bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deregulated Immune Pathway Associated with Palbociclib Resistance in Preclinical Breast Cancer Models: Integrative Genomics and Transcriptomics
Authors: PANDEY KAMAL , Lee Eunbyeol , Park Nahee , Hur Jin , Cho Young Bin , Kim Seung Ki , Lee Seung Ah , Kim Isaac , An Hee-Jung , Hwang Sohyun , Wha Yong Wha 
Published: August 2020

Abstract
Background: Recently, cyclin-dependent kinase (CDK) 4/6 inhibitors have been widely used to treat advanced hormone receptor-positive breast cancer. Despite promising clinical outcomes, almost all patients eventually acquire resistance to CDK4/6 inhibitors. Hence, understanding the mechanisms of acquired resistance to CDK4/6 inhibitors is crucial for developing alternative treatment strategies. Therefore, the present study screened genes associated with palbociclib resistance through genomics and transcriptomics in preclinical breast cancer models. Methods: Palbociclib-resistant cells, MCF7-PR and T47D-PR, were generated by exposing MCF7 and T47D cells to palbociclib. After confirming acquired resistance through in vitro assays, whole-exome sequencing (WES) and mRNA microarray were performed to compare the genomic and transcriptomic landscape between palbociclib-sensitive and resistant cells. Real time-PCR was performed to confirm differentially expressed genes.Results: Microarray analysis comparing MCF7 and MCF7-PR cells revealed 651 differentially expressed genes (DEGs) (fold change >2 or <0.5), while WES comparing T47D and T47D-PR cells revealed 107 mutated genes. Furthermore, pathway analysis of both DEGs and mutated genes revealed immune pathway deregulation commonly observed in MCF7-PR and T47D-PR cells. Notably, DEG annotation revealed activation of type I interferon pathway, activation of immune checkpoint inhibitory pathway, and suppression of immune checkpoint stimulatory pathway in palbociclib-resistant cells. Moreover, mutations in NCOR1, MUC4 and MUC16 genes found in palbociclib-resistant cells were annotated to be related to the immune pathway. Conclusions: Palbociclib resistance was found to be associated with deregulated immune pathway in preclinical breast cancer models. Further studies are warranted to evaluate whether immune pathways may be a therapeutic target to overcome CDK4/6 inhibitor resistance.
Killing process on the nutrient content, product stability and in vitro digestibility of black soldier fly (Hermetia illucens) larvae meals
Authors: Zhen Yongkang , Kovitvadhi Attawit , Chundang Pipatpong , Zhang Yu , Wang Mengzhi , Vongsangnak Wanwipa , Pruksakorn Chantima 
Published: August 2020

Abstract
BACKGROUNDBlack soldier fly (BSF; Hermetia illucens) is considered as a potential sustainable insect alternative source of protein for animal feed; however, the quality of BSF meal is greatly influenced by the killing method. Therefore, the purpose of this article is to compare the quality of BSF obtained by different killing methods.RESULTSBSF at the 18-day-old prepupae stage were separated into six different killing methods (n = 3): 1. blending, 2. freezing, 3. CO2 treatment, 4. vacuum, 5. Blanching and 6. humane method. After killing, were obtained by hot air oven drying and grinding. The chemical composition and in vitro digestibility calculated from sediment was not affected by the killing method, except that blending provided the worst BSF quality for all measured parameters (P < 0.05). The highest quality of BSF was obtained from the heat treatment procedures (blanching and the humane method), as they produced lower acidity after killing, total viable counts, browning reaction (enzymatic and non-enzymatic), darkness, moisture, fat acidity, protein and lipid oxidation during storage compared with other killing procedures (P < 0.05). Interestingly, the highest of free amino acids in the supernatant after in vitro digestibility of BSF samples was observed with the humane killing method (P < 0.05), whereas other parameters were similar to those obtained with blanching.CONCLIUSIONBlanching and humane method produce BSF with the nutritional quality, safety and stability. humane method did not produce clearly different outcomes to blanching; therefore, the selection of one of these techniques over the other should depend on the regulations in each country.
Repeatability of Two Artificial Intelligence Approaches for Tumor Segmentation in PET
Authors: Pfaehler Elisabeth , Mesotten Liesbet , Kramer Gem , Thomeer Michiel , Vanhove Karolien , de Jong Johan , Adriaensens Peter , Hoekstra Otto S. , Boellaard Ronald 
Published: August 2020

Abstract
Background: Positron Emission Tomography (PET) is routinely used for cancer staging and treatment follow up. Metabolic active tumor volume (MATV) as well as total MATV (TMATV - including primary tumor, lymph nodes and metastasis) and/or total lesion glycolysis (TLG) derived from PET images have been identified as prognostic factor or for the evaluation of treatment efficacy in cancer patients. To this end a segmentation approach with high precision and repeatability is important. However, the implementation of a repeatable and accurate segmentation algorithm remains an ongoing challenge. Methods: In this study, we compare two artificial intelligence (AI) based segmentation methods with conventional segmentation approaches in terms of repeatability. One segmentation approach is based on a textural feature (TF) segmentation approach designed for accurate and repeatable segmentation of primary tumors and metastasis. Moreover, a Convolutional Neural Network (CNN) is trained. The algorithms are trained, validated and tested using a lung cancer PET dataset. The segmentation accuracy of both segmentation approaches is compared using the jaccard coefficient (JC). Additionally, the approaches are applied on a fully independent test-retest dataset. The repeatability of the methods is compared with the repeatability of two majority vote (MV2, MV3) approaches, 41%SUVMAX, and a SUV>4 segmentation (SUV4). Repeatability is assessed with test-retest coefficients (TRT%) and intraclass correlation coefficient (ICC). A TRT% of 0 indicates perfect repeatability and an ICC>0.9 was regarded as representing excellent repeatability.Results: The accuracy of the segmentations with the reference segmentation was good (JC median TF: 0.7, CNN: 0.73) Both segmentation approaches outperformed together with the MV2 approach the other conventional segmentation methods in terms of test-retest coefficient (TRT% mean: TF: 13.0%, CNN: 13.9%, MV2: 14.1%, MV3: 28.1%, 41%SUVMAX: 28.1%, SUV4: 18.1% ) and ICC (TF: 0.98, MV2: 0.97, CNN: 0.99, MV3: 0.73, SUV4: 0.81, and 41%SUVMAX: 0.68).Conclusion: The AI based segmentation approaches used in this study provided better repeatability than conventional segmentation approaches. Moreover, both algorithms lead to accurate segmentations for both primary tumors as well as metastasis and are therefore good candidates for PET tumor segmentation.
Pregnancy-Related Ecological Shifts of Salivary Microbiota and its Association with Salivary Sex Hormones
Authors: Niu Chenguang , Dong Ting , Jiang Wenxin , Gao Li , Yuan Keyong , Hu Xuchen , Lin Wenzhen , Zhou Xuedong , Xu Changen , Huang Zhengwei 
Published: August 2020

Abstract
Background: The interactions between hosts, oral microbiomes and microenvironments have been the subject of much research in recent years. Yet, whether the alterations in the host impact the oral microbiome is not understood well. The fluctuation of sex hormone levels during pregnancy is a dramatic change in the host, and is closely related to pregnancy-associated gingivitis. In this study, salivary estradiol and progesterone level were measured at three trimesters of pregnancy and after delivery (t1: ≤ 14weeks；t2: 20–25 weeks；t3: 33–37 weeks; t4: 42 days after delivery) from 11 pregnant and 7 non-pregnant volunteers, and their salivary microbiome were collected and profiled by 16S rDNA gene sequencing. Results: The diversity of the salivary microbiome increased significantly in t3, compared to the t1 (P<0.05), and a close parallel to the shift is found in the elevation of salivary sex hormones. Addionally, Capnocytophaga gingivalis, Peptoniphilus sp.oral taxon 386, Prevotella baroniae, Simonsiella muelleri and Lactobacillus reuteri were correlated to the fluctuation of sex hormone levels. Conclusions: The diversity of the salivary microbiome in pregnant women was elevated with the gestation weeks, which was found parallel to the changes in estradiol and progesterone levels in saliva. Rather than highly abundant bacteria, the low abundant bacteria were more vulnerable to the host impact.
Patterns of Flea Infestation in Rodents and Insectivores From Intensified Agro-ecosystems, Nw Spain
Authors: Herrero-Cófreces Silvia , Flechoso Manuel Fabio , Rodríguez-Pastor Ruth , Luque-Larena Juan José , Mougeot Francois 
Published: August 2020

Abstract
Background: Fleas frequently infest small mammals and play important vectoring roles in the epidemiology of (re)emerging zoonotic disease. Rodent outbreaks in intensified agroecosystems of NW Spain have been recently linked to periodic zoonotic disease spillover to local human populations. Obtaining qualitative and quantitative information about the composition and structure of the whole flea and small mammal host coexisting communities is paramount to understand disease transmission cycles and to dilucidate the disease-vectoring role of flea species. Methods: Here we report on a large spatial (6 locations) and temporal (6 years with 3 samplings/year) survey conducted in intensively farmed landscapes in NW Spain, aiming to: (i) characterise the flea community parasitizing the small mammal host guild (Microtus arvalis, Apodemus sylvaticus, Mus spretus, Crocidura russula) in terms of flea-host specificity, abundance, prevalence, intensity and aggregation; (ii) evaluate patterns of co-infection by different flea species in hosts; and (iii) study the variation of flea abundance according to season and host sex. Results: Three flea species dominated the system (99.4%): Ctenophthalmus apertus, Leptopsylla taschenbergi and Nosopsyllus fasciatus. Results showed a high aggregation pattern of fleas in all hosts. C. apertus and N. fasciatus were shared by all host species in the guild, but L. taschenbergi mainly parasitized mice (M. spretus, A. sylvaticus). We found significant male-bias infestation patterns in mice, and significant seasonal variations in flea abundances for all rodent hosts (M. arvalis, M. spretus, A, sylvaticus). Simultaneous infections by 2 or 3 flea species were found in 36.8% of all hosts, and N. fasciatus was the most common flea co-infecting hosts. Conclusions: Our study shows that flea infestation patterns differ among hosts and seasons, influencing their potential vectoring role of diseases. Further investigation should be carried out on abundant and polyphagous fleas (e.g. N. fasciatus), since they may have higher competence to circulate zoonoses in natural systems.
Impact Involving the Community in Entomological Surveillance of the Triatoma Infestans Vectorial Control
Authors: Abrahan Luciana , Cavallo Maria José , Amelotti Ivana 
Published: August 2020

Abstract
BackgroundVectorial transmission is the principal way of Trypanosoma cruzi infection, the parasite that cause Chagas disease. In Argentina, Triatoma infestans is the principal vector, for this reason, vector control is the main strategy for the prevention of this illness. Provincial Program of Chagas La Rioja (PPCHLR) carries out entomological evaluation of domiciliary units (UD) and spraying those where T. infestans are found. The lack of government funds generated low visit frequency of PPCHLR, especially in areas with a low infestation that they were not prioritized. For this reason, seeking possible alternatives to complement control activities are necessary. Involving householders in entomologic evaluation would be a control alternative. The major objective was to determine the cost of entomological evaluation with and without community participation.Methods For entomological evaluation with community participation, 434 DU corresponding to nine localities of Castro Barros Department (CBD) were selected in November 2017. T. infestans infestation of DUs selected was determined involving the community in triatomines detection. Each householder was trained in the insect collection that were kept in labelled plastic bags and recovered after two weeks to analyse T. cruzi presence in laboratory. For entomological evaluation without community participation, PPCHLR data collected in February 2017 over 359 DU of CBD were used. Entomological evaluation costs with and without community participation over DU visited number, over DU evaluated number, and over DU sprayed were calculated and compared between methodologies. In addition, DU evaluated number out DU visited number was compared. The infestation in the area was 13.8%, with relative risk differences by zones. ResultsThe results showed that the triatomines did not show evidence of T. cruzi infection. Costs in relation to DU visited, to those evaluated and to those sprayed, were lowered with community participation (p< 0.05). In addition, a greater number of DU evaluated in relation to those visited as well as greater surface were covered with community participation. ConclusionThe participation of the community in the infestation survey is more efficient, allowing the spraying to be focused on infested houses and thus reducing costs and intervention times by PPCHLR.
Detection of Diarrheagenic Pathogens in Improved Water Using PCR-Based Specific Techniques in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis Protocol
Authors: Gemeda Shibabaw Tadesse , Soboksa Negasa Eshete , Desta Adey Feleke , Gari Sirak Robele 
Published: August 2020

Abstract
Background: Effective application of Polymerase Chain Reaction (PCR) based methods in detecting pathogenic microorganisms in improved water samples were limited in low- and middle-income countries. This limitation initiated this systematic review to assess the effective characterization method that could be applied in low- and middle-income countries. Therefore, the aim of this review and analysis is to pullout the available evidences in characterization of pathogenic microorganisms in improved drinking water that could be effectively applied in low- and middle-income countries. Methods: We will search for published literatures using Google Scholar, PubMed or Medline, Scopus and Cochrane Library databases to explore the various PCR based methods recommended for the detection and enumeration of pathogens to examine quality of drinking water provided for communities. All studies conducted in low- and middle-income countries that use any types of PCR methods in water samples without publication date restriction were included in the review. The primary outcome of this study is assessing the magnitude of diarrheagenic pathogens detected in improved water supplies by PCR application in low- and middle-income countries. Critical appraisal will be conducted on all papers selected for inclusion in the review. The studies selected will be assessed by the reviewers for retrieval prior to inclusion in the review. Discussion: This review will systematically discover and integrate the evidence available on the detection of diarrheagenic pathogens through the application of PCR based methods for water quality determination. This facilitates water quality monitoring activities. In this review, information about the applied PCR method, detected diarrheagenic pathogens, water sample size, effectiveness in terms of time and cost, will be gathered and summarized. The findings from this review and analysis will provide compiled data on the magnitude of the detected diarrheagenic pathogenic microbes by type and amount in improved water supply through the application of PCR techniques in low- and middle-income countries. It is envisaged that the study will promote the application of PCR methods for drinking water quality monitoring in these low- and middle-income countries.
4P Model for Dynamic Prediction of Covid-19 with statistical and machine learning approach: Social Dynamics, Government Roles and Pathogen Behavior on Bangladesh Perspective
Authors: Hasan Khandaker Tabin , Rahman Mohammed Mostafizur , Ahmmed Md. Mortuza , Chowdhury Anjir Ahmed , Islam Mohammad Khairul 
Published: August 2020

Abstract
Introduction: Around the world, scientists are racing hard to understand how Covid-19 epidemic is spreading and growing, thus trying to find ways to prevent it before medications come to pass. Many different models have been proposed so far correlating different factors. Some of them are too localized to indicate a general trend of the pandemic while some others have established transient correlations only.Methods: Hence, in this study, a 4P model has been proposed based on four probabilities (4P) which has been found to be true for all affected countries taking Bangladesh as a case. Efficiency scores have been estimated from survey analysis not only for governing authorities on managing the situation (P(G)) but also for the compliance of the citizens ((P(P)). Since the immune responses of all the people are not uniform to a specific pathogen, the probability of a person getting infected ((P(I)) after being exposed has also been estimated. And the vital one is the probability of Test Positivity ((P(T)) which is a strong indicator of how effectively the infected people are diagnosed and isolated from the rest of the group that affects the rate of growth.Results and Conclusion: All the four parameters have been fitted in a non-linear exponential model that partly updates itself periodically with everyday facts. Along with the model, all the four probabilistic parameters are engaged to train a recurrent neural network using Long-Short Term Memory neural network and the followed trial confirmed a ruling functionality of the 4Ps.
Assessment of the direct quantitation of SARS-CoV-2 by droplet digital PCR
Authors: Deiana Michela , Mori Antonio , Piubelli Chiara , Scarso Salvatore , Favarato Mose , Pomari Elena 
Published: August 2020

Abstract
Droplet digital PCR (ddPCR) is a sensitive and reproducible technology widely used for quantitation of several different viruses. The aim of this study was to compare the 2019-nCoV CDC ddPCR Triplex Probe Assay (BioRad) performance on the direct quantitation of SARS-CoV-2 on nasopharyngeal swab respect to the procedure applied to the extracted RNA. Moreover, the two widely used swab types were compared (UTM 3mL and ESwab 1mL, COPAN). A total of 50 nasopharyngeal swabs (n=25 UTM 3mL and n=25 ESwab 1mL) from SARS-CoV-2 patients collected during the pandemic from IRCCS Sacro Cuore Don Calabria Hospital (Veneto Region, North-East Italy) were used for our purpose. After heat inactivation, an aliquot of swab medium was used in order to perform the direct quantitation. Then, we compared the direct method with the quantitation performed on the RNA purified from nasopharyngeal swab by automated extraction. We observed that the direct approach achieved generally equal RNA copies compared to the RNA extracted. The results with the direct quantitation were more accurate on ESwab with a sensitivity of 93.33% [95% CI, 68.05 to 99.83] and specificity of 100.00% for both N1 and N2. On the other hand, on UTM we observed a higher rate of discordant results for N1 and N2. The human internal amplification control (RPP30) showed 100% of both sensitivity and specificity independent of swabs and approaches.In conclusion, we described a simple and fast approach for the quantitation of SARS-CoV-2 in nasopharyngeal swab. Our approach resulted in an efficient quantitation, without automated RNA extraction and purification. However, special care needs to be taken on the potential bias due to the conservation of samples as we used thawed material and to the heating treatment. Further studies on a larger cohort of samples are warranted to evaluate the clinical value of this direct approach.
Intestinal sepsis model of small animals
Authors: Reddy Ramesh , Rao Suman 
Published: August 2020

Objective: The goal of this paper was to develop a model of intestinal sepsis in the investigational animal.
Material and methods. Sprague-Dawley male rats of 4 weeks (N = 42) were used. Initially, a pilot study (N = 12) was performed and distributed in groups with .8 cc inoculum of Escherichia coli ATCC intraperitoneally administered at concentrations of 9, 7, 6. Subsequently, concentrations of 9 CFU are used in two groups of rats with reductions of 11 cc. Finally, a randomized trial of 28 rats was initiated in three treatment groups after intraperitoneal infection. Biological models of blood and peritoneal fluid were observed, and histopathological study of intraperitoneal tissues was done.
Results. Demise of 95% of the rats infected with E. coli UFC concentration was observed. The blood culture and peritoneal fluid culture was positive for the same strain in all of them. The formation of blisters on the liver surface and polymorphonuclear infiltration in organs were detected.
Conclusion. The fatal dose of E. coli should be diluted for intraperitoneal injection.
Saliva as the Stress Biomarker after Fasting Exposure on Adult Girls and Boys
Authors: Devi Arpana , Sharma Kriti , Giri Arup 
Published: August 2020

This experiment was conducted to determine the fasting effects on anthropometric parameters and salivary antioxidant properties in girls and boys. Saliva samples were collected from eighteen healthy girls (control-09 & fasting-09 girls) and twelve healthy boys (control-06 & fasting-06 boys). Saliva was collected four times from all the subjects at a time interval of two hours. For anthropometric parameters, body weight, body temperature, pulse rate (PR), systolic blood pressure (SBP), diastolic blood pressure (DBP) was measured during each saliva collection time. Antioxidant parameters of all the saliva samples were evaluated. Most of the anthropometric parameters like temperature, PR, SBP, and DBP of the fasting group was significantly (p<0.5) decreases than the control group of both boy's and girl's in the different time interval. Antioxidant properties were significantly (p<0.5) higher in the fasting group of girls, but the insignificantly different level was found in the boy's group. This study was indicating that fasting affected the anthropometric parameters (PR, SBP, and DBP), mainly in the girls. Salivary antioxidant properties were mostly lower in the girls' fasting group. Therefore, saliva may be a useful stress biomarker during fasting conditions.