bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep learning improves the ability of sgRNA off-target propensity prediction
Authors: Liu Qiaoyue , Cheng Xiang , Liu Gan , Li Bohao , Liu Xiuqin
Published: December 2019

Background CRISPR/Cas9 system, as the third-generation genome editing technology, has been widely applied in target gene repair and gene expression regulation. Selection of appropriate sgRNA can improve the on-target knockout efficacy of CRISPR/Cas9 system with high sensitivity and specificity. However, when CRISPR/Cas9 system is operating, unexpected cleavage may occur at some sites, known as off-target. Presently, a number of prediction methods have been developed to predict the off-target propensity of sgRNA at specific DNA fragment. Most of them use artificial feature extraction operations and machine learning techniques to obtain off-target scores. With the rapid expansion of off-target data and the rapid development of deep learning theory, the existing prediction methods can no longer satisfy the prediction accuracy at the clinical level. Results Here, we propose a prediction method named CnnCrispr to predict the off-target propensity of sgRNA at specific DNA fragments. CnnCrispr automatically trains the sequence features of sgRNA-DNA pairs with GloVe model, and embeds the trained word vector matrix into the deep learning model including biLSTM and CNN with five hidden layers. We conducted performance verification on the data set provided by DeepCrispr, and found that the auROC and auPRC in the "leave-one-sgRNA-out" cross validation could reach 0.957 and 0.429 respectively (the pearson value and spearman value could reach 0.495 and 0.151 respectively under the same settings). Conclusion Our results show that CnnCrispr has better classification and regression performance than the existing states-of-art models.
A new homozygous CACNB2 mutation has functional relevance and supports a role for calcium channels in autism spectrum disorder
Authors: Graziano Claudio , Despang Patrick , Palombo Flavia , Severi Giulia , Posar Annio , Cassio Alessandra , Pippucci Tommaso , Isidori Federica , Matthes Jan , Bonora Elena
Published: December 2019

BackgroundDiagnostic yield in patients with autism spectrum disorder (ASD) has improved over the last years, thanks to the introduction of whole genome arrays and next generation sequencing, but etiology is still unknown for the majority of cases. Among distinct cellular pathways, evidence implicating dysregulation of cellular calcium homeostasis in ASD pathogenesis has been accumulating, and specific mutations in voltage-gated calcium channels found in patients with autism were shown to be functionally relevant.MethodsWhole exome sequencing and Sanger sequencing were performed to identify and confirm variants in a girl with ASD, global developmental delay and precocious puberty, born of first-degree cousins. Site-directed mutagenesis was used to generate a human CaVβ2d calcium channel subunit carrying a CACNB2 mutation. Whole-cell patch-clamp recordings were performed to reveal functional effects of mutant CaVβ2d on Ba2+-currents mediated by L-type (CaV1.2) calcium channels in transiently transfected HEK-293 cells.ResultsIn an ASD patient, we identified a rare homozygous variant (p.Arg70Cys) in the CACNB2 gene coding for the auxiliary CaVβ2subunit of voltage-gated calcium channels. In a recombinant system, the CaVβ2 variant, which was not previously associated to ASD, was found to alter CaV1.2 calcium channel function by significantly affecting activation and inactivation of whole-cell Ba2+-currents.LimitationsAlthough the evidence of CACNB2 involvement in ASD is slowly accumulating, the number of reported patients is very limited. Deep clinical phenotyping and functional studies in larger sets of subjects will be instrumental to fully understand the penetrance and outcome of CACNB2 variants.ConclusionsThe p.Arg70Cys variant in CACNB2 shows functional consequences similar to other ASD-associated CaVβ2 mutations. These results support the idea of CACNB2 variations contributing to the development of ASD and hint to a rare form of Mendelian recessive autism with possible specific comorbidities.
Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago
Authors: Morgan Andrew , Brazeau Nicholas , Ngasala Billy , Mhamilawa Lwidiko , Denton Madeline , Msellem Mwinyi , Morris Ulrika , Filer Dayne , Aydemir Ozkan , Bailey Jeffrey , Parr Jonathan , Mårtensson Andreas , Bjorkman Anders , Juliano Jonathan
Published: December 2019

Background: Tanzania’s Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria’s persistence, but this paradigm has not been studied using modern genetic tools.Methods: We used whole-genome sequencing (WGS) to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. We assessed ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections.Results: We identified significant decreases in the effective population sizes in both populations in the timeframe of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared large sections of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling,, we demonstrate a pair of isolates between the mainland and Zanzibar that are related at the expected level of half-siblings, consistent with recent importation.Conclusions: These findings suggest that importation plays an increasing role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.
Stigma and Perceived Threat Regarding Peripartum Depression among Pregnant Women in a “Pregnancy Friendly” Community
Authors: Amarasinghe Gayani , Agampodi Suneth Buddhika , Agampodi Thilini
Published: December 2019

Background: Peripartum depression (PPD) is identified globally as a major maternal morbidity. Stigma and underlying perceptions such as perceived threat which includes perceived severity and perceived susceptibility regarding PPD can interfere with timely identification, help seeking and, treatment acceptance, hindering efforts to control maternal mortality and morbidity due to this disease.Methods: A cross sectional study was conducted among pregnant women with a period of gestation more than 12 weeks attending field antenatal clinics in Anuradhapura district, Sri Lanka. Multistage cluster sampling with probability proportionate to size was used for sampling. Self-completed questionnaire with a vignette describing a postpartum mother with symptoms of peripartum depression (part A) and accompanied suicidal ideation (part B) was given to participants. Based on the vignette, agreement on stigma and perception statements were marked in a five point likert scale. An exploratory factor analysis was conducted on stigma statements. Including the factor scores, agreement to perception statements and selected socio-demographic variables, a logistic regression model was run to explain the perceived susceptibility.Results: Out of the 624 participants, 60.7% (n-379) perceived that they are not susceptible to develop a mental health problem during antenatal or postnatal period of the pregnancy. Though 86.2 % (n-525) had heard about PPD, its symptoms and even suicidal ideation were normalized by 55.9% (n-260) and 49.5% (n-280) of participants respectively. About 79.1% (n-468) thought that symptoms would resolve without treatment. By exploratory factor analysis on stigma statements (c2 80.376, p<.001), a two factor solution was achieved. Factors were interpreted as judgmental and nonjudgmental stigma. Mainly nonjudgmental stigma was evident among participants. Direct logistic regression for predicting the perceiving personal susceptibility to a perinatal mental illness (2 =31.474, p= 0.017, N = 329) revealed that only factor score for nonjudgmental stigma became statistically significant in the model (OR -0.691 p=0.029).Conclusion: Perceived threat from symptoms of peripartum depression and even suicidal ideation is low in this community. Presence of nonjudgmental stigma in this community also shows the need for social interventions to address these issues related to PPD and related morbidities.
Co-regulation role of endogenous hormones and transcriptomics profiling under cold stress in Tetrastigma hemsleyanum
Authors: Peng Xin , Qiu Wenyu , Wu Hao , Chen Hongjiang , Zhang Zhongyi
Published: December 2019

Background: Tetrastigma hemsleyanum Diels et Gilg is a valuable medicinally herb, Chilling sensitivity is the dominant environmental factor limiting the artificial domestication of the plants. Hormone-related gene regulation and hormone signaling pathways in response to cold stress in T. hemsleyanum remain unknown.Results: Some key genes involved in hormones biosynthesis, such as ZEP and NCED genes of ABA biosynthesis, GA2ox, GA3ox, and GA20ox genes of GA biosynthesis, ACO genes of ET biosynthesis were screened to be crucial in cold response. Consistently, the response of ABA and ABA/GA1+3 to cold stress was prior to that of GA1+3, ZR, ABA/IAA, and ABA/ZR. The increasing changes in ABA/GA1+3 turned to a steep decline with the extension of stress time, which might be one factor contributing to cold-sensitivity of T. hemsleyanum under prolonged stress. The cold tolerance of T. hemsleyanum would be enhanced by endogenous ABA but repressed by GA3 when each phytohormone was applied alone. The ABA-mediated promotion and GA-mediated repression of cold tolerance could both be attenuated by the co-application of the two phytohormones within 6h. When the biosynthesis of endogenous ABA and GA were inhibited by FLU and PAC, respectively, the effects of GA and ABA treatment were reversed partially.Conclusions: In summary, we present the ﬁrst study of global expression patterns of hormone-regulated transcripts in T. hemsleyanum. This study suggested that GA and ABA work antagonistically to balance the responses to cold in T. hemsleyanum. PAC, a GA biogenesis inhibitor, as well as exogenous ABA, might be potential plant growth regulators that can promote cold tolerance of T. hemsleyanum. The study also provided valuable hints in revealing a new theoretical basis and potential candidate genes that govern cold tolerance of T. hemsleyanum.
An immunoinformatic approach driven by experimental proteomics: in silico design of a subunit candidate vaccine targeting secretory proteins of Leishmania donovani amastigotes
Authors: Khan Md Anik Ashfaq , Ami Jenifar Quaiyum , Faisal Khaledul , Chowdhury Rajashree , Ghosh Prakash , Hossain Faria , Wahed Ahmed Abd El , Mondal Dinesh
Published: December 2019

Background Visceral leishmaniasis (VL) caused by dimorphic Leishmania species is a parasitic fatal disease with high socio-economic burden in endemic areas worldwide. Sustaining control of VL in terms of proper and prevailing immunity development is a global necessity amid unavailability of a prophylactic vaccine. Screening of experimental proteome of human disease propagating form of L. donovani (amastigote) can be more pragmatic for in silico mining of novel vaccine candidates.Methods By using an immunoinformatic approach, CD4 and CD8 T-cell specific epitopes from experimentally reported L. donovani proteins having secretory potential and increased abundance in amastigotes were screened. A chimera linked with a toll-like receptor 4 (TLR4) peptide adjuvant was constructed and evaluated for physicochemical characteristics, binding interaction with TLR4 in simulated physiological condition and the trend of immune response following hypothetical immunization.Results Selected epitopes from physiologically important L. donovani proeins were found mostly conserved in L. infantum - covering theoretically more than 98% of global population. The multi-epitope chimeric vaccine was predicted as stable, antigenic and non-allergenic. Structural analysis of vaccine-TLR4 receptor docked complex and its molecular dynamics simulation suggest sufficiently stable binding interface along with prospect of non-canonical receptor activation. Simulation dynamics of immune response following hypothetical immunization indicate active and memory B- as well as CD4 T-cell generation potential, and likely chance of a more Th1 polarized response.Conclusions The methodological approach and results from this study could facilitate more informed screening and selection of candidate antigenic proteins for entry into vaccine production pipeline in future to control human VL.
Abnormal genome-wide DNA methylation induced by cisplatin may contribute to the chemo-resistance of human small cell lung cancer
Authors: Ji Fuyun , Yu Shilong , Wu Yi , Lv Jing , Zhang Peng , Li Xiaokang , Jiang Chaowen , Zhang Ruijie , Song Liyuan , Chen Yan , Guo Ruiling , Qian Guisheng , Li Xihua
Published: December 2019

Background: So far, the platinum-based chemotherapy (e.g. cisplatin-etoposide doublet) is still the backbone for SCLC management due to its high respond rate both in LS-SCLC and ES-SCLC. However, cisplatin treatment often results in the development of chemo-resistance, leading to therapeutic failure and becoming the main obstacle to improve the therapeutic efficacy. Currently, little has been known about the genome-wide abnormal methylation of SCLC induced by cisplatin, which might provide prospective layouts to discover the potential genes and the signal pathways related with chemo-resistance of SCLC.
Results: A total of 58,401 sites was identified to be differentially methylated (|Δβ| ≧ 0.20) in H446/DDP cells compared with that of H446 cells, of which 25,991 genes were found to be hypomethylated and 32,410 genes were shown to be hypermethylated. KEGG enrichment displayed that the differentially hypomethylated genes were mainly gathered in MAPK signaling pathway, ECM-receptor interaction, and Focal adhesion, while the differentially hypermethylated genes were clustered in Neuroactive ligand-receptor interaction, Type I diabetes mellitus, Focal adhesion, Allograft rejection, ECM-receptor interaction, CAMs, Graft-versus-host disease, Intestinal immune network for IgA production, ARVC, and Viral myocarditis (KEGG enrichment, qvalue < 0.05). Among the 152 genes which were selected as the MDR-related candidate genes for qRT-PCR to testify whether the abnormal methylation regulated the expression of related genes at the mRNA level, 69 hypomethylated genes were revealed to be significantly increased and the other 54 hypermethylated genes evidently decreased in H446/DDP cells compared with that of H446 cells. Moreover, the upregulated genes with the hypomethylated sites were found to be mainly clustered in Pathways in cancer, MAPK signaling pathway, Cytokine-cytokine receptor interaction, and Cell adhesion molecules (CAMs), while the downregulated genes with the hypermethylated sites were mainly clustered in MAPK signaling pathway, Pathways in cancer, Melanoma, Osteoclast differentiation, and Prostate cancer.
Conclusions: Cisplatin could induce a large-scale abnormal methylation in the whole genome of SCLC. Pathways in cancer, MAPK signaling pathway, Cytokine-cytokine receptor interaction, and Cell adhesion molecules (CAMs) were most likely to be affected by cisplatin via. methylation to contribute to the development of chemo-resistance and other malignant biological behavior of SCLC cells.
Determinants of anemia in children under five years in Angola, Malawi and Senegal: A comparative study
Authors: KHULU CHRIS , Ramroop Shuan
Published: December 2019

Background: Anemia is defined as a condition where there is an insufficient quantity of homoglobin, hematocrit or red cell in the human body [1, 2]. Unicef (2017) report urged all countries to reduce under ve years mortality by 2030, thereof there is a need of understanding and determining factors contributing to child mortality. The significance of this study underpins the improvement in collaboration among the three countries and recommend to government the area to invest in order to meet the SDG target.Method: The current study used demographic health survey data from Angola (2016), Malawi (2016) and Senegal (2016). Using World Health Organisation (WHO) classification guidelines of anemia, the ordinal dependent variable was developed. The three categories of anemia condition used in this study are Mild (10.0 - 10.9 g/dl), Moderate (7.0 - 9.9 g/dl) and severe (<7 g/dl). Results: Gamma measure and chi-square test of independence was conducted to explore the association between anemia status and factors. The score test and Brant test were used to test the proportional odds model assumption and it was satisfied.Results from ordinal survey logistic regression model found place of residence, age of the child, wealth index, mother level of education and nutritional status to be significant factors associated with anemic condition of under five year children in all three countries. Discussion: The health institutions of Angola, Malawi and Senegal need to monitor under five years children that are suffering from malnutrition condition. The study showed that there is a high chance for under five years children to suffer from both malnutrition and anemia condition. This finding is similar to the results of the study that was conducted in Bangladesh and Burma [27, 28].Conclusion: The study identifieed place of residence, age of the child, wealth index, mother level of education and nutritional status as common factors associated with anemia in Angola, Malawi and Senegal. This nding is in agreement with that of the studies conducted by [27, 26, 36]. The results showed the necessity of collaboration between Angola, Malawi and Senegal in order to achieve the SGD target.
Paradox of HIV stigma in an integrated chronic disease care in rural South Africa: viewpoints of users and providers
Authors: Ameh Soter , D'Ambruoso Lucia , GOMEZ-OLIVE Francesc , Kahn Kathleen , Tollman Stephen , Klipstein-Grobusch Kerstin
Published: December 2019

Background: An integrated chronic disease management (ICDM) model was introduced by the National Department of Health in South Africa to tackle the dual burden of HIV/AIDS and non-communicable diseases. One of the aims of the ICDM model is to reduce HIV-related stigma. There is a dearth of literature on reduction of HIV stigma attributable to the ICDM model. This paper describes the viewpoints of health care users and providers on HIV stigma in an ICDM model in rural South Africa.Methods: A qualitative case study of HIV stigmatisation in the context of the implementation of an ICDM model in seven primary health care (PHC) facilities and their catchment communities was conducted in 2013 in the rural Agincourt sub-district, South Africa. Eight Focus Group Discussions were used to obtain data from 61 purposively selected participants who were 18 years and above. Seven In-Depth Interviews were conducted with the nurses-in-charge of the facilities. The transcripts were thematically analysed using MAXQDA 2018 qualitative software. The emerging themes on HIV stigma and HIV-related concerns were inductively analysed. Results: Both service providers and users perceived implementation of the ICDM model may have led to reduced HIV stigma in the facilities. On the other hand, service users and providers thought HIV stigma increased in the communities because community members thought that home-based carers visited the homes of HIV-infected people. Service users thought that routine HIV testing, intended for pregnant women as stipulated in the World Health Organization guidelines, was associated with unwanted pregnancies among adolescents who wanted to use contraceptives but refused to take a HIV test as a precondition for receiving contraceptives. Caregivers of ill persons wanted full disclosures of the HIV status of their family members to enable them to protect their health and contribute to enhancing adherence to anti-retroviral therapy of HIV-infected family members.Conclusions: Although the ICDM model was perceived to have contributed to reducing HIV stigma in the health facilities, it was associated with stigma in the communities. Remodelling the community component of the ICDM model could contribute to HIV stigma reduction in the study setting and elsewhere in South Africa.
Cohort Profile: The Nigerian HIV Geriatric Cohort Study
Authors: Kayode Gbenga Ayodele , Dakum Patrick , Avong Yohanna Kambai , Odutola Michael Kolawole , Okuma James , Nta Iboro Ekpo , Ndembi Nicaise , Mensah Charles , Khamofu Hadiza , Okonkwo Prosper , Okpanachi John Oko , Ezeanolue Echezona
Published: December 2019

Background: An estimated 280,000 adults aged 50 years and above live with HIV in Nigeria, a population set to increase with ART efficacy and expanding coverage. To learn how elderly people living with HIV (EPLHIV) in Nigeria fare, despite not being prioritized by the national treatment program, and to deepen knowledge for their differentiated care and achieve better outcomes, the Nigerian HIV Geriatric Cohort (NHGC) was setup. Methods: Patient-level data spanning the period 2004 to 2018, obtained from comprehensive HIV treatment hospitals, that are supported by four major PEPFAR-implementing partners in Nigeria was used. These 4 entities collaborated as member organizations of the Nigeria Implementation Science Alliance. We defined geriatric/elderly as those aged 50 years and above. From de-identified treatment records, demographic and clinical data of EPLHIV ≥50-year-old at ART initiation during the review period was extracted, merged into a single REDcap® database, and described using STATA 13. Results: A total of 101,652 unique EPLHIV entries were analysed. This cohort’s data was of 53,608 (52.7%) women, 51,037 (71.4%) of EPLHIV identified as married and 33,446 (51.1%) unemployed. Mean age was 57.1 years (SD=6.9) with average duration on ART as 4.6 years (SD=3.5). ART profile showed that 88,792 (95.7%) were on 1st-line and 55,905 (64.9%) were on TDF-based regimens. Mean-body mass index (BMI) was 23.0 kg/m2 (SD=5.4 kg/m2) with 56,010(55.1%), 19,619(19.3%) and 8844 (8.7%) showing normal (18.5kg/m2–24.9kg/m2), overweight (BMI 25- <30kg/m2) and obese (BMI ≥30kg/m2) ranges respectively. Hypertensive readings (systolic-BP >140mmHg or diastolic-BP >90mmHg) was found in 21,550 (21.2%) ELHIV records. Mean CD4 count was 420cells/µL (SD=285cells/µL) and 83,660(82.3%) had a viral load result showing <1000copies/ml. As for treatment outcomes, available records showed that 54.1% were active-in-treatment, 28.4% were lost-to-follow-up and 6.8% died. Poor population death records and aversion to autopsies makes it almost impossible to estimate AIDS-related deaths. Conclusions: The study described the clinical and non-clinical profile of EPLHIV in Nigeria. This study provides vital information for stakeholders in HIV prevention, care and treatment to understand the characteristics of EPLHIV. Findings from further analysis of this cohort will be applied to improve the quality of health of EPLHIV.
Effects of a single interprofessional simulation session on medical and nursing students’ attitudes toward interprofessional learning and professional identity: A questionnaire study
Authors: Burford Bryan , Greig Paul , Kelleher Michael , Merriman Clair , Platt Alan , Richards Elize , Davidson Neil , Vance Gill
Published: December 2019

BackgroundParticipation in simulation-based interprofessional education (sim-IPE) may affect students’ attitudes towards interprofessional learning (through gaining experience with others) and their professional identity (by increasing the ‘fit’ of group membership by performing a role). We examined this in two questionnaire studies involving two sites, with students drawn from four universities. MethodQuestionnaire data were collected before and after students took part in a sim-IPE session consisting of three acute scenarios.Questionnaires included the Readiness for Interprofessional Learning Scale (RIPLS) and measures of professional identity derived from the social identity theory literature. In Study 1 only identification with professional group was measured, while in Study 2 identification with Student group and the immediate interprofessional team were also measured.Linear mixed effects regression analysis examined the effect of the simulation session, and differences between medical and nursing students, between sites and between measures of Professional, Student and Team identity.Results194 medical and 266 nursing students completed questionnaires across the two studies.In both studies RIPLS increased for all groups following participation in sim-IPE, although this was larger for nursing students in Study 1. Nursing students had consistently higher RIPLS scores than medical students at one site.Effects of the simulation session on identity measures varied between sites and different dimensions of identity. Notably, while positive emotions associated with group membership increased for Student group, Professional group and Team, the sense of belonging (Ingroup Ties) and centrality of the group increased only for Team. There were also differences between sites. Nursing students had consistently higher identification scores than medical students.ConclusionsParticipation in a single sim-IPE can improve attitudes towards interprofessional learning. It can also enhance aspects of professional identity, particularly those related to affect, with potential benefits for wellbeing. Changes in identification with an immediate Team may suggest positive psychological consequences of ad hoc Team formation in the workplace.Differences between medical and nursing students suggest that their differing opportunities to work with other professions during training may change baseline attitudes and identity, but a single sim-IPE session can still have an additive effect.
Does simulation suffice? Teaching procedural skills in undergraduate medical students- observational quasi-experimental study.
Authors: Naylor Katarzyna , Torres Kamil
Published: December 2019

Background. Medical simulation as a teaching method is concerned with close mirroring of the real clinical conditions, it is designed to develop skills from the clinical environment, under the guidance of experienced instructors, it allows standardization and repeatability of the skills taught. As a result, students acquire skills and competences, become acquainted with the medical equipment needed to perform a given procedure without endangering patients. The presented research attempts to evaluate the application of medical simulation techniques in the teaching of basic clinical skills using original instructional videos and the Peyton approach. Also, an attempt was made to assess how the applied interventions affect the assessment regarding the usefulness of the course by the students of medicine in comparison with the results of practical assessment in the form of OSCE. Materials. The research was conducted in the period from May 2015 to June 2017, among 750 students of the medical faculty of the Medical University in Lublin. The study used a self-reported questionnaire and documentation analysis with the results of practical assessment. The obtained results were statistically analyzed.Results. The overall students scored the BCS course high (good and very good). The highest values were assigned to Stage III of the research. The introduction of simulation techniques along with the original instructional videos and the Peyton approach positively reflected in the results obtained in the final assessment, OSCE, especially in case of invasive procedures: peripheral vein cannulation and urinary bladder catheterization. Conclusions. Consequently, obtained results allowed concluding that the use of medical simulation techniques in the teaching of basic clinical skills using modern methodologies and teaching interventions: original instructional videos and the Peyton approach affected the positive assessment of the usefulness of the simulation course by students, as well as improve and support the process of acquiring basic skills clinical in the early years of medical training.
Application of wastewater for production of lettuce (Lactuca sativa) in hydroponic system
Authors: Xavier Josilda France , Azevedo Carlos Alberto Vieira de , Azevedo Marcia Rejane de Queiroz Almeida , Dantas Josely Fernandes , Filho Antônio Fernandes Monteiro , Lima Vera Lúcia Antunes de
Published: December 2019

The study aimed to evaluate the agronomic performance of three varieties of lettuce subjected to different treatments of wastewater. The experimental design was a randomized block in a 7 x 3 split-plot with three replicates. The factors were 7 hydroponic and 3 cultivars of crisp lettuce. The solutions were formulated and optimized by considering Furlani solution as reference nutrient. The experimental portion consisted of the nutritive solutions (S). S1 = Furlani solution; S2 = domestic wastewater; S3 = optimized domestic wastewater; S4 = well water; = S5 optimized well water; S6 = wastewater from the UASB reactor and S7 = wastewater optimized from the UASB reactor, the subplot was constituted of three lettuce cultivars (Verônica, Vanda and Thais). The results showed that solutions with domestic wastewater (S2), optimized domestic wastewater (S3), optimized well water (S5) and the solution wastewater from the UASB reactor (S6) promoted the highest number of leaves per plant for the three cultivars. Solutions with enhanced domestic wastewater (S3), optimum water well (S5) and the solution formulated from the wastewater from the UASB reactor (S6) promoted the highest stem diameter in three cultivars. The highest value of total production was obtained from Vanda cultivar, when the wastewater from the UASB reactor (S6) was used as nutritive solution.
Salt stress in popcorn genotypes trigger changes of antioxidant enzymes
Authors: Trevizan Claudia Borsari , Bonacina Cristine , Lourenceto Letícia , Santos Tiago Benedito dos , Souza Silvia Graciele Hülse de
Published: December 2019

Salinity is a major problem in agriculture because it can alter the metabolism of plants and affect crop yield. This study aimed to evaluate the effect of NaCl on growth, key antioxidants and changes in the expression of genes encoding antioxidant enzymes. Two popcorn genotypes, IAC125 and UFMV2, experienced reduction in growth as the salt concentration increased. Increase in chlorophyll content and damage to the plasma membrane was observed. Consequently, changes in osmotic activity led to reduced water content in the leaves. Increased concentration of salt increased the activity of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) in two popcorn genotypes but maximum activity was observed in the IAC125 genotype. Such enzymatic activities occur in order to maintain the levels of lipid peroxidation under salt stress, indicating that this genotype is tolerant to salinity conditions. The ZmAPX, ZmCAT, ZmSOD (Cu/Zn) and ZmSOD (Mn) genes increased their expression as salinity increased. The ZmSOD (Fe) gene was highly regulated in the IAC125 genotype under salt stress, but low regulation was observed in the UFM2 genotype, regardless of the salt concentration. The enhancement in tolerance against salt stress indicates that the genes involved in the antioxidative process are triggered by oxidative stress induced by abiotic stresses. These results showed that the popcorn varieties have different levels of salt tolerance due to the differential expression pattern of the antioxidant genes. The up-regulation of antioxidant enzymatic activity could lead to increased scavenging of excessive free radicals and reduce oxidative stress.
Inoculation with arbuscular mycorrhizal fungi alters content and composition of essential oil of Sage (Salvia officinalis) under different phosphorous levels
Authors: Cruz Rayane Monique Sete da , Cruz Glaucia Leticia Sete da , Dragunski Douglas Cardoso , Junior Affonso Celso Gonçalves , Alberton Odair , Souza Silvia Graciele Hulse de
Published: December 2019

This study aimed at evaluating the growth and essential oil content of Salvia officinalis L. (sage) inoculated with two species of arbuscular mycorrhizal fungi (AMF) Rhizophagus clarus and Claroideoglomus etunicatum under different phosphorous (P) levels. The treatments were prepared in a sterile substrate (sand, vermiculite and organic compound (1: 1: 2, v:v) with high (200 mg kg−1) and low (20 mg kg−1) P levels at sowing, with and without AMF inoculation; the experiment was conducted in a greenhouse for four months. Plants were grown in pots with 3 kg of substrate in a 3 x 2 (3 mycorrhizal x 2 levels of P) factorial experiment, in a completely randomized design (with eight repetitions). Spore density, AMF root colonization, plant dry mass, P and N shoot content, yield and composition of essential oil (EO) were determined. Data were processed and submitted to analyses of hierarchical clustering and principal component. Plant biomass increased with addition of P in the substrate. EO content increased with AMF Rhizophagus clarus inoculation in high-P substrate. It was concluded that inoculation with R. clarus and the addition of P at sowing can boost the growth of sage and the content of its EO. Camphor, α-humulene, viridiflorol, manool, α-thujone and β- thujone were the main components of the EO.
Effect of Trichoderma spp. fungus for production of seedlings in Enterolobium Schomburgkii (Benth.) Benth
Authors: Santos Misael Freitas dos , Costa Daniele Lima da , Vieira Thiago Almeida , Lustosa Denise Castro
Published: December 2019

Enterolobium schomburgkii (monkey ear) is important Amazonic forest specie, being used for wood and medicinal purposes and environmental recuperation issues. Biological treatment such as Trichoderma fungus is alternative method that may improve performance of seeds germination and provide healthy seedlings. We aimed to assess effect of Trichoderma fungus on development of E. schomburgkii seedlings. Five isolates of Trichoderma spp., in the concentration of 1.0 x 107 conidia.mL-1, were assessed and applied through four methods: seeds; pre-planting substrate; post-planting substrate; and seed + pre-planting + post-planting substrate. The seedlings were produced in polypropylene bags and kept in nursery for 10 months. The experimental design was completely randomized, in a 5x4+1 factorial scheme, with 10 repetitions. We monthly assessed the plant height, collar diameter and number of leaves and leaflets. After 10 months, we assessed root length, dry matter of aerial part and dry matter of roots system. The results showed that variables were significantly influenced by Trichoderma isolates and its application modes, either individually or under interaction, except on the root length. Eight treatments boosted the plants height and five of them increased the collar diameter, compared with the control. The height of the seedlings was the variable that mostly influenced by the treatments. Application of Trichoderma in pre-planting substrate influenced the highest number of variables analyzed. Therefore, the isolates application used in this work is feasible for production of Enterolobium schomburgkii seedlings. Based on results of this experiment we do not recommended treatment of Enterolobium schomburgkii seeds with Trichoderma isolates, except using T. asperellum T09
Effect of debranching on sweet potato yield and quality
Authors: Santos Albertir Aparecido dos , Júnior Valter Carvalho de Andrade , Fialho Cíntia Maria Teixeira , Azevedo Alcinei Místico de , Brito Orlando Gonçalves , Viana Abraão José Silva , Guimarães Amanda Gonçalves
Published: December 2019

The objective of this study was to evaluate effect of branch removal on the yield and quality of sweet potato genotypes in different harvesting systems and two growing seasons. Two trials (2014 and 2016/17) were conducted in a randomized block design with three replicates in the factorial scheme composed of: three clones (Brazlândia Rosada, BD-31 TO and BD-65) and five harvesting systems (H): H1- total harvest of branch and root at 120 days after planting (DAP); H2- cut of the branches at 120 DAP, plus regrown branches and roots harvested at 210 DAP; H3 - total harvest of branches and roots at 165 DAP; H4 - cut of the branches at 165 DAP and harvest of regrown branches and roots at 210 DAP and H5- branches and roots total harvest at 210 DAP. For harvesting systems H2 and H4 the total production of branches at the end of the cycle was determined by the sum of the two cuts. The yield, dry matter of shoot and root, chemical-bromatological and nutrient quality were evaluated. The 2014 trial produced higher green mass yield of the branches, while in 2016/2017, higher root yield observed. H2 and H4 were shown to have better quality of the branches regarding the bromatological and nutrient characteristics, being recommended for animal feeding. The systems without regrowth (H3 and H5) allowed better yields and quality of roots, useful for human feeding. In general, the clone Brazlândia Rosada, produced the highest yield of roots and branches; therefore, recommended for planting.
Analisis Algoritma Apriori untuk Mendukung Strategi Promosi Perguruan Tinggi
Authors: Kusumo Haryo , Sediyono Eko , Marwata Marwata
Published: December 2019

Every company and organization that wants to survive needs to determine the effectiveness of the right promotion strategy. Determination of the right promotion strategy will be able to reduce the cost of promotion and achieve the right promotional goals. One way that can be done to determine the promotion strategy is to use data mining techniques. Data mining techniques used in this case are using the Apriori algorithm. A priori algorithm is one of the classic data mining algorithms. A priori algorithms are used so that computers can learn the rules of association, look for patterns of relationships between one or more items in a dataset. This study is conducted by observing several research variables that are often considered by universities in determining their promotion goals, namely school, region, and department. The results of this study are in the form of interesting patterns resulting from data mining which is important information to support the right promotion strategy in getting new students.
Effect of Meteorological Conditions on Storability of the Scab-Immune Columnar Apple Varieties
Authors: Nikitin Andrej , Makarkina Margarita
Published: December 2019

Introduction. Weather conditions during vegetative period have an effect on the duration of fruit storage, as well as the yield of commercial fruits unaffacted by physiological disorders or microbiological diseases. In this regard, new apple varieties demand a detailed study of economic and biological indicators, determination of storage period, and various factors that may affect it.

Study objects and methods. The research featured preservation capacity of five new scab-immune columnar apple varieties cultivated at the All-Russian Research Institute for Fruit Crop Breeding (Orlov Region, Russia), namely ‘Vostorg’, ‘Zvezda’ ‘Efira’, ‘Poezia’, ‘Priokskoye’, and ‘Sozvezdiye’. The apples were stored in an industrial refrigerator at +2°C. The Selyaninov’s hydrothermal coefficient (HTC) was used as a predictive indicator of the potentially effective storability.

Results and discussion. A set of experiments was conducted to determine the effect of the weather conditions during the vegetative period on the yield of commercial fruits. The best preservation was recorded for the fruits harvested in the years with sufficient rainfall during the growing season. The most comfortable conditions of seasonal humidification for the long-term storage of fruits were formed for ‘Zvezda Efira’ and ‘Sozvezdiye’ in 2014 and ‘Poezia’ and ‘Priokskoye’ in 2016 at HTC = 1.0. The storability depended on the weather conditions during the growing season and the variety. The ‘Sozvezdiye’ variety showed the highest commercial yield after storage in 2014 (96.7%), while the lowest commercial yield (64.2%) belonged to the ‘Vostorg’ apples in 2016. ‘Sozvezdiye’ had the highest effective persistence of commercial fruits (83.6–96.7%) during the whole study period (92.0% on average). ‘Vostorg’ and ‘Poezia’ demonstrated worse results than other varieties (76.2% and 76.8% on average, respectively).

Conclusion. Poor precipitation and excess heat in the period of 30 days before harvesting adversely affected the fruit storability, which led to scald. ‘Zvezda Efira’ and ‘Sozvezdiye’ were absolutely stable to scald. The dry year of 2012 had a positive effect on the apples as the level of ascorbic acid increased during storage (82.8% of the baseline). Therefore, it is advisable to use HTC to predict fruit quality and storage period.
Survival of emerging pathogen Acinetobacter baumannii in water environment exposed to different oxygen conditions
Authors: Dekic Svjetlana , Hrenovic Jasna , van Wilpe Erna , Venter Chantelle , Goic-Barisic Ivana
Published: December 2019

Bacterium Acinetobacter baumannii is a leading cause of hospital infections. Over the last decade, its occurrence in natural environments outside hospital settings has been reported. The aim was to examine the survival of A. baumannii in water media exposed to different ranges of oxygen supply in order to predict its behaviour in the environment. The abundance of five A. baumannii isolates was monitored in nutrient-depleted and nutrient-rich water media in aerated, intermediate and anaerobic conditions (oxygen saturation 96, 56 and 0%, respectively). A. baumannii survived in both media in all tested oxygen concentrations for 50 days. In nutrient-rich water survival of A. baumannii was lowest in anaerobic conditions, while in nutrient-depleted water there was no difference in survival regardless of oxygen availability. A. baumannii formed translucent small colony variants as the fast response (after 1 day) and dormant cells as the prolonged response (after 14 days) to anaerobic conditions. Transmission electron microscopy (TEM) images showed the outer membrane of coccobacillus dormant cells was up to four times thicker than in regular cells. Once in the environment, A. baumannii is able to survive regardless of the availability of dissolved oxygen, which represents a serious public health concern.
Lipoxygenase Inhibitors as Cancer Chemopreventives: Discovery, Recent Developments and Future Perspectives
Authors: Mahboubi-Rabbani Mohammad , Zarghi Afshin
Published: December 2019

Background:

Leukotrienes (LTs) constitute a bioactive group of Polyunsaturated Fatty
Acid (PUFA) metabolites molded by the enzymatic activity of lipoxygenase (LO) and have a pivotal
role in inflammation and allergy. Evidence is accumulating both by in vitro cell culture experiments
and animal tumor model studies in support of the direct involvement of aberrant metabolism of arachidonic
acid (ACD) in the development of several types of human cancers such as lung, prostate,
pancreatic and colorectal malignancies. Several independent experimental data suggest a correlation
between tumoral cells viability and LO gene expression, especially, 5-lipoxygenase (5-LO). Overexpressed
5-LO cells live longer, proliferate faster, invade more effectively through extracellular matrix
destruction and activate the anti-apoptotic signaling mechanisms more intensively compared to the
normal counterparts. Thus, some groups of lipoxygenase inhibitors may be effective as promising
chemopreventive agents.

Methods:

A structured search of bibliographic databases for peer-reviewed research literature regarding
the role of LO in the pathogenesis of cancer was performed. The characteristics of screened papers
were summarized and the latest advances focused on the discovery of new LO inhibitors as anticancer
agents were discussed.

Results:

More than 180 papers were included and summarized in this review; the majority was about
the newly designed and synthesized 5-LO inhibitors as anti-inflammatory and anticancer agents. The
enzyme’s structure, 5-LO pathway, 5-LO inhibitors structure-activity relationships as well as the
correlation between these drugs and a number of most prevalent human cancers were described. In
most cases, it has been emphasized that dual cyclooxygenase-2/5-lipoxygenase (COX-2/5-LO) or
dual 5-lipoxygenase/microsomal prostaglandin E synthase-1 (5-LO/mPGES-1) inhibitors possess
considerable inhibitory activities against their target enzymes as well as potent antiproliferative effects.
Several papers disclosing 5-lipoxygenase activating protein (FLAP) antagonists as a new group
of 5-LO activity regulators are also subject to this review. Also, the potential of 12-lipoxygenase (12-
LO) and 15-lipoxygenase (15-LO) inhibitors as chemopreventive agents was outlined to expand the
scope of new anticancer agents discovery. Some peptides and peptidomimetics with anti-LT activities
were described as well. In addition, the cytotoxic effects of lipoxygenase inhibitors and their adverse
effects were discussed and some novel series of natural-product-derived inhibitors of LO was also
discussed in this review.

Conclusion:

This review gives insights into the novel lipoxygenase inhibitors with anticancer activity
as well as the different molecular pharmacological strategies to inhibit the enzyme effectively. The
findings confirm that certain groups of LO inhibitors could act as promising chemopreventive agents.
Co-expression Network Analysis Revealing the Potential Regulatory Roles of LncRNAs in Atrial Fibrillation
Authors: Shen Lishui , Shen Guilin , Lu Xiaoli , Ding Guomin , Hu Xiaofeng
Published: December 2019

Background:

Atrial fibrillation (AF) is one of the most common heart arrhythmic disorders
all over the world. However, it is worth noting that the mechanism underlying AF is still dimness.

Methods:

In this study, we implemented a series of bioinformatics methods to explore the
mechanisms of lncRNAs underlying AF pathogenesis. The present study analyzed the public
datasets (GSE2240 and GSE115574) to identify differentially expressed long non-coding RNAs
(lncRNAs) and mRNAs in the progression of AF.

Results:

Totally, 71 differentially expressed lncRNAs and 390 DEGs were identified in AF.Next,
we performed bioinformatics analyses to explore the functions of lncRNAs in AF. Gene Ontology
(GO) analysis indicated that differentially expressed lncRNAs were involved in regulating multiple
key biological processes, such as cell cycle and signal transduction. Kyoto Encyclopedia of Genes
and Genomes (KEGG) pathway analysis demonstrated these lncRNAs were associated with the
regulation of MAPK and Wnt signaling pathways. Eight lncRNAs (RP5-1154L15.2, RP11-
339B21.15, RP11-448A19.1, RP11-676J12.4, LOC101930415, MALAT1, NEAT1, and PWAR6)
were identified to be key lncRNAs and widely co-expressed with a series of differentially expressed
genes (DEGs).

Conclusion:

Although further validation was still needed, our study may be helpful to elucidate the
mechanisms of lncRNAs underlying AF pathogenesis and providing further insight into identifying
novel biomarkers for AF.