bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Production and Secretion of Potentially Toxigenic Extracellular Proteins From A Hypervirulent Strain of Aeromonas Hydrophila
Authors: Barger Priscilla Carmen , Liles Mark R , Beck Benjamin H , Newton Joseph C 
Published: September 2020

Abstract
Background: Hypervirulent Aeromonas hydrophila (vAh) is a pathogen in freshwater aquaculture that results in the loss of over 3 million pounds of marketable channel catfish, Ictalurus punctatus, and catfish hybrids (I. punctatus, ♀ x blue catfish, I. furcatus, ♂) each year from freshwater catfish production systems in Alabama, U.S.A. vAh isolates are clonal in nature and are genetically unique from, and significantly more virulent than, traditional A. hydrophila isolates from fish. Even with the increased virulence, natural infections cannot be reproduced in aquaria challenges making it difficult to determine modes of infection and the pathophysiology behind the devastating mortalities that are commonly observed. Despite the intimate connection between environmental adaptation and plastic response, the role of environmental adaption on vAh pathogenicity and virulence has not been previously explored. In this study, secreted proteins of vAh cultured as free-living planktonic cells and within a biofilm were compared to elucidate the role of biofilm growth on virulence. Results: Functional proteolytic assays found significantly increased degradative activity in biofilm secretomes; in contrast, planktonic secretomes had significantly increased hemolytic activity, suggesting higher toxigenic potential. Intramuscular injection challenges in a channel catfish model showed that in vitro degradative activity translated into in vivo tissue destruction. Identification of secreted proteins by HPLC-MS/MS revealed the presence of many putative virulence proteins under both growth conditions. Biofilm grown vAh produced higher levels of proteolytic enzymes and adhesins, whereas planktonically grown cells secreted higher levels of toxins, porins, and fimbrial proteins. Conclusions: This study is the first comparison of the secreted proteomes of vAh when grown in two distinct ecological niches. These data on the adaptive physiological response of vAh based on growth condition increase our understanding of how environmental niche partitioning could affect vAh pathogenicity and virulence. Increased secretion of colonization factors and degradative enzymes during biofilm growth and residency may increase bacterial attachment and host invasiveness, while increased secretion of hemolysins, porins, and other potential toxins under planktonic growth (or after host invasion) could result in increased host mortality. The results of this research underscore the need to use culture methods that more closely mimic natural ecological habitat growth to improve our understanding of vAh pathogenesis.
Neutrophil-to-lymphocyte ratio has limited predictive value for determining outcomes in perforated colon cancer: a retrospective study.
Authors: Wu Chunyi , Chiang Jy-Ming , You Jeng-Fu , Tang Reiping , Chen Jinn-Shiun , Yeh Chien-Yuh , Hsieh Pao-Shiu , Tsai Wen-Sy , Hung Hsin-Yuan , Chiang Sum-Fu , Lai Cheng-Chou 
Published: September 2020

Abstract
Background: The neutrophil-to-lymphocyte ratio (NLR) is a significant prognostic marker in resectable colorectal cancer; however, there are no equivalent findings for perforated colon cancer. Using our colorectal cancer database, we retrospectively analyzed the data from 1995 to 2015 to determine if preoperative NLR was associated with survival outcomes in patients with perforated colon cancer. Methods: One-to-one propensity score matching (PSM) was applied to minimize the difference between the higher- (>5) and lower- (≤5) NLR groups. Clinicopathological factors, long-term overall survival (OS), and disease-free survival (DFS) were analyzed and compared between the two groups. The main outcome measures were OS and DFS. Results: Before PSM, the higher-NLR group had significantly higher prevalence of leukocytosis (lower- vs. higher-NLR groups: 12 [12.9%] vs. 46 [59.7%], p<0.001), lower serum albumin levels (lower- vs. higher-NLR groups: 30 [32.3%] vs. 42 [54.5%], p=0.003), and higher emergent operation rate (lower- vs. higher-NLR groups: 5 [5.4%] vs. 20 [26.0%], p<0.001). After one-to-one PSM, the groups comprised 41 patients each; none of the parameters were significantly different. The mean follow-up period was 76.3 months. Five-year OS and DFS were not significantly different (OS: p=0.637; DFS: p=0.827) between the higher- and lower-NLR groups. Conclusion: NLR have limited predictive value for outcomes in patients with perforated colon cancer.
A New Risk Score Model Based on Lactate Dehydrogenase Predicting Prognosis in Esophageal Squamous Cell Carcinoma Treated With Chemoradiotherapy
Authors: Han Jinmin , Zhou Tao , Liu Chengxin , Li Baosheng 
Published: September 2020

Abstract
Purpose: The current study was to assess the prognostic value of the lactate dehydrogenase (LDH) in esophageal squamous cell cancer (ESCC) patients and to generate a risk score model to predict prognosis in patients who undergone chemoradiotherapy.
Patients and Methods: 614 ESCC patients who received chemoradiotherapy were performed from 2012 to 2016.The optimal cutoff points for continuous variables were calculated by the X-tile program. We analyzed the association between LDH level and clinicopathological characteristics. And a 1:3 propensity score matching analysis was used to compensate for differences in baseline characteristics. The Kaplan-Meier methods and Cox regression models were used to explore the prognostic factors for overall survival (OS) and progression-free survival (PFS). Based on the results, we developed a corresponding risk score model and assessed its predictive capacity in the subgroups.
Results: The optimal cutoff points of age, CEA, Cyfra21-1, tumor length, total dose and LDH were defined as follows:69 years, 2.4 ng/ml, 6.4 ng/ml, 6.5 cm, 58.8Gy and 134 U/L, respectively. A high level of LDH was associated with advanced M stage (p=0.005) and larger tumor length (p=0.026). Patients in the high-LDH group had shorter PFS and worse OS than those in the low-LDH group. Multivariate survival analysis indicated that pretreatment serum LDH level (p=0.039)，Cyfra21-1 level (p=0.003), tumor length (p=0.013), clinical N stage (p=0.047) and clinical M stage (p=0.011) were independent predictors for OS. Furthermore, a risk score model based on these five prognostic factors was established to divide patients into three groups with obvious prognosis (χ2 = 20.53, p< 0.0001).
Conclusion: Pretreatment serum LDH levels may be a reliable factor in predicting the therapeutic effect of chemoradiotherapy in ESCC. A risk score model combined LDH, Cyfra21-1 and other prognostic factors could help to guide a personalized management. Further validation is needed before widely used in clinical practice.
Hypofractionated Proton Beam Radiotherapy in Patients With Unresectable Liver Tumors: Multi-institutional Prospective Results From the Proton Collaborative Group
Authors: Parzen Jacob S , Hartsell William , Chang John , Apisarnthanarax Smith , Molitoris Jason , Durci Michael , Tsai Henry , Urbanic James , Ashman Jonathan , Vargas Carlos , Stevens Craig , Kabolizadeh Peyman 
Published: September 2020

Abstract
Background: Recent advances in radiotherapy techniques have allowed ablative doses to be safely delivered to inoperable liver tumors. In this setting, proton beam radiotherapy (PBT) provides the means to escalate radiation dose to the target volume while sparing the uninvolved liver. This study evaluated the safety and efficacy of hypofractionated PBT for liver tumors, predominantly hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC).Methods: We evaluated the prospective registry of the Proton Collaborative Group for patients undergoing definitive PBT for liver tumors. Demographic, clinicopathologic, toxicity, and dosimetry information were compiled.Results: To date, 63 patients have been treated at 9 institutions between 2013-2019. Thirty (48%) had HCC and 25 (40%) had ICC. The median dose and biological equivalent dose (BED) delivered was 58.05 GyE (range, 32.5-75) and 80.5 GyE (range, 53.6-100), respectively. The median mean liver BED was 13.9 GyE. Three (4.8%) patients experienced at least one grade ³3 toxicity. With median follow-up of 5.1 months (range, 0.1-40.8), the local control (LC) rate at 1 year was 91.2% for HCC and 90.9% for ICC. The 1-year LC was significantly higher (95.7%) for patients receiving BED greater than 75.2 GyE than for patients receiving BED of 75.2 GyE or lower (84.6%, p = 0.029). The overall survival rate at 1 year was 65.6% for HCC and 81.8% for ICC. Conclusions: Hypofractionated PBT results in excellent LC, sparing of the uninvolved liver, and low toxicity, even in the setting of dose-escalation. Higher dose correlates with improved LC, highlighting the importance of PBT especially in patients with recurrent or bulky disease.
Identification of Long Non-Coding RNAs Involved in Fat Deposition in Pigs Using Two High-Throughput Sequencing Methods
Authors: Liu Yibing , Ao Hong , Zhang Fengxia , Zhao Xitong , Liu Huatao , Shi Yong , Xing Kai , Yu Ying , Wang Chuduan 
Published: September 2020

Abstract
Background: Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been proven in previous studies. In this study, we focused on lncRNAs associated with fattening traits in pigs. The adipose tissue of six Landrace pigs with either extremely-high or -low backfat thickness ( n high = 3, n low = 3) was collected, after which we performed strand-specific RNA sequencing using biological replicates and pooling methods. Results: A total of 19,631 genes and 2,013 lncRNAs were identified using the coding potential calculator, coding-non-coding index, and Pfam database, including 334 known transcripts and 1,679 novel transcripts. Using edgeR, we determined that 220 lncRNAs and 1,512 genes were differentially expressed (|Fold Change| > 2 and false discovery rate < 0.05) between the two groups in biological replicate RNA sequencing (RNA-seq), and 127 lncRNAs and 2,240 genes were differently expressed in pooling RNA-seq. Further Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analysis of the differentially expressed genes found that some of the genes were involved in several key pathways related to fat development. After targeting gene prediction, we determined that some cis-target genes of the differentially expressed lncRNAs play an important role in fat deposition. For example, ACSL3 is cis-targeted by lncRNA TCONS-00052400, and it can activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 was up-regulated in the high backfat thickness group, and its cis-target gene ACACB was also up-regulated in this group. It has been reported that ACACB is the rate-limiting enzyme in fatty acid oxidation. Conclusions: Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect fat deposition in pigs through regulation of their target genes. In summary, our study explored the regulation of lncRNA and their target genes on fat deposition in pigs and provided new insights for further investigation of the biological functions of lncRNA.
Synthesis,Surface Morphology, Optical Properties and Photocatalyst Activities of TiO2/ZnO/Fe2O3 Nanocomposites.
Authors: Parambil Juliya Acha , V.M Abdul Mujeeb , Karazhanov S. Zh. , Peediyekkal Jayaram 
Published: September 2020

Abstract
The photocatalytic degradation of methylene blue in aqueous solutions is enhanced significantly by formulating multiphase TiO2/ZnO/Fe2O3 nanocomposites. The photocatalytic activity of unary TiO2, binary TiO2/ZnO, and ternary TiO2/ZnO/Fe2O3 compounds are compared and reported. Using TiO2/ZnO/Fe2O3, methylene blue degradation became rapid and the reaction followed first-order kinetics. The consequences of the phase transition, surface features, and optical properties are compared and elucidated. The reduced photoluminescence intensity and decreased optical band gap energy in tertiary compounds impose higher degradation of methylene blue under irradiation.
Cell Banking of HEK293T Cell Line for Clinical-Grade Lentiviral Particles Manufacturing
Authors: Perpiña Unai , Herranz Cristina , Martin-Ibañez Raquel , Boronat Anna , Chiappe Felipe , Monforte Verónica , Orpella-Arecet Gemma , González Ester , Olive Myriam , Castella María , Suñe Guillermo , Urbano-Ispizua Alvaro , Delgado Julio , Juan Manel , Canals Josep M. 
Published: September 2020

Abstract
Background: Cell banks have been widely used to preserve cell properties as well as to record and control cell line access in research. However, the generation of cell banks involved in the manufacturing of Advanced therapy medicinal products such as cell or gene therapy products must comply with the current Good Manufacturing Practice regulation. Similarly, the quality of those cell lines used as starting materials in viral-vector manufacturing processes must be also evaluated.Methods: Three batches of both Master Cell Bank and Working Cell Bank of the HEK293T cell line were manufactured under the current Good Manufacturing Practices regulation. Quality control test were performed according to the product specifications. The process validation includes previous qualification of the manufacturing personnel by performing simulation tests as well as the continuous measure of environmental parameters during manufacturing such as air particles and microorganism. Cell number and viability of cryopreserved cells were periodically measured in order to define the stability of these cellular products.Results: All batches of Master Cell Bank and Working Cell Bank fulfilled the acceptance criteria of their specifications showing the robustness and homogeneity of the processes. In addition, both Master and Working cell bank maintain the defined viability and cell number 37 months after cryopreservation. Conclusions: Manufacturing cell banks under Good Manufacturing Practices regulation for its use as raw material or final cellular product is feasible. HEK293T cell banks have been used to manufacture clinical-grade lentiviral particles for Chimeric Antigen Receptor T-cell based clinical trials.
Identification of the Role of GLS2&nbsp;in&nbsp;the Development and Progression of Clear Cell Renal Cell Carcinoma.
Authors: sun dantong , tian lu , wo yang , zhao han , yan weihua , wei xiaojuan , Li Hong , Hou Helei 
Published: September 2020

Abstract
Background The incidence of RCC has drastically increased in recent years. The large intratumor heterogeneity of RCC, especially ccRCC, usually leads to treatment failure. In addition, single biomarkers have a limited ability to predict prognosis. Therefore, we performed this study to select variables and provided a simple but efficient way to predict prognosis.MethodThree studies from GEO database were involved in the DEGs selection. A total of 840 RCC patients and 524 ccRCC patients from TCGA database were involved in the prognostic analyses. Nomograms based on Cox regression model were used to select variables to predict the prognosis, and GSEA was used to demonstrate the potential pathways altered by gene expression.ResultOur study suggested that DEGs existed between metastatic and primary tumor tissues. Loss of GLS2 was related to poor prognosis in RCC and ccRCC. These results revealed that GLS2 expression, combined with basic characteristics, including age and TNM stage, could efficiently predict prognosis. GLS2 serves as a tumor suppressor in ccRCC, loss of GLS2 function endows cells with oncogenic functions and is related to advanced disease. According to the GSEA results, loss of GLS2 function may alter the cell cycle by activating the E2F pathway.ConclusionGLS2 is a tumor suppressor in RCC. Loss of GLS2 function in ccRCC predicts a poor prognosis via the underlying E2F pathway. Nomograms based on DEGs and clinical features provide physicians with a simple but efficient way to predict prognosis. Further studies are needed to verify the pathway in our study.
Characteristics and outcomes of culture-negative versus culture-positive with fungus in sepsis patients: a retrospective analysis of the MIMIC-III database
Authors: Zou Zhiye , Wu Ming 
Published: September 2020

Abstract
BACKGROUND: We compared the characteristics of culture-positive and culture-negative with fungi in septic patients to determine whether fungi culture status is associated with mortality and the relationship between antifungal therapy and sepsis patient mortality.METHODS: The study was based on the Medical Information Mart for Intensive Care (MIMIC) III database, we included all intensive care unit (ICU) admissions between 2001 and 2012 with sepsis, which met the Martin’s criteria. The primary outcome was hospital mortality. Secondary outcomes included the usage of antifungal drugs, duration of mechanical ventilation and hospital stay. Multivariable logistic regression and propensity score matching were used to investigate any association.RESULTS: The study population included 836 fungi-positive patients (16.6%) and 4191 fungi-negative patients (83.4%). Fungi-positive patients had more congestive heart failure and chronic pulmonary, higher sequential organ failure assessment (SOFA), and more need for renal replacement therapy on day one than fungi-negative patients. There was no correlation between antifungal therapy and hospital mortality (adjusted odds ratio = 1.03, 95% CI [0.89, 1.20]; P=0.676）. Hospital mortality was lower in the fungi-negative group (25.5%) than in the fungi-positive group (37.3%, P<0.001). After propensity score matching, 613 cases from each group were matched. The hospital mortality remained significantly higher in the fungi-positive group (167/613 vs. 216/613, p=0.003).CONCLUSIONS: Although residual confounding cannot be excluded, significant differences between fungi-positive and fungi-negative sepsis are identified, with the former group having more comorbidities, worse severity of illness, longer hospitalizations, and higher mortality. Antifungal therapy does not affect the outcome.
An External Pilot Cluster Randomised Controlled Trial of a Theory-based Intervention to Improve Appropriate Polypharmacy in Older People in Primary Care (Polyprime): Study Protocol
Authors: Rankin Audrey , Cadogan Cathal A , Barry Heather E , Gardner Evie , Agus Ashley , Molloy Gerard J , Gorman Ashleigh , Ryan Cristín , Leathem Claire , Maxwell Marina , Gormley Gerard J , Ferrett Alan , McCarthy Pat , Fahey Tom , Hughes Carmel M 
Published: September 2020

Abstract
Background: The use of multiple medications (polypharmacy) is a concern in older people (≥65 years) and is associated with negative health outcomes. For older populations with multimorbidity, polypharmacy is the reality and the key challenge is ensuring appropriate polypharmacy (as opposed to inappropriate polypharmacy). This external pilot cluster randomised controlled trial (cRCT) aims to further test a theory-based intervention to improve appropriate polypharmacy in older people in primary care in two jurisdictions, Northern Ireland (NI) and the Republic of Ireland (ROI).Methods: Twelve GP practices across NI (n=6) and the six counties in the ROI that border NI will be randomised to either the intervention or usual care group. Members of the research team have developed an intervention to improve appropriate polypharmacy in older people in primary care using the Theoretical Domains Framework of behaviour change. The intervention consists of two components: 1) an online video which demonstrates how a GP may prescribe appropriate polypharmacy during a consultation with an older patient; and 2) a patient recall process, whereby patients are invited to scheduled medication review consultations with GPs. Ten older patients receiving polypharmacy (≥4 medications) will be recruited per GP practice (n=120). GP practices allocated to the intervention arm will be asked to watch the online video and schedule medication reviews with patients on two occasions; an initial and a 6-month follow-up appointment. GP practices allocated to the control arm will continue to provide usual care to patients. The study will assess the feasibility of recruitment, retention and study procedures including collecting data on medication appropriateness (from GP records), quality of life and health service use (i.e. hospitalisations). An embedded process evaluation will assess intervention fidelity (i.e. was the intervention delivered as intended), acceptability of the intervention and potential mechanisms of action.Discussion: This pilot cRCT will provide evidence of the feasibility of a range of study parameters such as recruitment and retention, data collection procedures and the acceptability of the intervention. Pre-specified progression criteria will also be used to determine whether or not to proceed to a definitive cRCT.Trial registration: ISRCTN, ISRCTN41009897. Registered 19 November 2019, https://doi.org/10.1186/ISRCTN41009897. Clinicaltrials.gov, NCT04181879. Registered 02 December 2019, https://clinicaltrials.gov/ct2/show/NCT04181879.
Do they really wash their hands? Prevalence estimates for personal hygiene behaviour during the coronavirus crisis based on indirect questions
Authors: Mieth Laura , Mayer Maike , Hoffmann Adrian , Buchner Axel , Bell Raoul 
Published: September 2020

Abstract
Background: During the so-called coronavirus crisis, billions of people have to change their behaviours to slow down the pandemic. Protective measures include self-isolation, social (physical) distancing and compliance with personal hygiene rules, particularly regular and thorough hand washing. To adjust public information campaigns to the level of people’s commitment and to evaluate the effectiveness of these campaigns, valid information about the degree to which people comply with protective measures is desirable.Methods: However, during a health crisis there is strong public pressure to comply with health and safety regulations so that people’s responding in direct questionings may be seriously compromised by social desirability. Here we use an indirect questioning technique to test whether the prevalence of hygiene practices may be lower when confidentiality of responding is guaranteed.Results: In the direct questioning group 94.5 % of the participants claimed to practice proper hand hygiene; in the indirect questioning group a significantly lower estimate of only 78.1 % was observed.Conclusions: These results indicate that estimates of the degree of commitment to measures designed to counter the spread of the disease may be significantly inflated by social desirability in direct questionings. Indirect questioning techniques with higher levels of confidentiality seem helpful in obtaining more realistic estimates of the degree to which people follow the recommended personal hygiene measures.