bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significance of neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio for predicting clinical outcomes in COVID-19
Authors: Zhang Ting , Huang Shaoping , Liu Min , Li Xiaolu , Shang Zhiyin , Lu Hongzhou 
Published: June 2020

Abstract
Background

The epidemic of 2019 novel coronavirus (COVID-19) struck China in late December,2019, resulting in about 200000 deaths all over the world. Numerous observational studies have suggested that the neutrophil-to-lymphocyte ratio (NLR) and lymphocyte proportion and the platelet-to-lymphocyte ratio (PLR) are inflammatory markers. Our study aimed to detect the role of NLR, PLR in predicting the prognosis of COVID-19.
Results

Four hundred and fifteen consecutive patients were enrolled in Shanghai Public Health Clinical Center affiliated to Fudan University, between 20 January and 11 April 2020 with confirmed COVID-19,among which 386 (93%) patients were not severe, and 27 (7%) were severe. The proportion of males in severe cases is higher than in non-severe cases (75.86% vs. 50.52%, P = 0.008). The age between the two groups is different (p = 0.022). Compared with non-severe patients, severe patients exhibited more comorbidities, including hypertension (48.28% vs. 19.43%, p < 0.001), diabetes (20.69% vs. 6.99%, p = 0.009), chronic obstructive pulmonary disease (51.72% vs. 6.22%, p < 0.001), and fatty liver (37.93% vs. 15.8%, p = 0.002), respectively. NLR and PLR showed significant difference (p < 0.001). Diabetes (OR 0.28; 95% CI 15.824-187.186), fatty liver (OR 21.469; 95% CI 2.306-199.872), coronary heart disease (OR 18.157; 95% CI 2.085-158.083), NLR (OR 1.729; 95% CI 1.050–2.847) were significantly associated with severe cases with COVID-19. The NLR of patients in severe group had a 1.729-fold higher than that of no-severe group (OR 1.729; 95% CI 1.050–2.847, P = 0.031).
Conclusions

NLR is an independent risk factor of severe COVID-19 patients. PLR, NLR were significantly different between severe and non-severe patients, so assessment of NLR, PLR may help identify high risk cases with COVID-19.
Microskeletal stiffness promotes aortic aneurysm by sustaining pathological vascular smooth muscle cell mechanosensation via Piezo1&nbsp;&nbsp;&nbsp;&nbsp;
Authors: Qian Weiyi , Hadi Tarik , Ma Xiao , Silvestro Michele , Rivera Cristobal , Bajpai Apratim , Zhang Zijing , Qu Hengdong , Corsica Annanina , Miscovich Bradley , Aykut Berk , Miller George , Ramkhelawon Bhama , Chen Weiqiang 
Published: June 2020

Abstract
Mechanical overload of the vascular wall is a pathological hallmark of life-threatening abdominal aortic aneurysms (AAA). However, how this mechanical stress resonates at the unicellular level of vascular smooth muscle cells (VSMC) in AAA is undefined. Here, we combined novel ultrasound tweezers-based micromechancal system and single-cell RNA sequencing to map defective mechano-phenotype signature of VSMC niched in AAA. VSMC gradually adopted a mechanically solid-like state by upregulating cytoskeleton (CSK) crosslinker, α-actinin2, which stiffened VSMC cell membrane thereby directly powering the activity of mechano-sensory ion channel Piezo1 during AAA development. Theoretical modelling predicted that in AAA, such CSK alterations fueled cell membrane tension thereby blocking physiological mechanoallostatic responses of VSMC. Single-cell mechanical measurements and frequency spectrum analysis validated the mechanosensation deficiency in VSMC during AAA development. Our findings demonstrate that deviations of mechanosensation behaviors of VSMC is detrimental for AAA and identifies Piezo1 as a novel target to curb AAA onset.
Bioinformatics Analysis Reveals Biomarkers With Prognostic Benefits in Diffuse Type Gastric Cancer
Authors: Li Sheng , Yu Chao , Cheng Yuanguang , Du Fangchao , Wen Gang 
Published: June 2020

Abstract
BackgroundGastric cancer (GC) is one of the most common malignancies in digestive system, among which the differentiation of diffuse type GC is relatively poor, the probability of distant metastasis and lymph node metastasis is relatively high, and the clinical prognosis is relatively poor. The purpose of this study is to explore potential signaling pathways and key biomarkers that drive the development of diffuse type GC. Methods Using the “limma” package in R to screen Differentially expressed genes. Screening hub genes by PPI analysis. Immunohistochemistry analysis and qRT-PCR analysis was carried out to detect genes expression. Using Kaplan-Meier Plotter database analyzed the prognostic roles of hub genes.ResultsA total of 355 DEGs consisting of 293 diffuse type DEGs and 62 intestinal type DEGs were selected according to screening criteria, 3 hub genes were chosen from diffuse type DEGs according to the degree of connectivity by using protein-protein interaction (PPI) networks and Cytoscape software including AGT, CXCL12 and ADRB2. Immunohistochemistry analysis and qRT-PCR results showed that the expression of three genes was related to the different GC lauren types. The Kaplan Meier analysis showed that the expression values of these three genes were related to prognosis of diffuse type GC. ConclusionsAGT, CXCL12 and ADRB2 might contribute to the progression of diffuse type GC, which could have potential as biomarkers or therapeutic targets for diffuse type GC.
Comparative chloroplast genomes of the tea plants and the implications for the different origins of the two Assam teas
Authors: li LI , Hu Yunfei , He Min , Zhang Bo , Hong Yongcong , Wu Wei , Cai Pumo , Huo Da 
Published: June 2020

Abstract
Background
Tea plants belong to the genus Camellia, whose species are taxonomically complex due to frequent hybridization and polyploidy nature. The genetic genealogy of Camellia has always been a focus of botanical and ecological research, including a debate about whether Assam tea has two different domestication origins (Chinese Assam type and Indian Assam type). The chloroplast genome resources were able to provide useful data for the analysis of the plastome evolutionary relationship and species classification. Here, we determined the first chloroplast genome of the natural triploid tea plant (Camellia sinensis cv. Wuyi Narcissus) and conducted the genome comparison with Chinese type tea (Camellia sinensis var. sinensis), Chinese Assam type tea (Camellia sinensis var. assamica) and Indian Assam type tea (Camellia assamica) to improve our understanding of the evolutionary mechanism and the taxonomic classification of Camellia.
Results
This study presented detailed sequences and structural variations of chloroplast genomes of four tea plants. The chloroplast genome of the natural triploid tea showed no obvious sequence difference from that of other two types of Chinese teas, while that of Chinese tea and Indian tea was significant sequence difference. The natural selection probably dominated in shaping the codon bias of the chloroplast genome in tea plant, and the codon usage distribution of genome in Indian tea was obviously different from that in Chinese tea. The phylogenetic status of Chinese and Indian Assam teas was in the different branches of the tea plant. Phylogenetic tree clustering was not consistent with the current some taxonomy of Camellia.
Conclusions
The sequence variation of the chloroplast genome of tea plant was mainly ascribed to the expansion and contraction of the border regions (IR/ SC), which were mainly due to the sequence repeat and indel mutation events of the genome. The codon usage pattern and phylogenetic analysis supported Chinese Assam type and Indian Assam type tea might have different domestication origins and suggested the current some taxonomy of Camellia might need revision.
Mapping the architecture of regulatory variation provides insights into the evolution of complex traits
Authors: Lupo Offir , Krieger Gat , Jonas Felix , Barkai Naama 
Published: June 2020

Abstract
Background : Organisms evolve complex traits by recruiting existing programs to new contexts, referred as co-option. Within a species, single upstream regulators can trigger full differentiation programs. Distinguishing whether co-option of differentiation programs results from variation in single regulator, or in multiple genes, is key for understanding how complex traits evolve. As an experimentally accessible model for studying this question we turned to budding yeast, where a differentiation program (filamentous) is activated in S. cerevisiae only upon starvation, but used by the related species S. paradoxus also in rich conditions. Results : To define expression variations associated with species-specific activation of the filamentous program, we profiled the transcriptome of S. cerevisiae, S. paradoxus and their hybrid along two cell cycles at 5-minutes resolution. As expected in cases of co-option, expression of oscillating genes varies between the species in synchrony with their growth phenotypes and was dominated by upstream trans-variations. Focusing on regulators of filamentous growth, we identified gene-linked variations (cis) in multiple genes across regulatory layers, which propagated to affect expression of target genes, as well as binding specificities of downstream transcription factor. Unexpectedly, variations in regulators essential for S. cerevisiae filamentation were individually too weak to explain activation of this program in S. paradoxus . Conclusions : Our study reveals the complex architecture of regulatory variation associated with species-specific use of a differentiation program. Based on these results, we suggest a new model in which evolutionary co-option of complex traits is stabilized in a distributed manner through multiple weak-effect variations accumulating throughout the regulatory network.
A Dual-Targeting Ruthenium Nanodrug that Inhibits Primary Tumor Growth and Lung Metastasis by the PARP/ATM Pathway
Authors: Lu Yu , Zhu Di , Gui Lin , Li Yuanming , Wang Wenjing , Liu Jiawang , Wang Yuji 
Published: June 2020

Abstract
Many studies have found that ruthenium complexes have unique biochemical characteristics and thus inhibit tumor growth or metastasis. Our aim was to report a novel dual-targeting ruthenium candidate 2b with both antitumor and antimetastatic functions that could target tumor sites using both EPR effects and TF/TFR. It was composed of ruthenium-complexed carboline acid and four chloride ions. In vitro, 2b could trigger DNA cleavage and thus block the cell cycle and cause apoptosis by the PARP/ATM pathway. In vivo, 2b could inhibit not only LLC tumor growth but also lung metastasis. We found apoptosis and decrease in CD31 expression in tumor tissue. In addition, we also found that 2b could collect in tumor tissue. Thus, we concluded that 2b could target tumors, inhibit tumor growth and prevent lung metastasis.
Water Loss During the Handwashing During Covid-19 Pandemic in Bangladesh
Authors: Sayeed Abu , Ahmed Fahad , Tariq Mohammad Raihan , Rahman Faujhia , Joy Md. Tarikul Islam , Abid Mohammad Tazrian , Rahman Md Hafizur 
Published: June 2020

Abstract
Hand washing is an important measure of public health to prevent COVID-19 pandemic from speared. But the increase in hand washing causes tremendous pressure on overstretched water resources, as the loss of water during handwashing increases. As there is no previous study to evaluate water loss during hand washing, the study aimed to determine the water loss during the COVID-19 pandemic during hand washing. Sociodemographic data were collected using a web based survey tool and an experiment was conducted to estimate the amount of water wasted during hand washing. 77.9% of participants washed their hands regularly after returning home from outside. 4 of the 7 participants generally did not turn off their tap when washing their hands.A single participant, who kept their tap on throughout the hand washing process, wasted approximately 14.88 L of water per day. The loss of water during hand washing is an alarming but less attentional issue. Hand washing is necessary during the COVID-19 situation, but behavioral adjustments are required to shut down the faucet at times when water is not being used.
Localization of recurrent lesions ileocolic resection for Crohn's disease
Authors: Ikeuchi Hiroki , Uchino Motoi , Bando Toshihiro , Horio Yuki , Kuwahara Ryuichi , Minagawa Tomohiro , Goto Yoshiko , Kusunoki Kurando , Ikeda Masataka , Beppu Naohito , Takesue Yoshio 
Published: June 2020

Abstract
Background
Crohn’s disease (CD) recurrence can occur not only at the site of anastomosis but also elsewhere in the bowel following ileocolic resection (ICR). The aims of the present study were to assess long-term outcomes of a primary ICR procedure for CD in consecutive patients and examine the location of the reoperation causative lesion.
Methods
We examined cases of surgery with ICR initially performed at our institution. Those with a simultaneous multiple bowel resection or bowel resection with strictureplasty were excluded.
Results
A total of 169 patients who underwent ICR due to CD were enrolled. The median follow-up period was 12.6 years (range 4–27 years). A reoperation was needed in 45 (26.6%), of whom 14 had lesions causative of the reoperation at other than the anastomotic site. The most common causative lesion location was in the colon rather than the oral side of the small intestine. Furthermore, we investigated the relationship between presence of residual lesions following the initial surgery and lesions causative of reoperation. In the group without residual disease (n = 31), 29.0% (n = 9) had non-anastomotic lesions involved in indications for reoperation, while that was 35.7% (n = 5) in the group with residual disease (n = 14).
Conclusions
Anastomotic site lesion is not the only causative factor for reoperation following ICR. Regular examinations and applicable treatment with awareness that the cause of reoperation is not limited to the site of anastomosis are important in these cases.
Pulmonary Epithelial–Myoepithelial Carcinoma Without AKT1, HRAS or PIK3CA Mutations: A case report
Authors: Yanagawa Naoki , Sato Ayaka , Nishiya Masao , Suzuki Masamichi , Sugimoto Ryo , Osakabe Mitsumasa , Uesugi Noriyuki , Saito Hajime , Sugai Tamotsu 
Published: June 2020

Abstract
Background: Pulmonary epithelial–myoepithelial carcinoma is a rare subtype of lung cancer. Because of its rarity, the molecular information on this carcinoma is insufficient.Case presentation: We report a case of pulmonary epithelial–myoepithelial carcinoma without AKT1, HRAS or PIK3CA mutations in a 76-year-old woman. Computed tomography revealed a tumor located in the left lower lung. Thoracoscopic left lower lobectomy was performed. Histopathologically, the tumor consisted of duct-like structures and polygonal-to-spindle-cell features. The duct-like structures were composed of two distinct cell layers. Immunohistochemically, the inner layer consisted of cuboidal cells that were positive for pan-cytokeratin and negative for p63, whereas the outer layer consisted of polygonal and spindle cells that were positive for p63 and weakly positive for pan-cytokeratin. We evaluated mutations in AKT1, BRAF, CTNNB1, HRAS, KRAS and PIK3CA but did not detect any mutations.Conclusion: Pulmonary epithelial–myoepithelial carcinoma is a rare subtype of lung cancer, with only 56 previous cases reported in the English literature. The genetic alterations in pulmonary epithelial–myoepithelial carcinoma are still unclear. To our knowledge, only one study described HRAS mutations in pulmonary epithelial–myoepithelial carcinoma, detected in all three tumors evaluated. However, our case did not show any mutations in any of the above-examined genes.
Ultrasonographic Diagnosis of Rare Primary Cervical Cancer
Authors: Li Jiaoling , Gu Congmin , Zheng Haiqing , Liu Xiaofang , Geng Xiuping , Wu Haiying 
Published: June 2020

Abstract
Background: To summarize ultrasonographic features of rare primary and common cervical cancer and the association of these cancers with HPV infection so as to diagnose rare primary cervical cancer.METHODS: Sixty-five cases with cervical cancer suspected by ultrasonography and three cases with clinical symptoms treated at our department underwent cervical biopsy. Sixty-four diagnosed cases were retrospectively analyzed and divided into common-type (CTCC) and rare-type (RTCC) cervical cancers.RESULTS: Sixty-one cases were diagnosed, four misdiagnosed, three missed the diagnosis by ultrasonography, the sensitivity of which was 95.31% (61/64). The common-type cervical cancer had 43 cases of squamous cell carcinoma. The rare-type cervical cancer had 15 cases of adenocarcinoma, four of small-cell carcinoma, and two of adenosquamous carcinoma. The demographic characteristics of the two groups were not significantly different (P > 0.2). The tumor size in RTCC was smaller than those in CTCC (P < 0.05). Hypoechoic lesions in CTCC and isoechoic lesions in RTCC composed 74.42% (32/43) and 61.90% (13/21), respectively (P < 0.001). Exophytic in CTCC and endophytic in RTCC composed 67.44% (29/43) and 66.67% (14/21), respectively (P = 0.01). HPV infection composed 83.72% (36/43) in CTCC and 47.62% (10/21) in RTCC, respectively (P = 0.003). Color Doppler blood signals were found in all cases, as compared with normal cervical tissue. The consistency between ultrasonography and pathology staging diagnosis of RTCC was good (Weighted kappa (95%CI) = 0.87).CONCLUSION: Most of patients in RTCC have isoechoic lesions. There is a good consistency between ultrasonography and pathology staging diagnosis of RTCC.
Co-infection of SARS-CoV-2 with Chlamydia or Mycoplasma pneumoniae: a case series and review of the literature
Authors: Oliva Alessandra , Siccardi Guido , Migliarini Ambra , Cancelli Francesca , Carnevalini Martina , D'Andria Maria , Attilia Ilenia , Danese Vittoria Carmela , cecchetti Veronica , Romiti Roberto , Ceccarelli Giancarlo , Mastroianni Claudio M , Palange Paolo , Venditti M. , Venditti M. 
Published: June 2020

Abstract
The novel coronavirus SARS-CoV-2 has spread all over the world causing a global pandemic and representing a great medical challenge. Nowadays, there is limited knowledge on the rate of co-infections with other respiratory pathogens, with viral co-infection being the most representative agents. Co-infection with Mycoplasma pneumoniae has been described both in adults and pediatrics whereas only 2 cases of Chlamydia pneumoniae have been reported in a large US study so far. In the present report, we describe a series of 7 patients where co-infection with C. pneumoniae (n=5) or M. pneumoniae (n=2) and SARS-CoV-2 was detected in a large teaching hospital in Rome. An extensive review of the updated literature regarding the co-infection between SARS-CoV-2 and these atypical pathogens is also performed.
Awareness and Impact of Hydroxychloroquine / Chloroquine prophylaxis among the Healthcare Workers during the COVID-19 Pandemic: An observational study.
Authors: Dhamija Silky , Joshi Yayati , Nandhakumar Amar 
Published: June 2020

Abstract
Background Various modalities are under study for prevention and treatment of novel coronavirus. One such modality is use of Hydroxychloroquine/Choloroquine. The objective of survey was to understand the awareness and impact of HCQ/CQ prophylaxis among the health care workers (HCWs) including surgeons and anaesthetists.Methods A web-based, cross-sectional survey was conducted for HCWs globally. Participation was voluntary and confidentiality was maintained by making participants' information anonymous. The questionnaire consisted of 28 items. Data were tabulated in excel, and descriptive statistics were performed. Results Survey was taken by 344 HCWs from all over the world. 98% participants heard about the use of HCQ/CQ prophylaxis against COVID 19 infection. 301 HCWs knew about the side effects of HCQ/CQ. 54 1% participants agree there is not adequate research done. 122 participants took HCQ/CQ prophylaxis. Out of 29 5% participants who received the medicine from hospital under hospital protocol, 66 7% were given medication without baseline investigations and 30 5% HCWs were not even briefed about the drug and its side effects by the hospitals. 36 2% participants developed side effects. 8 7% HCWs were tested for COVID19 out of 344 participants.Conclusion The drug taken by HCWs was without adequate evidence, prior investigations, supervision and follow-up. Most of the participants self prescribed the drug. No separate guidelines were stated for people who had co-morbid conditions. Hospitals neither conducted baseline investigations and nor briefed HCWs about HCQ/CQ. These are some serious concerns we are looking into as who will be answerable in case of adverse events.
The quest for better machine learning models to forecast COVID-19-related infections: A case study in the state of Pará-Brazil
Authors: Torres Renato Hidaka , Soares Wilson Rogério , Ohashi Orlando Shigueo , Pessin Gustavo 
Published: June 2020

Abstract
COVID-19 disease has become an unprecedented public health crisis. Although a relatively small percentage of people require intensive care, due to the high degree of contagion of the disease, the public system quickly collapses. Due to the highly complex nature of this disease and variation in its behavior depending on the characteristics of each geographic region, in this work, we analyze data from the Amazon region in Brazil (Pará). We applied several machine learning models to forecast the contagious curve to up 10 days. The Linear SVM and Multilayer Perceptron presented the best overall performances. Until the discovery of a vaccine, every effort is needed to understand and anticipate this disease.
Detection of COVID-19 Cases In Chest X-ray Images Using Wavelets And Support Vector Machines
Authors: Sarhan Ahmad M 
Published: June 2020

Abstract
This paper presents a novel technique for the detection of COVID-19 cases in chest X-ray scans. The proposed system uses the Wavelet transform (WT) to find discriminative features in the X-ray images and Support Vector Machines (SVM) to classify the extracted features. The WT is well-known for its energy compression capability. The proposed system preprocesses the chest X-ray image with WT which produces a set of approximation coefficients that include a limited number of high-magnitude coefficients. The proposed system introduces a novel threshold scanning technique that extracts only selected high-energy approximation coefficients. The thresholded coefficients are encoded using a modified version of the run-length encoding (RLE) scheme. The resulting code vector is used as the features representing the input image. These limited features are then presented to a SVM for classification (normal or COVID-19). The use of limited features in the proposed system significantly simplifies the work of the SVM classifier and increases its accuracy. Another advantage of diminishing the number of features is the reduction of the time complexity of the system. The proposed system produces a maximum accuracy of 94.5% when the decomposition level is 2 and the threshold level is 903.