bluuebunny/crossref_metadata_2025 huggingface dataset:
Randomized, Double-Blind Trial on the Impact of Word Count in Cancer Clinical Trial Consent Forms
Authors: Almodallal Yahya , Duong Quyen , Satele Daniel , Novotny Paul , Cook Kathryn D. , Chauhan Cynthia , Daiss Michelle K. , Le-Rademacher Jennifer , Looker Sherry , Martin Nichole , Smestad Michanda F. , Winham Stacey J. , Mandrekar Sumithra J. , Jatoi Aminah
Published: June 2021

PURPOSE:

This randomized, double-blind study sought to understand whether cancer clinical trial consent form verbosity detracts from patients' decision making on trial enrollment.

METHODS:

This trial tested mock consent forms of 2,000, 4,000, and 6,000 words. The first two comprised the two experimental arms and the third the control arm. Phase II was conducted to identify the promising arm, which, in phase III, was compared with the control arm. Each consent form described the same trial. Eligible adult patients reported a cancer history and English literacy. The primary end point used a patient-reported Likert scale to assess the relationship between information in the consent form and trial decision making.

RESULTS:

In phase II, 93 patients were accrued and prompted the selection of the 2,000-word consent form for phase III. In phase III, 182 patients were recruited, resulting in 240 total evaluable patients to compare the 2,000-word versus the 6,000-word arm (control). For the primary end point, 103 (84%) and 107 (91%) patients in the 2,000- and 6,000-word arms, respectively, strongly agreed or agreed with the following: “The information in this consent form helped me make a decision about whether or not to enroll in the trial” (two-sided, P = .14). Median time to read each consent form was 8 and 12 minutes, respectively (two-sided, P < .0001). Among those assigned these consent forms, 84% and 73%, respectively (two-sided, P = .04) signed or expressed a willingness to sign.

CONCLUSION:

This study's primary end point was not met. However, secondary outcomes suggest a need to further study the efficiency and efficacy of shorter consent forms for cancer clinical trial enrollment.
Toward a Lowest Effective Dose of Cyproterone Acetate in Trans Women: Results From the ENIGI Study
Authors: Kuijpers Suzanne M E , Wiepjes Chantal M , Conemans Elfi B , Fisher Alessandra D , T’Sjoen Guy , den Heijer Martin
Published: June 2021

Context

Cyproterone acetate (CPA) is a competitive inhibitor of the androgen receptor and exerts negative hypothalamic feedback. It is often used in combination with estrogens in trans women to achieve feminization. However, CPA has been associated with side effects such as changes in liver enzyme concentrations and increases in prolactin concentrations. The question is whether the testosterone-lowering effect, as well as these side effects, are dose dependent.

Objective

To assess the lowest effective dose of CPA in trans women to prevent side effects.

Methods

This longitudinal study, conducted at gender identity centers in Amsterdam, Ghent, and Florence, is part of the European Network for the Investigation of Gender Incongruence (ENIGI), a multicenter prospective cohort study. Participants were trans women (n = 882) using estrogens only or in combination with 10, 25, 50, or 100 mg CPA daily. The primary outcome measure was the concentration of testosterone at 3 and/or 12 months of hormone therapy.

Results

Using estrogens only (without CPA) led to testosterone concentrations of 5.5 nmol/L (standard error of the mean [SEM] 0.3). All doses of CPA resulted in testosterone concentrations below the predefined threshold of suppression of 2 nmol/L (10 mg, 0.9 nmol/L, SEM 0.7; 25 mg, 0.9 nmol/L, SEM 0.1; 50mg, 1.1 nmol/L, SEM 0.1; 100 mg, 0.9 nmol/L, SEM 0.7). Higher prolactin and lower high-density lipoprotein concentrations were observed with increasing doses of CPA. No differences in liver enzyme concentrations were found between the doses.

Conclusion

Compared with higher doses of CPA, a daily dose of 10 mg is equally effective in lowering testosterone concentrations in trans women, while showing fewer side effects.
Circadian Rhythms Within the Female HPG Axis: From Physiology to Etiology
Authors: Shao Shuyi , Zhao Huanqiang , Lu Zhiying , Lei Xiaohong , Zhang Ying
Published: June 2021

Declining female fertility has become a global health concern. It results partially from an abnormal circadian clock caused by unhealthy diet and sleep habits in modern life. The circadian clock system is a hierarchical network consisting of central and peripheral clocks. It not only controls the sleep–wake and feeding–fasting cycles but also coordinates and maintains the required reproductive activities in the body. Physiologically, the reproductive processes are governed by the hypothalamic–pituitary–gonadal (HPG) axis in a time-dependent manner. The HPG axis releases hormones, generates female characteristics, and achieves fertility. Conversely, an abnormal daily rhythm caused by aberrant clock genes or abnormal environmental stimuli contributes to disorders of the female reproductive system, such as polycystic ovarian syndrome and premature ovarian insufficiency. Therefore, breaking the “time code” of the female reproductive system is crucial. In this paper, we review the interplay between circadian clocks and the female reproductive system and present its regulatory principles, moving from normal physiology regulation to disease etiology.
Global proteomic analyses of human cytotrophoblast differentiation/invasion
Authors: Chen Hao , Williams Katherine E. , Kwan Elaine Y. , Kapidzic Mirhan , Puckett Kenisha A. , Aburajab Rayyan K. , Robinson Joshua F. , Fisher Susan J.
Published: June 2021

During human pregnancy, cytotrophoblasts (CTBs) from the placenta differentiate into specialized subpopulations that play crucial roles in proper fetal growth and development. A subset of these CTBs differentiate along an invasive pathway, penetrating the decidua and anchoring the placenta to the uterus. A crucial hurdle in pregnancy is the ability of these cells to migrate, invade and remodel spiral arteries, ensuring adequate blood flow to nourish the developing fetus. Although advances continue in describing the molecular features regulating the differentiation of these cells, assessment of their global proteomic changes at mid-gestation remain undefined. Here, using sequential window acquisition of all theoretical fragment-ion spectra (SWATH), which is a data-independent acquisition strategy, we characterized the protein repertoire of second trimester human CTBs during their differentiation towards an invasive phenotype. This mass spectrometry-based approach allowed identification of 3026 proteins across four culture time points corresponding to sequential stages of differentiation, confirming the expression dynamics of established molecules and offering new information into other pathways involved. The availability of a SWATH CTB global spectral library serves as a beneficial resource for hypothesis generation and as a foundation for further understanding CTB differentiation dynamics.
Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein
Authors: Rao Shilpa , Hoskins Ian , Tonn Tori , Garcia P. Daniela , Ozadam Hakan , Sarinay Cenik Elif , Cenik Can
Published: June 2021

Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a nonstructural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation levels. We discover that a functionally coherent subset of human genes is preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5′ UTRs from TOP transcripts can drive preferential expression in the presence of Nsp1. Finally, we found that LARP1, a key effector protein in the mTOR pathway, may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine-tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
Fermented medicinal herbs improve the hematological and physiological profile of Striped catfish (Pangasionodon hypophthalmus)
Authors: Syawal Henni , Kurniawan Ronal , Effendi Irwan , Austin Brian
Published: June 2021

This study sought to determine the effect of fermented medicinal herbs (FMH), i.e. cutchery (Kaempferia galanga), tumeric (Curcuma longa) and curcuma (Curcuma xanthorrhiza) in combination with molasses and probiotic drink (Yakult), administered orally on the hematological and physiological profile of striped catfish (Pangasionodon hypophthalmus). A complete randomized design (CRD) experiment was used with four levels of treatments, namely P0 (control), P1 (FMH 100 ml/kg), P2 (FMH 200 ml/kg) and P3 (FMH 300 ml/kg) of feed. The fish were kept in a farm in cages at 75 fish/m3, and fed with the experimental diets for 60 days. The results revealed that FMH (P2) dietary administration improved hematological and physiological profile of catfish, i.e total erythrocytes of 2.81 x 106 cells/mm3, hematocrit values of 39.00 %, hemoglobin levels of 10.73 g/dl, total leukocytes of 11.41 x 104 cells/mm3, blood glucose 97.33 mg/dl, and total serum protein 4.10 mg/dl compared to controls with 1.89 x 106 cells/mm3, 32.33 %, g/dl, 9.67 x 104 cells/mm3, 67.33 mg/dl, and total serum protein of 3.10 mg/dl, respectively. Moreover, the diet improved special growth rate, feed conversion ratio, feed efficiency and the survival rate of catfish
Parent priorities for research and communication concerning childhood outcomes following preterm birth
Authors: Ginnell Lorna , Boardman James P. , Reynolds Rebecca M. , Fletcher-Watson Sue
Published: June 2021

Background: Children born preterm (before 37 weeks of gestation) are at risk for several adverse childhood outcomes. Parent priorities for research into these outcomes, and preferences for receiving information about these risks, have not previously been established. Here we report the results of an online survey designed to understand parent priorities for research and their preferences for receiving information about childhood outcomes.

Methods: An online survey was circulated through social media and was completed by 148 parents of preterm children between the ages of 0 and 12 years from around the United Kingdom (UK). Survey questions were in the form of rating scale, multiple choice, ranking or open-ended free text questions. Descriptive analysis was applied to the quantitative data. Illustrative quotes were extracted from the qualitative free text data and a subset of these questions were analysed using framework analysis.

Results: Parent priorities for research centre around identification of factors which can protect against or improve adverse cognitive or developmental outcomes. The majority of parents would prefer for communication to begin within the first year of the child’s life. Parents reported a knowledge gap among health visitors, early years educators and schools.

Conclusions: In order to align with parent preferences, research should prioritise identification of protective factors and the development of effective interventions to improve outcomes. Training for health visitors and educational professionals could improve the experiences of families and children.
Assessment of bacteria and archaea levels in Çakalburnu Lagoon (İzmir) sediments by real-time PCR
Authors: Omuzbüken Burcu , Kaçar Aslı
Published: June 2021

Coastal lagoons are shallow water masses, discredited from the marines as a barrier that permits water to change through one or more inputs. These fragile ecosystems have a specific type of sediments with their own characteristics. Biogeochemical processes, mostly intervened by the benthic microbial loop, are significant for understanding the relationships among the lagoon and the contiguous coastal partition. This study was conducted in the Çakalburnu Lagoon (İzmir) area, which is located at the Bay of İzmir and the area covers 67 hectares. The aim of the present study is to constitute of determining the number of different microbial communities in the lagoon sediments. We collected from lagoon sediments samples at 7 stations and we applied a Real-time qPCR assay to determine levels of archaea (ARC), methanogenic archaea (MCRA), anaerobic methane oxidation archaea (ANME 1, ANME 2a, ANME 2c), bacteria (BAC) and sulfate-reducing bacteria (SRB2) in the study. The amount of maximum abundance of archaeal and bacterial 16S rRNA gene in sediments are 2,66x1010 gene copy numbers/g and 3,89x107 gene copy numbers/g, respectively. So, it was established that the archaeal abundance was intense in the lagoon sediments. The characterization of microbial diversity is significant for the comprehension of the biological fundamentals of the ecosystem. The data presented in our study contributes to the studies on preserving ecological and microbiological balance and determining biogeochemical cycles in sensitive ecosystems such as lagoons. The research will be conducted on studies to determine the abundance levels of seasonal and annual microbial groups in the future.
Heavy metal and Al bioaccumulation in the anemone Actinia equina Linnaeus, 1758 (Cnidaria: Actiniidae) from İskenderun Bay, North-Eastern Mediterranean, Turkey
Authors: Duysak Önder , Mazlum Yavuz , Uğurlu Erkan
Published: June 2021

The purpose of this study was to determine the accumulation levels of ten metals (Fe, Zn, Cd, Cu, Co, Ni, Al, Mn, Pb, and Cr) in the muscle tissues of Actina equina indvduals. A total of 120 individuals of A. equina were collected at six different stations in İskenderun Bay in spring 2013. The accumulation levels of heavy metals in the tissues were found to vary significantly among stations. The mean concentrations of Fe were the highest at Samandağ station (105.11 ± 74.28 mg/kg) whereas the lowest average value of Co (0.84 ± 0.10 mg/kg) was obtained at Dörtyol station. Heavy metal concentratıons in muscle tissue of A. equina were ordered as Fe>Zn>Mn>Al>Cr>Cu>Pb>Ni>Cd>Co, respectively. This study is the first detailed bioaccumulation study conducted with A. equina in İskenderun Bay.
Optical characterization of chromophoric dissolved organic matter at eutrophic and oligotrophic parts of a semi-enclosed bay (İzmir, Aegean Sea)
Authors: Alyürük Hakan , Kontaş Aynur
Published: June 2021

Optical characterization of chromophoric dissolved organic matter (CDOM) from İzmir Bay (Aegean Sea) waters was investigated. For sampling, surface and subsurface seawater from 7 stations were collected in summer 2015. Excitation-emission matrix (EEM) spectra of each sample were recorded on a fluorescence spectrophotometer. The results showed that dissolved organic carbon (DOC) concentrations and EEM peaks were increased from the outer bay to inner bay stations. EEM peaks indicated the presence of both humic-like and protein-like components which were higher at middle-inner bays than outer bay. Spearman’s rank correlation coefficients for EEM peak intensities and DOC concentrations were highly positive (p<0.05). HIX found between 0.73-3.51, whereas BIX ranged from 0.31 to 0.96 in the bay. Humification degree of CDOM in the middle-inner bays were higher compared to outer bay stations. High HIX values in the middle-inner bays could be linked to the presence of Melez stream (heavily polluted), other streams, rain run-offs and maritime activities at İzmir Bay. High BIX values in the middle-inner bays indicated presence of freshly produced DOM from bacterial origin. Optical characterization of CDOM could be used for tracing fluorescent DOM components and determining different DOM sources (autochthonous or allochthonous) in further studies.
Age estimation and the best growth model selection of the tentacled blenny Parablennius tentacularis (Brünnich, 1768) in the southeastern Black Sea
Authors: Van Ayşe , Gümüş Aysun , Özpiçak Melek , Süer Serdar
Published: June 2021

By the study's coverage, 522 individuals of tentacled blenny (Parablennius tentacularis (Brünnich, 1768)), were caught with the bottom trawl operations (commercial fisheries and scientific field surveys) between May 2010 and March 2012 from the southeastern Black Sea. The size distribution range of the sample varied between 4.8-10.8 cm. The difference between sex length (K-S test, Z=3.729, P=0.000) and weight frequency distributions (K-S test, Z=3.605, P=0.000) was found to be statistically significant. The length-weight relationship models were defined as isometric with W = 0.009L3.034 in male individuals and positive allometric with W = 0.006L3.226 in female individuals. Otolith and vertebra samples were compared for the selection of the most accurate hard structure that can be used to determine the age. Otolith was chosen as the most suitable hard structure. The current data set was used to predict the best growth model. For this purpose, the growth parameters were estimated with the widely used von Bertalanffy, Gompertz and Logistic growth functions. Akaike's Information Criterion (AIC), Lmak./L∞ ratio, and R2 criteria were used to select the most accurate growth models established through these functions. Model averaged parameters were calculated with multi-model inference (MMI): L'∞ = 15.091 cm, S.E. (L'∞) = 3.966, K'= 0.232 year-1, S.E. (K') = 0.122.
Expression of cytochrome P450 aromatase isoforms in female Alburnus tarichi (Guldenstaedtii, 1814)
Authors: Unal Guler , Marquez Emily , O'brien Mara H. , Stavropoulos Pericles , Callard Ian P.
Published: June 2021

In this study, we aimed to clone brain-derived Cyp19b and ovary-derived Cyp19a the P450 aromatase gene isoforms and to indicate the expression levels of these genes in the hypothalamus and ovary tissues from reproductively arrested ovarian development (RA) and non-arrested ovarian development (RN) Alburnus tarichi from Lake Van, Turkey. The expression levels of Cyp19b and Cyp19a genes were predominant in the hypothalamus and ovary, respectively. The level of Cyp19b mRNA was significantly lower in the hypothalamus and ovary from RA fish than in the hypothalamus and ovary from RN fish (P<0.05). The expression level of Cyp19a was significantly lower in the ovary of RA fish (P<0.05) than RN fish while no difference was found in the hypothalamus of both RA and RN fish (P<0.05). According to these findings, we suggest that the RA fish represent a segment of the population and these fish may be more sensitive to endocrine disruption compound/s than others.
Padrão de deslocamento ativo da região metropolitana de Campinas, Brasil
Authors: Goulardins Guilherme Stefano , Sá Thiago Hérick de , Kokubun Eduardo
Published: June 2021

Analisar o padrão do deslocamento ativo da Região Metropolitana Campinas, levando em consideração particularidades dos residentes e suas viagens. Utilizando as bases de dados obtidas através da Pesquisa Origem e Destino da Região Metropolitana de Campinas dos anos de 2003 e 2011, foram realizadas estatísticas descritivas e temporais a partir das características dos sujeitos, municípios e viagens. Para identificarmos diferenças adotamos o intervalo de confiança de 95% (IC 95%). Utilizamos a regressão de Poisson para verificação da correlação entre características individuais e o desfecho ser ciclista ou caminhante, adotando o valor de p < 0,05. Todos os dados foram analisados levando-se em consideração os procedimentos de amostragem para que a amostra fosse representativa. Constatou-se que a frequência de ciclistas e caminhantes e suas respectivas viagens caíram. Encontramos associação positiva para ciclista ser homem e classes econômicas mais baixas, para os caminhantes houve associação positiva ser mulher e crianças/adolescentes. Quanto ao tempo de viagem, notou-se aumento na mediana para os ciclistas e queda para os caminhantes. Não encontramos nenhuma viagem de bicicleta que faça integração com outro modo de transporte. Quanto ao porte do município, observou-se uma queda em viagens de bicicleta tanto nos municípios pequenos, médios e grandes, e os residentes de Campinas apresentaram as menores frequências.
Additive interaction of levetiracetam with lamotrigine in the mouse 6 Hz psychomotor seizure model – an isobolographic analysis
Authors: Łuszczki Jarogniew J. , Wlaź Aleksandra , Marzęda Ewa , Durmowicz Dariusz , Florek-Łuszczki Magdalena
Published: June 2021

The aim of this study was to characterize the anticonvulsant effects of levetiracetam (LEV) in combination with lamotrigine (LTG – a second-generation antiepileptic drug), in the mouse 6 Hz psychomotor seizure model. Limbic (psychomotor) seizure activity was evoked in albino Swiss mice by a current (32 mA, 6 Hz, 3 s stimulus duration) delivered via ocular electrodes and isobolographic analysis for parallel dose-response relationship curves (DRRCs) was used to characterize the consequent anticonvulsant interactions between the drug combinations. Results indicated that LEV administered singly was associated with a DRRC that was parallel to that for LTG. With isobolography for parallel DRRCs, the combination of LEV with LTG at three fixed-ratios of 1:3, 1:1 and 3:1 exerted additive interaction. LEV combined with LTG exerted additive interaction in the mouse 6 Hz psychomotor seizure model.
A review of TTS – development, types and preparations
Authors: Naleśniak Magdalena , Iwaniak Karol , Kasperek Regina , Poleszak Ewa
Published: June 2021

Transdermal Therapeutic Systems (TTS) are elastic multi-layer patches applied to the skin in order to deliver active substances into the bloodstream. One advantage of a transdermal drug delivery route over other types of medication delivery is that the patch provides a noninvasive therapy, longer duration of drug activity, and improves most of bioavailability. TTS consist of a backing layer, a drug, an adhesive, and a release liner. TTS can be divided into five basic types of systems: reservoir, matrix, microreservoir, single-layer drug in adhesive, and multi-layer drug in adhesive. In order to improve the penetration of drugs through the skin, passive and active methods are used. The researchers are constantly developing new methods of improving the delivery of drugs applied by transdermal route.
Adsorptive Studies for the Removal of Crystal Violet Dye from Aqueous Solution by Using Cicca Acida L. Stem - Activated Carbon
Authors: Ramasamy Sharmila , Kaliyaperumal Anbarasu , Pommanaickar Thamilarasu
Published: June 2021

Textile industries discharge wastewater containing various dyes including Crystal Violet dye. These dyes are very harmful for human beings, animals and plants. Therefore, the attempt is made for adsorption framework on elimination of crystal violet dye by using Cicca acida L. stem-activated carbon from aqueous solution carried out under various experimental methods and optimization conditions. Adsorption data modeled with Freundlich, Langmuir and Tempkin adsorption isotherms. Thermodynamic factors like as âˆ†Ho, âˆ†So and âˆ†Go were calculated, which indicated that the adsorption was spontaneous and endothermic nature. Based on kinetic study, pseudo-second order kinetic model was fit compared to the pseudo-first order kinetic model. The adsorbent has been characterized by SEM before and after adsorption of crystal violet dye solution.
Get smart – technological innovations in endodontics. Part 1: 3D imaging, 3D treatment planning and guided endodontics
Authors: Shah Pratik Kamalkant , Zhang Qianni , Chong Bun San
Published: June 2021

Endodontic treatment can be technically challenging, requiring a high level of clinical precision and skill to avoid mishaps, to achieve a quality result and to ensure a favourable outcome. Understandably, dentists vary in competency and ability to manage challenging endodontic cases. Coupled with patients' desire to retain their natural dentition, the demand for endodontic treatment exceeds service provision. Secondary and tertiary care providers are inundated with referrals. Access to privately funded services may also be restricted due to availability and locality. The scientific and technological revolution in healthcare has benefited many medical and dental disciplines, including endodontics: solutions may be found within these technological innovations to improve and facilitate the delivery of endodontic care.

CPD/Clinical Relevance: Technological innovations can contribute and facilitate the assessment, management and treatment of challenging endodontic cases in everyday clinical practice.
Technique tips: the lap-to-lap (knee-to-knee) examination in paediatric dentistry
Authors: Dzyuba Nikita , Reynolds Laura , Barry Siobhan
Published: June 2021

CPD/Clinical Relevance: The lap-to-lap technique is very useful and can greatly help all dentists in conducting dental examinations in young and uncooperative patients, in both primary and secondary care settings.
Development of phenotypic markers and contrast genotype candidates of target minerals related to cassava
Authors: Pratama Sylvia Nosya , SUDARSONO Sudarsono , Ardie Sintho Wahyuning , KHUMAIDA NURUL , Sukma Dewi
Published: June 2021

Abstract. Pratama SN, Sudarsono, Ardie W, Khumaida N, Sukma D. 2021. Development of phenotypic markers and contrast genotype candidates of target minerals related to cassava. Biodiversitas 22: 3049- 3056. Cassava leaves have various macro and micro-nutrients with varying levels, such as magnesium, iron, and zinc. The differences in genotypes of cassava may result in different mineral content in cassava leaves. This study aims to determine the estimator phenotypic markers and contrast genotype candidate selection related to target minerals. This study used a one-factor treatment composed of 12 cassava genotypes and arranged in a randomized block design (RBD) which each treatment was repeated 3 times. The observation was conducted on the leaves' qualitative and quantitative characters such as plant growth, leaf morphology, and leaf mineral content characters. The observation was performed at 3 and 6 months after planting. The results showed that the quantitative and qualitative characters that could be used as estimator for mineral content in cassava leaves are the Soil Plant Analysis Development (SPAD)- Chlorophyll value and leaf color. Genotypes G6-1-15-4-3, G6-2-15-1-1, G6-2-15-3-3 (lowest) and Malang (G4D0), G4D1-222, G3D2-413 (highest) could be categorized as contrast genotypes based on SPAD-value and mineral content. The strong positive correlation between Mg and Fe content with SPAD suggested that SPAD is a possible marker for high Mg and Fe content in leaves. Adversely, a weak relationship between SPAD and Zn content in leaves showed that SPAD is a weak marker for Zn content in leaves. Further research related to molecular markers development can be carried out based on these results.
Effect of light exposure on secondary metabolites production of an endophytic fungus Arthrinium rasikravindrae and its antioxidant and anticancer activities
Authors: Eltivitasari Andita , Rahmawati Rahmawati , Gemantari Baiq Maylinda , Romadhonsyah Fitra , Nurrochmad Arief , Wahyuono Subagus , Astuti Puji
Published: June 2021

Abstract. Eltivitasari A, Rahmawati, Gemantari BM, Romadhonsyah F, Nurrochmad A, Wahyuono S, Astuti P. 2021. Effect of light exposure on secondary metabolites production of an endophytic fungus Arthrinium rasikravindrae and its antioxidant and anticancer activities. Biodiversitas 22: 3156-3163. Endophytic microorganisms are one of the promising sources in producing bioactive compounds, to be developed for new drug candidates. They are found to have the ability to generate the same compounds as their host plant. Metabolite producing capacity of the endophytes is known to be affected by light exposure during fermentation process. This study focused on an endophytic fungus Arthrinium rasikravindrae isolated from Coleus amboinicus stem to reveal out its metabolite profiles due to light exposure as well as its bioactivity consequences. A. rasikravindrae was cultured on potato dextrose broth medium for 14 days and fermented in dark and exposed to natural light. Metabolite profiling was performed using TLC and GC-MS analysis. The activities were observed using DPPH assay for antioxidant and MTT assay for cytotoxicity potential. The results showed that A. rasikravindrae ethyl acetate extract produced during dark and exposed to light fermentation conditions contained different compounds but there was some which showed similarity with their host plant. Methyl octadec-9-enoate was found in all fermentation conditions as well as in C. amboinicus stem extract. Besides methyl octadec-9-enoate, methyl palmitate was also found present in both A. rasikravindrae extract fermented exposed to light and its host plant. The antioxidant activity of extract generated from dark fermentation condition was better as compared to that exposed to light with IC50 value of 66.36±0.53 vs 556.92±34.37 µg/mL. However, cytotoxic activity screening against several cancer cell lines exhibited opposing results in which extract from light-exposed fermentation resulted in better cytotoxic activity (IC50 value of 291.40 ± 2.34 µg/mL on WiDr, 336.80 ± 5.05 µg/mL on T47D, and 404.73 ± 3.46 µg/mL on Hela cell lines). Extract obtained from dark fermentation condition showed IC50 value of more than 500 µg/mL in all tested cancer cell lines. Preliminary examination on cytotoxic activity against WiDR cells suggested that the extract from light-exposed fermentation might induce cell death through mechanisms involving cell cycle arrest.
Short Communication: Assessment of Pteridophytes’ composition and conservation status in sacred groves of Jhargram District, South West Bengal, India
Authors: Uday Dr. Uday Kumar Sen , BHAKAT RAM KUMAR
Published: June 2021

Abstract. Uday UKS, Bhakat RK.. 2021. Short Communication: Assessment of Pteridophytes’ composition and conservation status in sacred groves of Jhargram District, South West Bengal, India. Biodiversitas 22: 3171-3178. Sacred groves are significant as community-preserved areas and have contributed to the conservation of biodiversity, thereby playing a key role in environmental management. The ecological and related cultural values of the species and the activities of local communities would make it possible to understand the importance of the protection of the sacred groves and also to prepare integrated approaches to biodiversity at the ecosystem level. Thus, this study aimed to investigate the status of pteridophyte diversity in the sacred groves of Jhargram district, West Bengal, India. The study showed that 77 pteridophyte species belonging to 44 genera and 15 families were collected and described, of which nine species were classified as Lycopodiopsida and sixty-eight species as Polypodiopsida. The floristic analysis revealed the dominance of the order Polypodiales (70.13%) followed by Aspleniaceae (23.38%), and Polypodiaceae (23.38%). The results also showed the predominance of the genera Selaginella with five species. Of the total species, 76.62% were terrestrial species, 14.29% were epiphytes, and 9.09% were aquatic species. The highest frequency is shown by Class C (25.97%) and major pteridophyte plants (81.81%) were not been evaluated till now.
The earthworm’s diversity and their relationship to the soil physicochemical properties under the stands of perennial plant at the Mount Merapi forest, Yogyakarta, Indonesia
Authors: Minarsih Sri , Hanudin Eko - , Nurudin Makruf
Published: June 2021

Abstract. Minarsih S, Hanudin E, Nurudin M. 2021. The earthworm’s diversity and their relationship to the soil physicochemical properties under the stands of perennial plant at the Mount Merapi forest, Yogyakarta, Indonesia. Biodiversitas 22: 3237-3244. The study was to propose earthworm as bioindicator and its correlation to the soil physicochemical properties underneath some perennial plants. Soil samples and earthworm observation was taken out at a depth of 0-10 cm and 10-20 cm under the stands of Acacia decurrens, coffee, Albizia chinensis, bamboo, snake fruit, and Acacia mangium. Soil moisture, temperature and Physico-chemical properties were measured, such as texture, pH, organic C, mineralized C, total N, mineralized N, available P, and base cations (Ca, Mg, K, Na). The results revealed that the earthworms density underneath of the stands of coffee was 105.4 ind.m-2 > snake fruit 92.6 ind.m-2 > Albizia chinensis  66.7 ind.m-2 > A. decurrens ? bamboo 40.7 ind.m-2 > A. mangium 37.0 ind.m-2. The dominant species of the earthworms found at a depth of 0-10 cm consisted of four species, namely: Pheretima hamayana, Pheretima californica, Eudrillus eugeniae, and Eiseniella tetraeda. Meanwhile, the earthworms diversity underneath the stands of coffee was H’=1.26 > A. mangium H’=1.03 > Albizia chinensis  H'=0.69 > ?H'=0.69 > bamboo H'=0.59. The soil physicochemical properties was positively correlated to the earthworms density was C-mineralized (r = 0.823) ? soil moisture (r = 0.585) ? available K (r = 0.529) ? available Ca (r = 0.505) ? available Mg (0.494). The results could be concluded that labile organic carbon, water, and alkaline cations were the important factors in improving soil biological fertility in the active volcano area.
Short Communication: Phytochemical diversity and bioactivity of Malaysian Premna cordifolia (Lamiaceae)
Authors: DAUD DZULSUHAIMI , MD DEWA MUHAMMAD SHAFIQ AZAMUDIN , MOHAMAD MAHBOB EMI NORZEHAN , WAN ABDUL RAZAK WAN RAZARINAH
Published: June 2021

Abstract. Daud D, Dewa MSAM, Mahbob ENM, Razak WRWA. 2021. Short Communication: Phytochemical diversity and bioactivity of Malaysian Premna cordifolia (Lamiaceae). Biodiversitas 22: 3245-3248. The aims of the present study are to determine the chelation potential and protective effect of Premna cordifolia leaves ethanolic extract in lead intoxicated mice. Twenty-four male mice were divided into four groups with six animals each. Group 1 was healthy mice and received 2 ml/kg bwt distilled water. Group 2 was healthy mice and supplemented with 200 mg/kg bwt P. cordifolia leaves ethanolic extract. Group 3 was lead intoxicated mice and received 2 ml/kg bwt distilled water. Group 4 was lead intoxicated mice and supplemented with 200 mg/kg bwt P. cordifolia leaves ethanolic extract. All treatments were given for 14 days. Chelation activity was determined by measuring the concentrations of lead in the liver, kidney and testis by using atomic absorption spectroscopy. Sperm quality was tested according to World Health Organization manual and testosterone was estimated by using ELISA kit. Spectroscopic data showed that P. cordifolia leaves ethanolic extract was able to lower lead concentrations in liver, kidney and testis of lead intoxicated mice. Following a decrease in lead concentrations, sperm quality and testosterone levels were restored in lead intoxicated mice supplemented with P. cordifolia leaves ethanolic extract. In conclusion, P. cordifolia leaves ethanolic extract has the potential to be developed as an alternative remedy for treating lead poisoning effects.
The performance and genetic variation of first and second generation tropical alfalfa (Medicago sativa)
Authors: Suwignyo Bambang , ARIFIN LUKMANA , UMAMI NAFIATUL , MUHLISIN MUHLISIN , SUHARTANTO BAMBANG
Published: June 2021

Abstract. Suwignyo B, Arifin L, Umami N, Muhlisin, Suhartanto B. 2021. The performance and genetic variation of first and second generation tropical alfalfa (Medicago sativa). Biodiversitas 22: 3265-3270. This study aimed to compare the growth performance, nutrient content, seed viability, and genetic variation of first- and second-generation alfalfa (Medicago sativa L.). First and second-generation alfalfa seeds were obtained from the Forage and Pasture Science Laboratory, Department of Animal Nutrition and Feed Science, Faculty of Animal Science, Universitas Gadjah Mada (UGM), Yogyakarta, Indonesia. First generation alfalfa (F1) seeds were obtained from cross breeding of two different parental alfalfa varieties, namely, Canadian and local. The second-generation (F2) seeds were obtained from plants of the first-generation alfalfa (F1). A randomized design experiment was conducted using the two types of alfalfa (first- and second generation). Alfalfa from Canada as female parent was used as the baseline in the genetic masker test. Seeds were planted in a polybag, watered twice a day, and received 12 hours of daylight and 4 hours of artificial light. Plants were then harvested 8 weeks after planting by cutting the plant canopy. Genetic variation was examined using the Inter Simple Sequence Repeat (ISSR) method followed by descriptive analysis. Germination, plant height, dry matter content, organic matter, and crude protein were assessed as variables using a Student’s T-test. Our results showed that germination, plant height, leaf color, and nutrient content (dry matter, organic matter, and crude protein) of the first- and second-generation alfalfa plants were not significantly different. However, the second-generation alfalfa demonstrated better seed viability than the first generation plants, then it can be categorized as a new genotype (tropical alfalfa) based on genetic variation analysis.
Antimicrobial resistance in coagulase-negative staphylococci isolated from subclinical mastitis in Ettawa Crossbred goat (PE) in Yogyakarta, Indonesia
Authors: Suwito Widodo , NUGROHO WIDAGDO SRI , WAHYUNI AGNESIA ENDANG TRI HASTUTI , SUMIARTO BAMBANG
Published: June 2021

Abstract. Suwito W, Nugroho WS, Wahyuni AETH, Sumiarto B. 2021. Antimicrobial resistance in coagulase-negative staphylococci isolated from subclinical mastitis in Ettawa Crossbred goat (PE) in Yogyakarta, Indonesia. Biodiversitas 22: 3418-3422. Subclinical mastitis (SCM) in Ettawa Crossbred Goat (PE) is most frequently caused by staphylococci with a significant reduction in milk yield. The aim of this study is to determine antimicrobial resistance patterns of coagulase-negative staphylococci (CoNS) from PE goat SCM. A total of 36 CoNS isolates originating from PE goat SCM were collected in semisolid tube use in this study. All CoNS isolates were further examined for antimicrobial susceptibility testing by the Kirby-Bauer disc diffusion method. Antibiotic susceptibility of CoNS isolated samples according to Clinical Laboratory Standards Institute (CLSI). The CoNS isolates showed the highest resistance rate against sulfamethoxazole (65%), ampicillin (55.56%), penicillin (45%), cefoxitin (33.33%), erythromycin (25%), oxytetracycline (20%), tetracycline (15%), gentamicin and neomycin (11.11%), while oxacillin was sensitive. The highest of multiple antimicrobials resistance observed 15% in ampicillin, penicillin and tetracycline, then 5-10% in ampicillin, penicillin, erythromycin, tetracycline and oxytetracycline. The majority of CoNS in this study were resistant to sulfamethoxazole and then, followed by ampicillin, penicillin, cefoxitin, erythromycin, oxytetracycline, tetracycline, gentamicin and neomycin. In addition, most isolates were penicillin-resistant and multidrug-resistant (MDR).
Biostatistics of fall armyworm Spodoptera frugiperda in maize plants in Bogor, West Java, Indonesia
Authors: RUSSIANZI WANDA , Anwar Ruly , TRIWIDODO HERMANU
Published: June 2021

Abstract. Russianzi W, Anwar R, Triwidodo H. 2021. Biostatistics of fall armyworm Spodoptera frugiperda in maize plants in Bogor, West Java, Indonesia. Biodiversitas 22: 3463-3469. Fall Armyworm (FAW) Spodoptera frugiperda (J.E. Smith) is an invasive species that has become important pest of maize in Indonesia since 2019. This research was aimed to study the biology and demographic statistics of FAW in maize at Bogor. Daily observations of 132 FAW individuals from egg to death were carried out as the basis for compiling biology and life table. The demographic statistics of FAW were calculated using the Jackknife approach from the basic life table data. ImagoFAW actives at night. Mating activity occurs between 06.00 pm – 04.00 am, while egg-laying activity occurs between 06.00 pm-10.00 pm. Most hatching occurs between 00.00 am - 02.00 am. FAW has 6 larvae instars and there is no difference in stage between larvae that develop into male and female, which is around 15 days. The male pupae stage was longer than the female pupae, 8.78 ± 0.12 days and 7.81 ± 0.15 days. Male and female imagoes have the same life cycle, which is about 10 days. The life cycle of FAW was 32.26 ± 0.41 days, with a preoviposition period of 2.56 ± 0.45 days. Fecundity of FAW reaches 1012.62 ± 99.12 eggs per female imago. The population of FAW in Bogor has an intrinsic growth rate of 0.154 ± 0.001 individuals/day, with gross reproduction rate of 0.154 ± 0.001 individuals per generation, and net reproduction rate of 104.781 ± 0.155 individuals per imago per generation and a generation time of 30.114 ± 0.002 days.
Antiplasmodial activity, biosynthetic gene clusters diversity, and secondary metabolite constituent of selected Indonesian Streptomyces
Authors: Damayanti Ema , Lisdiyanti Puspita , Sundowo Andini , Ratnakomala Shanti , Dinoto Achmad , Widada Jaka , MUSTOFA Mustofa
Published: June 2021

Abstract. Damayanti E, Lisdiyanti P, Sundowo A, Ratnakomala S, Dinoto A, Widada J, Mustofa. 2021. Antiplasmodial activity, biosynthetic gene clusters diversity, and secondary metabolite constituent of selected Indonesian Streptomyces. Biodiversitas 22: 3478-3487. Actinobacteria of the genus Streptomyces are known as the primary candidate antibiotics, but still limited for antiplasmodial drugs. This study aimed to investigate the antiplasmodial activity, the biosynthetic gene clusters (BGCs) diversity, and the secondary metabolites constituent of selected Indonesian Streptomyces. The bacteria were isolated from various habitats: karst soil (GMR22), mangrove sediments (BSE7F and SHP 22-7), and marine sediment (GMY01). Molecular identification by 16S rDNA sequencing were performed for confirmation and morphological characterization by scanning electron microscope (SEM) were performed for identification. In vitro antiplasmodial assay was performed on human Plasmodium falciparum FCR-3. The BGCs which encode secondary metabolites were analysed using antiSMASH version 5 based on available whole genome sequence (WGS) data. The secondary metabolites were obtained from liquid fermentation followed by extraction using methanol and ethyl acetate. The secondary metabolites constituent was determined by liquid chromatography tandem mass spectrometry (LC-MS/MS). The molecular identification showed that GMR22 had similarity to Streptomyces lactacystinicus (98.02%), while BSE7F was similar to Streptomyces althioticus (97.06%), SHP 22-7 was similar to Streptomyces rochei (94.84%), and GMY01 to Streptomyces odonnellii (98.57%). All of isolates had morphological characteristics as the genus Streptomyces bacteria. The highest Plasmodium inhibition (81.84 ± 3.5%) was demonstrated by ethyl acetate extract of marine-derived Streptomyces sp. GMY01 (12.5 µg/mL). Non-ribosomal polyketide synthetase (NRPS), polyketide synthase (PKS) and hybrid of NRPS-PKS were the major BGCs in all Streptomyces. Majority of the Streptomyces produced compounds containing CHON elements with molecular weight approximately 100-400 Da. The active extract of GMY01 bacterium had five major detected compounds, namely kuraramine (C12H18N2O2), laminine (C9H20N2O2) 2-ethylacetanilide (C10H13NO), propoxur (C11H15NO3), and 3-methyl-1,2-diphenylbutan-1-one (C17H18O). This Indonesian marine bacterium is potential for bioassay guided isolation of antiplasmodial compounds in the future studies.
500  W peak power cavity dumped 2  µm GaSb-based VECSEL
Authors: Hoehler Jacob , Gibson Ricky , Reed Jennifer M. , Bedford Robert
Published: June 2021

A single transverse mode high-pulse-energy vertical-external-cavity
surface-emitting laser (VECSEL) was developed. The GaSb-based VECSEL
emits at a wavelength of 2.04 µm with a peak power exceeding 500 W
while maintaining good beam quality. The cavity employs a Pockels cell
combined with a low-loss thin film polarizer to selectively dump the
intracavity energy into a 10 ns pulse. The laser has promise for
incoherent LIDAR, materials processing, gas sensing, and nonlinear
optics.
Modeling turbulence in underwater wireless optical communications based on Monte Carlo simulation: erratum
Authors: Vali Zahra , Gholami Asghar , Ghassemlooy Zabih , Michelson David G. , Omoomi Masood , Noori Hamed
Published: June 2021

Corrections are given for errors in the presentation of equations in
J. Opt. Soc. Am.
A 34, 1187
(2017)JOAOD60740-323210.1364/JOSAA.34.001187.
Experimental investigation of the angular symmetry of optical force in a solid dielectric
Authors: Xi Xiang , Ma Jingwen , Zhou Zhong-Hao , Hu Xin-Xin , Chen Yuan , Zou Chang-Ling , Dong Chun-Hua , Sun Xiankai
Published: June 2021

The textbook-accepted formulation of electromagnetic force was proposed by Lorentz in the 19th century, but its validity has been challenged due to incompatibility with the special relativity and momentum conservation. The Einstein–Laub formulation, which can reconcile those conflicts, was suggested as an alternative to the Lorentz formulation. However, intense debates on the exact force are still going on due to lack of experimental evidence. Here, we report the first experimental investigation of angular symmetry of optical force inside a solid dielectric, aiming to distinguish the two formulations. The experiments surprisingly show that the optical force exerted by a Gaussian beam has components with the angular mode numbers of both 2 and 0, which cannot be explained solely by the Lorentz or the Einstein–Laub formulation. Instead, we found that a modified Helmholtz theory by combining the Lorentz force with additional electrostrictive force can explain our experimental results. Our results represent a fundamental leap forward in determining the correct force formulation and will update the working principles of many applications involving electromagnetic forces.