bluuebunny/crossref_metadata_2025_split huggingface dataset:
CNA profiling of single CTCs in locally advanced esophageal cancer patients during therapy highlights unexplored molecular pathways.
Authors: Gallerani Giulia , Rossi Tania , Valgiusti Martina , Angeli Davide , Fici Pietro , De Fanti Sara , Bandini Erika , Cocchi Claudia , Frassineti Giovanni Luca , Bonafè Massimiliano , Fabbri Francesco 
Published: August 2021

Abstract
Locally advanced esophageal cancer (EC) is an aggressive disease with a dismal prognosis. The role of circulating tumor cells (CTC) in the EC metastatic process is still an unaddressed question. Here we monitored the evolution of CTCs spread in 11 patients affected by locally advanced EC who were undergoing neoadjuvant chemo-radio therapy followed by surgery. We developed an ad hoc assay named ‘Grab-all’ assay using DEPArray system. Longitudinal monitoring allowed the identification of CTCs expressing epithelial, mesenchymal or mixed phenotype markers, in at least one time-point per patient. Through single cell copy number aberration (CNA) analysis, we revealed that individual CTCs from relapsed patients displayed higher degree of genomic imbalance compared to disease-free patients' ones. Post-neoadjuvant therapy CTCs show genomic aberrations previously reported in EC, namely 23/23 amplifications and 13/19 deletions. Notably the phenomenon was not restricted to the group of relapsed patients. In-depth analysis showed that networks enrichment in all time-points CTCs were inherent to innate immune system. At variance, transcription/gene regulation, post-transcriptional and epigenetic modifications were uniquely affected in CTCs of relapsed patients. Collectively, our data add clues to the comprehension of the role of CTCs in EC aggressiveness: chromosomal aberrations on genes related to innate immune system behave as relevant to the onset of CTC-status, whilst pathways of transcription / gene regulation, post-transcriptional and epigenetic modifications seem linked to patients’ outcome.
Assessment of Deep Learning Algorithms to Predict Histopathological Diagnosis of Breast Cancer: First Moroccan Prospective Study on a Private Dataset
Authors: AGOURI HAJAR EL , Azizi Mohammed , Attar Hicham El , Khannoussi Mohammed El , Ibrahimi Azeddine , Kabbaj Rachad , Kadiri Habiba , BEKARSABEIN Salma , ECH-CHARIF Soumaya , Mounjid Chaimaa , Khannoussi Basma El 
Published: August 2021

Abstract
Objective: Breast cancer is a critical public health issue and a leading cause of cancer-related deaths among women worldwide. Its early diagnosis and detection can effectively help in increasing the chances of survival rate. The aim of this work is to develop a computational approach based on deep convolutional neural networks for an efficient classification of breast cancer histopathological images by using our own created dataset. Two models of deep neural network architectures were used combined to gradient boosted trees classifier. Images were classified in three classes, normal tissue-benign lesions, in situ carcinoma and invasive carcinoma. Results: Both Resnet50 and Xception models achieved comparable results, with a small advantage to Xception extracted features. The proposed classification allowed us to obtain high degree of precision, a good generalization performance and avoided an eventual overfitting scenario due to the limited size of the data. In addition, we reported high sensitivity for detection of carcinoma cases, which is important for diagnostic pathology workflow in order to assist pathologists for diagnosing breast cancer with precision.
The trajectory of early disengagement: A longitudinal learning analytics study over a full program
Authors: Saqr Mohammed , López-Pernas Sonsoles 
Published: August 2021

Abstract
Research on online engagement is abundant. However, most of the available studies have focused on a single course. Therefore, little is known about how students’ online engagement evolves over time. Previous research in face-to-face settings has shown that early disengagement has negative consequences on students’ academic achievement and graduation rates. This study examines the longitudinal trajectory of students’ online engagement throughout a complete college degree. The study followed 99 students over 4 years of college education including all their course data (15 courses and 1383 course enrollments). Students’ engagement states for each course enrollment were identified through Latent Class Analysis (LCA). Students who were not engaged at least one course in the first term were labeled as “Early Disengagement”, whereas the remaining students were labeled as “Early Engagement”. The two groups of students were analyzed using sequence pattern mining methods. The stability (persistence of the engagement state), transition (ascending to a higher engagement state or descending to a lower state), and typology of each group trajectory of engagement are described in this study. Our results show that early disengagement is associated with higher rates of dropout, lower scores and lower graduation rates whereas early engagement is relatively stable. Our findings indicate that it is critical to proactively address early disengagement during a program, watch the alarming signs such as presence of disengagement during the first courses, declining engagement along the program or history of frequent disengagement states.
Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale
Authors: Cao Dong , Wang Dongxia , Li Shiming , Li Yun , Hao Ming , Liu Baolong 
Published: August 2021

Abstract
Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.Abstract Triticale (×Triticosecale Wittmack) is an economically important grain-forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.
Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations
Authors: Geibel Johannes , Praefke Nora Paulina , Weigend Steffen , Simianer Henner , Reimer Christian 
Published: August 2021

Abstract
BackgroundStructural variants (SV) are causative for some prominent phenotypic traits of livestock as different comb types in chickens or color patterns in pigs. Their effects on production traits are also increasingly studied. Nevertheless, accurately calling SV remains challenging. It is therefore of interest, whether close-by single nucleotide polymorphisms (SNPs) are in strong linkage disequilibrium (LD) with SVs and can serve as markers. Literature comes to different conclusions on whether SVs are in LD to SNPs on the same level as SNPs to other SNPs. The present study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate LD patterns between the called SV and surrounding SNPs.ResultsThe final callset consisted of 12,294,329 bivariate SNPs, 4,301 deletions (DEL), 224 duplications (DUP), 218 inversions (INV) and 117 translocation breakpoints (BND). While average LD between DELs and SNPs was at the same level as between SNPs and SNPs, LD between other SVs and SNPs was strongly reduced (DUP: 40 %, INV: 27 %, BND: 19 % of between-SNP LD). A main factor for the reduced LD was the presence of local minor allele frequency differences, which accounted for 50 % of the difference between SNP – SNP and DUP – SNP LD. This was potentially accompanied by lower genotyping accuracies for DUP, INV and BND compared with SNPs and DELs. An evaluation of the presence of tag SNPs (SNP in highest LD to the variant of interest) further revealed DELs to be slightly less tagged by WGS SNPs than WGS SNPs by other SNPs. This difference, however, was no longer present when reducing the pool of potential tag SNPs to SNPs located on four different chicken genotyping arrays.ConclusionsThe results imply that genomic variance due to DELs in the chicken populations studied can be captured by different SNP marker sets as good as variance from WGS SNPs, whereas separate SV calling might be advisable for DUP, INV, and BND effects.
A POLÍTICA E A PRÁTICA DA GESTÃO DO CURRÍCULO EM SÃO PAULO: ENSINAMENTOS DE PAULO FREIRE À FRENTE DA SECRETARIA MUNICIPAL DE EDUCAÇÃO (1989-1991)
Authors: Saul Ana Maria , Saul Alexandre , Voltas Fernanda Corrêa Quatorze 
Published: August 2021

Paulo Freire foi Secretário da Educação na cidade de São Paulo (1989-1991). Comprometeu-se com a construção de uma escola pública popular e democrática, com qualidade social. Neste texto apresenta-se a gestão do currículo na administração Freire, destacando princípios que permearam ações concretas para ‘mudar a cara da escola’. A metodologia para elaboração desse artigo foi a pesquisa bibliográfica. Ao final, o texto destaca que a política e a prática curricular, na perspectiva freireana, seguem requeridas para compreender e superar desafios atuais.
Current and future transboundary water cooperation over the YarlungZangbo/Brahmaputra River basin: from an interdisciplinary perspective
Authors: He Yanmei 
Published: August 2021

Abstract
While all riparian states in the YarlungZangbo/Brahmaputra River basin have conducted or planned dam-building, water diversion or other water-related activities to meet their respective national policy goals, they are also undertaking fragmented cooperation to solve conflicts and disputes as they arise. Mainly using a combination of natural, economic, social, environmental, political and legal factors affecting transboundary water cooperation as its analytical framework, this article explores the features of the current cooperation practice among the riparian states, then analyses manifold challenges the practice faces. The author lastly envisions an available path where all riparian states develop multilateral cooperation to address the challenges in the future. This article suggests that the rationale for future cooperation is the policy of preventive diplomacy with the aim of avoiding water conflicts and significant transboundary harm; the basic prerequisite for future potential cooperation is trust building among the riparian states, especially between China–India and between India–Bangladesh; the suitable form of future cooperation is expected to be an inclusive, comprehensive and coordination-oriented River Basin Organization; and the focus areas for future cooperation are supposed to be data sharing and riparian activities that all or most of the riparian states are suffering from.
Improving flood and drought management in agricultural river basins: an application to the Mun River Basin in Thailand
Authors: Prabnakorn Saowanit , Ruangpan Laddaporn , Tangdamrongsub Natthachet , Suryadi F. X. , de Fraiture Charlotte 
Published: August 2021

Abstract
Agriculture productivity is regularly affected by floods and droughts, and the severity is likely to increase in the future. Even if significant efforts are spent on water development projects, ineffective project planning often means that they continue to occur or are only partly mitigated, for example, in the Mun River Basin, Thailand, where 1,000 s of water projects have been implemented. Despite this, the basin regularly experiences floods and droughts. In this study, an analysis of the adverse impacts of basin-scale floods and droughts on rice cultivation in the Mun River Basin is conducted, and an estimation of the coping capacity of existing measures. The results demonstrate that while the total storage capacity of in-situ and ongoing projects would be sufficient to tackle both hazards, it can only be achieved if the projects are effectively utilised. Based on this, proposed solutions for the region include small farm ponds, a subsurface floodwater harvesting system, and oxbow lake reconnections. The suggested measures are practicable, economical, environmentally low-impact, and their implementation (if executed with appropriate care) would reduce flood and drought problems in the basin. Notably, the measures and calculation methods proposed for this basin can also be applied to other crops and regions.
Change the original microbial community structure in the hydrolysis acidification tank to enhance the COD removal performance of oily wastewater
Authors: Zhao Mengshi , Fu Qiang , Yang Yu , Zhang Li , Shan Si 
Published: August 2021

Abstract
The hydrolysis acidification tank mainly relies on microorganisms to treat oily sewage, but in many cases the chemical oxygen demand (COD) of the effluent from the hydrolysis acidification tank does not decrease or even increase. In this work, about 50 L of oily wastewater is treated in a facultative anaerobic hydrolysis acidification tank with a temperature of 29 °C, pH 6, high-throughput sequencing technology analyzes found that after long-term operation of the hydrolysis and acidification tank, the dominant bacterial Pseudomonas accounted for only 2.87%, at this time, the effluent COD of the hydrolysis and acidification tank was 450 mg/L. Pseudomonas stutzeri LH-42 a strain screened in the laboratory, was domesticated and colonized in the hydrolysis acidification tank. High-throughput sequencing and bioinformatics analysis showed that the proportion of Pseudomonas in the hydrolysis acidification tank reached 5.89%, the effluent COD of the hydrolysis and acidification tank was 200 mg/L. The above results indicate the importance of the proportion of Pseudomonas in the hydrolysis and acidification tank for the COD degradation of oily wastewater.
Prevalence and Molecular Characterization of Microbial Contaminants in
Raw Cow Milk of Tangail District in Bangladesh
Authors: Mohiuddin A.K.M. , Mahmud Shahin , Ali Md. Firoz , Faruque Md. Omar , Wasim Muhammad , Evamoni Fatematuz Zuhura , Chowdhury Kamal , Napis Suhaimi 
Published: August 2021

Objectives:
The aim of this study is to evaluate the microbial quality and associated
health risk of raw milk from the Tangail region of Bangladesh.

Methodology:
An intensive study was carried out from January to October 2019 at the Tangail
district of Bangladesh to assess bacterial contamination of raw milk. A total of 60 samples
were examined by following the standard bacteriological methods and the health impact was
evaluated with the help of a semi-structured-based questionnaire. Molecular characterization of
isolated bacteria was carried out by PCR.

Results:
Results revealed the mean values of TVC and TCC in raw milk, udder, oil, and utensil
samples were 7.6×106, 8.8×106, 4.6×106, and 1.3×106 cfu/ml and 3.7×105, 1.4×106, 4.4×105,
and 8.9×104 cfu/ml, respectively. The yeast and mold in raw milk, udder, and oil were 1.5×103,
1.8×103, and 1.3×102cfu/ml, respectively, and the mean values of E. coli in the abovementioned
samples were 1.9×103, 1.8×104, 2.1×103, and 1.6×103cfu/ml, respectively. On the
other hand, the mean values of Salmonella spp. in raw milk, udder, oil, and utensil samples
were 2.4×102, 7.9×102, 1.5×102, and 1.1×102cfu/ml, respectively. Some selected isolates confirmed
by molecular identification were tested for their sensitivity against some common antibiotics
used in Bangladesh. Escherichia coli showed 70% resistance to Amoxicillin and 90%
sensitivity to Ciprofloxacin whereas Salmonella spp. and Staphylococcus aureus showed 90%
resistance to Ampicillin and both were 80% and 90% sensitive to Ciprofloxacin, respectively.

Conclusion, Significance, and Impact of Study:
Milk producers should be appropriately
trained to monitor the overall hygienic conditions surrounding the production and handling of
milk until it reaches the consumer. Frequent monitoring of the milk production facility, occasional
testing of raw milk, and minimal use of antibiotics will ensure the quality of milk. Consumption
of quality milk and avoidance of raw milk consumption will reduce the health risk of
the consumers.
HPLC Tests in Quality Control under the Market Surveillance Program
for Medicinal Products Containing Amlodipine and Valsartan
Authors: Ilieva-Tonova Dessislava , Pencheva Ivanka , Serbezova Assena 
Published: August 2021

Background:
Quality is one of the three main characteristics of medicinal products.
The quality assurance process is multi-stage: during the manufacturing, quality control is the
commitment of the manufacturer, but after medicinal products become part of the distribution and
pharmacy network, analytical quality control is carried out within the program for Market Surveillance.
There are different approaches in conducting quality control of medicinal products under
the Market Surveillance Program.

Aim:
The aim of the study is to compare the results obtained under two approaches: individual
testing and testing by groups with the same active substance.

Methods:
In this study, comparative tests for assay and purity were carried out within two groups
of medicinal products from the antihypertensive group containing Amlodipine besilate and
Valsartan. Analyses were performed in accordance with the available pharmacopoeial monographs,
as well as those from literature sources.

Results:
The results from the assay tests show a significant difference in the same product tested.
Analytical methods for the determination of impurities also show different results when analyzing
the same medicinal product.

Conclusion:
Considering the performed analytical tests, the obtained results can be used to make
several conclusions and suggestions concerning the optimisation of the Annual Market Surveillance
Program.
Anti-Vascular Endothelial Growth Factor Therapy as an Adjunct to Diabetic Vitrectomy
Authors: Karimov Mushfig , Akhundova Lala 
Published: August 2021

Introduction:

The purpose of this work is to study the efficacy of the preoperative intravitreal administration of bevacizumab as an adjunct to vitrectomy in patients with Proliferative Diabetic Retinopathy (PDR).

Methods:
This retrospective comparative study was performed on 118 eyes (118 patients) with proliferative diabetic retinopathy (PDR), which underwent vitrectomy surgery at the Department of Diabetic Eye Disease at Zarifa Aliyeva National Ophthalmology Centre (Baku, Azerbaijan) in 2015-2019. The main group (the bevacizumab group) included 48 eyes with PDR that received intravitreal administration of bevacizumab (Avastin; Genentech Inc., USA) within one week before vitrectomy; the control group included 70 eyes that did not receive a bevacizumab injection for at least 3 months before the vitrectomy. The minimum follow-up was 12 months.

Results:
In both groups, complete retinal attachment after primary vitrectomy was achieved in all eyes (100%). Clinically significant intraoperative haemorrhage was observed in the preoperative bevacizumab injection group in 31.2% and the control group- 51.4%, p = 0.030. The preoperative bevacizumab injection reduced the risk of clinically significant haemorrhage by 2.3 times and the need for endodiathermy by 2.7 times (p = 0.031 and p = 0.024, respectively). Early vitreous cavity haemorrhage was observed in 15.0% in the bevacizumab group and in 35.5% in the control group (p = 0.038). The preoperative injection of bevacizumab before vitrectomy reduced the risk of vitreous cavity haemorrhage in the early postoperative period by 3.0 times (p = 0.036).

Conclusion:
The preoperative use of bevacizumab as an adjunct to diabetic vitrectomy can help reduce the incidence of intraoperative and early postoperative vitreous cavity haemorrhage, which leads to better functional results in the early postoperative period. Over the long-term follow-up period, the effect of the preoperative bevacizumab injections decreases.
Machine Learning Methods for Predicting Postpartum Depression: Scoping Review
Authors: Saqib Kiran , Khan Amber Fozia , Butt Zahid Ahmad 
Published: August 2021

Background
Machine learning (ML) offers vigorous statistical and probabilistic techniques that can successfully predict certain clinical conditions using large volumes of data. A review of ML and big data research analytics in maternal depression is pertinent and timely, given the rapid technological developments in recent years.

Objective
This study aims to synthesize the literature on ML and big data analytics for maternal mental health, particularly the prediction of postpartum depression (PPD).

Methods
We used a scoping review methodology using the Arksey and O’Malley framework to rapidly map research activity in ML for predicting PPD. Two independent researchers searched PsycINFO, PubMed, IEEE Xplore, and the ACM Digital Library in September 2020 to identify relevant publications in the past 12 years. Data were extracted from the articles’ ML model, data type, and study results.

Results
A total of 14 studies were identified. All studies reported the use of supervised learning techniques to predict PPD. Support vector machine and random forest were the most commonly used algorithms in addition to Naive Bayes, regression, artificial neural network, decision trees, and XGBoost (Extreme Gradient Boosting). There was considerable heterogeneity in the best-performing ML algorithm across the selected studies. The area under the receiver operating characteristic curve values reported for different algorithms were support vector machine (range 0.78-0.86), random forest method (0.88), XGBoost (0.80), and logistic regression (0.93).

Conclusions
ML algorithms can analyze larger data sets and perform more advanced computations, which can significantly improve the detection of PPD at an early stage. Further clinical research collaborations are required to fine-tune ML algorithms for prediction and treatment. ML might become part of evidence-based practice in addition to clinical knowledge and existing research evidence.