi Madiha , Taqi Arshad , Memon Muhammad Iqbal , Ali Syed Muneeb , Khaskheli Saleh , Sheharyar Muhammad , Hayat Muhammad , Shiekh Mohiuddin , Kodippily Chamira , Gamage Dilanthi , Dondorp Arjen M , Haniffa Rashan , Beane Abi 
Published: April 2020

AbstractPurposeTo describe the extent and variation of critical care services in PakistanMaterials and methodsA cross-sectional survey was conducted in all CCUs recognised for postgraduate training to determine administration, infrastructure, equipment, staffing, and training.ResultsThere were 220 CCUs registered for training, providing 2166 CCU beds and 1473 ventilators. Regional distribution of CCU beds per 100,000 population ranged from 1.0 in Sindh to none in Gilgit Baltistan (median 0.7). A senior clinician trained in critical care was available in 19 (12.1%) of units, giving a ratio of one trained intensivist for every 82 CCU beds and 0.009 trained intensivists per 100,000 population. One to one nurse to bed ratio during the day was available in 84 (53.5%) of units, dropping to 75 (47.8%) at night. Availability of 1:1 nursing also varied between provinces, ranging from 56.5% in Punjab compared to 0% in Azad Jamu Kashmir. All CCUs had basic infrastructure (electricity, running water, piped oxygen) and basic equipment (electronic monitoring and infusion pumps).ConclusionPakistan, a lower middle-income country has an established network of critical care facilities with access to basic equipment, but inequalities in its distribution. Investment in critical care training for doctors and nurses is needed.
Randomized clinical trial quality has improved over time but is still not good enough: an analysis of 176,620 randomized controlled trials published between 1966 and 2018
Authors: Vinkers Christiaan H. , Lamberink Herm J. , Tijdink Joeri K. , Heus Pauline , Bouter Lex , Glasziou Paul , Moher David , Damen Johanna A. , Hooft Lotty , Otte Willem M. 
Published: April 2020

AbstractBackgroundMany randomized controlled trials (RCTs) are biased and difficult to reproduce due to methodological flaws and poor reporting. There is increasing attention for responsible research practices including reporting guidelines, but it is unknown whether these efforts have improved RCT quality (i.e. reduced risk of bias). We therefore mapped trends over time in trial publication, trial registration, reporting according to CONSORT, and characteristics of publication and authors.MethodsMeta-information of 176,620 RCTs published between 1966 and 2018 was extracted. Risk of bias probability (four domains: random sequence generation, allocation concealment, blinding of patients/personnel, and blinding of outcome assessment) was assessed using validated risk-of-bias machine learning tools. In addition, trial registration and reporting according to CONSORT were assessed with automated searches. Characteristics were extracted related to publication (number of authors, journal impact factor, medical discipline) and authors (gender and Hirsch-index).FindingsThe annual number of published RCTs substantially increased over four decades, accompanied by increases in the number of authors (5.2 to 7.8), institutions (2.9 to 4.8), female authors (20 to 42%, first authorship; 17 to 29%, last authorship), and Hirsch-indices (10 to 14, first authorship; 16 to 28, last authorship). Risk of bias remained present in most RCTs but decreased over time for the domains allocation concealment (63 to 51%), random sequence generation (57 to 36%), and blinding of outcome assessment (58 to 52%). Trial registration (37 to 47%) and CONSORT (1 to 20%) rapidly increased in the latest period. In journals with higher impact factor (>10), risk of bias was consistently lower, higher levels of trial registration more frequent, and mentioning CONSORT.InterpretationThe likelihood of bias in RCTs has generally decreased over the last decades. This may be driven by increased knowledge and improved education, augmented by mandatory trial registration, and more stringent reporting guidelines and journal requirements. Nevertheless, relatively high probabilities of bias remain, particularly in journals with lower impact factors. This emphasizes that further improvement of RCT registration, conduct, and reporting is still urgently needed.FundingThis study was funded by The Netherlands Organisation for Health Research and Development (445001002).
SARS-CoV-2 On-the-Spot Virus Detection Directly from Patients
Authors: Ben-Assa Nadav , Naddaf Rawi , Gefen Tal , Capucha Tal , Hajjo Haitham , Mandelbaum Noa , Elbaum Lilach , Rogov Peter , Daniel King A. , Kaplan Shai , Rotem Assaf , Chowers Michal , Szwarcwort-Cohen Moran , Paul Mical , Geva-Zatorsky Naama 
Published: April 2020

AbstractMany countries are currently in a lockdown state due to the SARS-CoV-2 pandemic. One key aspect to transition safely out of lockdown is to continuously test the population for infected subjects. Currently, detection is performed at points of care using quantitative reverse-transcription PCR (RT-qPCR), and requires dedicated professionals and equipment. Here, we developed a protocol based on Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP) for detection of SARS-CoV-2. This protocol is applied directly on SARS-CoV-2 nose and throat swabs, with no RNA purification step required. We tested this protocol on over 180 suspected patients, and compared its results to the standard method. We further succeeded to apply the protocol on self-sampled saliva from confirmed cases. Since the proposed protocol provides results on-the-spot, and can detect SARS-CoV-2 from saliva, it can allow simple and continuous surveillance of the community.
Inf-Net: Automatic COVID-19 Lung Infection Segmentation from CT Images
Authors: Fan Deng-Ping , Zhou Tao , Ji Ge-Peng , Zhou Yi , Chen Geng , Fu Huazhu , Shen Jianbing , Shao Ling 
Published: April 2020

AbstractCoronavirus Disease 2019 (COVID-19) spread globally in early 2020, causing the world to face an existential health crisis. Automated detection of lung infections from computed tomography (CT) images offers a great potential to augment the traditional healthcare strategy for tackling COVID-19. However, segmenting infected regions from CT slices faces several challenges, including high variation in infection characteristics, and low intensity contrast between infections and normal tissues. Further, collecting a large amount of data is impractical within a short time period, inhibiting the training of a deep model. To address these challenges, a novel COVID-19 Lung Infection Segmentation Deep Network (Inf-Net) is proposed to automatically identify infected regions from chest CT slices. In ourInf-Net, a parallel partial decoder is used to aggregate the high-level features and generate a global map. Then, the implicit reverse attention and explicit edge-attention are utilized to model the boundaries and enhance the representations. Moreover, to alleviate the shortage of labeled data, we present a semi-supervised segmentation framework based on a randomly selected propagation strategy, which only requires a few labeled images and leverages primarily unlabeled data. Our semi-supervised framework can improve the learning ability and achieve a higher performance. Extensive experiments on ourCOVID-SemiSegand real CT volumes demonstrate that the proposedInf-Netoutperforms most cutting-edge segmentation models and advances the state-of-the-art performance.
COVID-19: One-month impact of the French lockdown on the epidemic burden
Authors: Roux Jonathan , Massonnaud Clément , Crépey Pascal 
Published: April 2020

1AbstractOn March 16 2020, French authorities ordered a large scale lockdown to counter the COVID-19 epidemic wave rising in the country, stopping non-essential economic, educational, and entertainment activities, maintaining mainly food retailers and healthcare institutions. One month later, the number of new hospitalizations and ICU admissions had reached a plateau and were beginning a slow descent.We developed a spatialized, deterministic, age-structured, and compartmental SARS-CoV-2 transmission model able to reproduce the pre-lockdown dynamic of the epidemic in each of the 13 French metropolitan regions. Thanks to this model, we estimate, at regional and national levels, the total number of hospitalizations, ICU admissions, hospital beds requirements (hospitalization and ICU), and hospital deaths which may have been prevented by this massive and unprecedented intervention in France.If no control measures had been set up, between March 19 and April 19 2020, our analysis shows that almost 23% of the French population would have been affected by COVID-19 (14.8 million individuals). Hence, the French lockdown prevented 587,730 hospitalizations and 140,320 ICU admissions at the national level. The total number of ICU beds required to treat patients in critical conditions would have been 104,550, far higher than the maximum French ICU capacity. This first month of lockdown also permitted to avoid 61,739 hospital deaths, corresponding to a 83.5% reduction of the total number of predicted deaths.Our analysis shows that in absence of any control measures, the COVID-19 epidemic would have had a critical morbidity and mortality burden in France, overwhelming in a matter of weeks French hospital capacities.