bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of prenatal central nervous system anomalies: obstetric management, fetal outcomes and chromosome abnormalities
Authors: Tan Ann Gee , Sethi Neha , Sulaiman Sofiah
Published: March 2022

Objective

To study the outcomes of fetuses who were diagnosed with central nervous system (CNS) anomalies during prenatal period and to describe the obstetric management of those pregnancies.

Methods

In this retrospective study, fetuses who were detected to have central nervous system anomalies by prenatal ultrasound from January 2010 to December 2019 were recruited. Data regarding prenatal diagnosis and obstetric outcomes were retrieved from maternal and paediatric records. The prognosis of fetuses who were born alive was classified based on their neurodevelopmental outcome within two years of life.

Results

There were a total of 365 fetuses with CNS anomalies within the 10-year study period, with a mean gestational age of 24.65±7.37 weeks at diagnosis. Ventriculomegaly (23.36%) was the commonest CNS anomalies seen. 198 (54.20%) of these fetuses had associated extra-CNS anomalies, with cardiovascular being the most common system involved. Fetal karyotyping was performed in 111 pregnancies, with chromosomal aberrations detected in 53 (49.07%) cases and culture failure in 3 cases. Majority of the chromosomal abnormalities were Edward syndrome (trisomy 18) and Patau syndrome (trisomy 13). Fetuses with congenital CNS anomalies and abnormal chromosomal karyotyping were more likely to be diagnosed earlier by prenatal ultrasound and tend to have poorer obstetric and neurocognitive prognosis. Prenatally, 86 (23.56%) of the cases were lost to follow up and likely to deliver elsewhere. Among the 279 cases whom their pregnancy outcomes were available, 139 (49.82%) pregnancies resulted in live births, 105 (37.63%) pregnancies were electively terminated, while the remaining 35 (12.54%) pregnancies ended in spontaneous loss. The decision of termination of pregnancy largely depends on mean diagnostic gestational age, presence of chromosomal aberrations and abnormal amniotic fluid volume in those fetuses. Two years after delivery, only 75 (53.96%) children out of 139 live births were still alive, 43 (30.93%) died and 21 (15.11%) cases were lost to follow-up. 32 (23.02%) children with prenatally diagnosed CNS anomalies had normal neurodevelopmental outcome. The presence of multiple CNS anomalies and involvement of extra-CNS anomalies indicated a poorer neurodevelopmental prognosis.

Conclusion

Less than 50% of fetuses with prenatally diagnosed CNS anomalies resulted in live births. Even if they survive till delivery, 36.45% of them passed away within 2 years and 62.79% of children who survived till 2 years old had neurodevelopmental disability.
Suicidal ideation among recently arrived refugees in Germany
Authors: Nesterko Yuriy , Haase Elisa , Schönfelder Antje , Glaesmer Heide
Published: March 2022

Background

Refugees are considered a high-risk population for developing mental health disorders. Yet little research has been conducted on suicidal ideation among refugees resettled in Western high-income countries. In the present hstudy, suicidal ideation and its association with different socio-demographic, flight-related, and mental health-related factors were analyzed in recently arrived refugees in Germany.

Methods

The study was conducted in a reception facility for asylum-seekers in Leipzig, where 564 newly arrived adult residents participated. The questionnaire included socio-demographic and flight-related questions as well as standardized instruments for assessing suicidal ideation (item 9 from PHQ-9), a variety of traumatic experiences (LEC-5), posttraumatic stress disorder (PCL-5), depression (PHQ-8), and somatic symptoms (SSS-8). Multiple logistic regression models were run to predict suicidal ideation in relation to different socio-demographic, flight, and mental health-related factors.

Results

In total, 171 (30.3%) participants who had just or very recently arrived in Germany reported having experienced suicidal ideation within the two weeks prior to being assessed. Those who reported suicidal ideation also reported higher prevalence of somatic symptoms, posttraumatic stress disorder, depression, and experiences of sexual violence, as well as worse self-rated mental and physical health. In addition, there were significant independent associations between suicidal ideation and (1) younger age, (2) longer flight duration, (3) experiences of sexual violence, (4) symptoms of posttraumatic stress disorder, and (5) symptoms of depression.

Conclusions

The results emphasize the association between suicidal ideation and different clinically relevant mental health symptoms among newly arrived refugees in Germany. Special attention should not only be given to refugees suffering from symptoms of poor mental health, but also to those of younger age as well as refugees who have experienced sexual violence, as they might be affected by suicidal ideation whether or not they suffer from other mental health problems.
The effect of the number of hepatic inflow occlusion times on the prognosis of ruptured hepatocellular carcinoma patients after hepatectomy
Authors: Xia Feng , Huang Zhiyuan , Ndhlovu Elijah , Zhang Mingyu , Chen Xiaoping , Zhang Bixiang , Zhu Peng
Published: March 2022

Background and aim

It has been previously reported that inflow occlusion does not affect postoperative outcomes in hepatocellular carcinoma patients. However, for patients with ruptured hepatocellular carcinoma(rHCC), the effect of hepatic inflow occlusion and the number of occlusion times on the prognosis is unknown.

Methods

203 patients with ruptured hepatocellular carcinoma were enrolled in this study. They were first divided into the non-hepatic inflow occlusion (non-HIO) group and the hepatic inflow occlusion (HIO) group. The Kaplan–Meier method was used to compare the recurrence-free survival and overall survival between the two groups. Patients in the HIO group were further divided into one-time HIO and two times HIO groups. KM method was also used to compare the two groups. Finally, independent risk factors affecting RFS and OS were determined by multivariate Cox regression analysis.

Result

In the non-HIO group, 1-,3- and 5-year OS rates were 67.0%, 41.0%, and 22.0%respectively, and RFS rates were 45.0%, 31.0%, and 20.0% respectively; In the one-HIO group, the 1-,3-, and 5-year OS rates were 55.1%, 32.1%, and 19.2% respectively, and RFS rates were 33.3%, 16.7%, and 7.7% respectively; In the two-HIO group, 1-,3-, and 5-year OS rates were 24.0%, 0.0%, and 0.0% respectively, and RFS rates were 8.0%, 0.0%, and 0.0% respectively. By Cox regression analysis, HIO was an independent risk factor for a poor prognosis in rHCC patients.

Conclusion

One time hepatic inflow occlusion did not affect postoperative OS, but negatively affected the RFS of rHCC patients; two times hepatic inflow occlusion negatively affected the postoperative OS and RFS in patients with rHCC.
A simplified Gibson assembly method for site directed mutagenesis by re-use of standard, and entirely complementary, mutagenesis primers
Authors: Olszakier Shunit , Berlin Shai
Published: March 2022

Background

Site-directed mutagenesis (SDM) is a key method in molecular biology; allowing to modify DNA sequences at single base pair resolution. Although many SDM methods have been developed, methods that increase efficiency and versatility of this process remain highly desired.

Method

We present a versatile and simple method to efficiently introduce a variety of mutation schemes using Gibson-assembly but without the need to design uniquely designated Gibson primers. Instead, we explore the re-use of standard SDM primers (completely overlapping in sequence) in combination with regular primers (~ 25 bps long) for amplification of fragments flanking the site of mutagenesis. We further introduce a rapid amplification step of the Gibson-assembled product for analysis and quality control, as well as for ligation, or re-ligation at instances the process fails (avoiding expenditure of added Gibson reaction mixtures).

Results

We first demonstrate that standard SDM primers can be used with the Gibson assembly method and, despite the need for extensive digestion of the DNA past the entire primer sequence, the reaction is attainable within as short as 15 min. We also find that the amount of the assembled Gibson product is too low to be visualized on standard agarose gel. Our added amplification step (by use of the same short primers initially employed) remedies this limitation and allows to resolve whether the desired Gibson-assembled product has been obtained on agarose gel or by sequencing of amplicons. It also provides large amounts of amplicons for subsequent ligations, bypassing the need to re-employ Gibson mixtures. Lastly, we find that our method can easily accommodate SDM primers with degenerate sequences.

Conclusion

We employ our alternative approach to delete, replace, insert, and degenerate sequences within target DNA sequences, specifically DNA sequences that proved very resistant to mutagenesis by multiple other SDM methods (standard and commercial). Importantly, our approach involves the re-use of SDM primers from our primer-inventory. Our scheme thereby reduces the need (and time and money) to design and order new custom Gibson-primers. Together, we provide a simple and versatile protocol that spans only 4 days (including the added amplification step), requires minimal primer sets and provides very high yields and success rates (> 98%).
Being fast or cautious? Sociocultural conditions influencing the sexual pathways of Black females in the United States
Authors: Crooks Natasha , King Barbara , Tluczek Audrey
Published: March 2022

Background

Black females in the United States face unique sociocultural conditions that impact their sexual development and increase their risk for sexually transmitted infections (STI), including but not limited to chlamydia, gonorrhea, and HIV. Research has not adequately explained how sociocultural conditions contribute to this increased risk. The purpose of our investigation was to explore the sociocultural conditions that influence Black cisgender females risk for STI.

Methods

This grounded theory study involved in-depth audio-recorded interviews with 20, primarily heterosexual, Black females ages 19–62.

Results

Findings informed a conceptual model that builds on previous theory about the sexual development of Black females and explains how sociocultural conditions impact two, participant identified, sexual pathways: Fast and Cautious. Movement on these sexual pathways was not always a linear trajectory; some participants shifted between pathways as their sociocultural contexts changed (i.e., sexual assault, STI, and level of protection). The Fast sexual pathway often led to greater STI risk.

Conclusions

This model may inform future research designed to prevent STI/HIV and promote the sexual health of Black females across the life course.
The public impact of academic and print media portrayals of TMS: shining a spotlight on discrepancies in the literature
Authors: Scheper Abigail , Rosenfeld Cynthia , Dubljević Veljko
Published: March 2022

Background

Transcranial magnetic stimulation (TMS) is an FDA approved treatment for major depression, migraine, obsessive compulsive disorder, and smoking addiction. TMS has gained popular media support, but media coverage and commercial reporting of TMS services may be contributing to the landscape of ethical issues.

Methods

We explore the differences between the academic and print media literature portrayals of TMS to evaluate their ethical impact for the public. We performed a comprehensive literature review using PubMed and NexisUni databases to evaluate the literature available on TMS from 2014 to 2019. Our sample consisted of 1632 academic articles and 468 print media articles for a total of 2100 articles. We then coded each article for seven specific top-level codes: (1) type of source, (2) year of publication, (3) purpose of TMS application, (4) age of subjects, (5) population, (6) overall tone, and (7) specification of TMS parameters. We also made some additional notes of the TMS parameters where specified and the breakdown of mental health applications.

Results

Our results indicated several discrepancies between the academic and the print media reporting about TMS technology, particularly with regards to tone and specificity. Namely, the academic sample was largely neutral and specific about the parameters under which TMS was being applied, while the print media sample was heavily optimistic and presented the application of TMS with far less specificity. There was some convergence between the two samples, such as the focus of both on therapy as the predominant TMS application.

Conclusions

We call upon the academic community to increase scrutiny of TMS services in order to ensure that people’s knowledge of health technologies is not unduly influenced by sensational claims and a general lack of adequate information.
Fat mass and obesity–associated protein promotes liver steatosis by targeting PPARα
Authors: Wei Xiaohui , Zhang Jielei , Tang Min , Wang Xuejiao , Fan Nengguang , Peng Yongde
Published: March 2022

Background

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide. The fat mass and obesity–associated protein (FTO) has been shown to be involved in obesity; however, its role in NAFLD and the underlying molecular mechanisms remain largely unknown.

Methods

FTO expression was first examined in the livers of patients with NAFLD and animal and cellular models of NAFLD by real-time PCR and Western blotting. Next, its role in lipid accumulation in hepatocytes was assessed both in vitro and in vivo via gene overexpression and knockdown studies.

Results

FTO expression was obviously elevated in the livers of mice and humans with hepatic steatosis, probably due to its decreased ubiquitination. FTO overexpression in HepG2 cells induced triglyceride accumulation, whereas FTO knockdown exerted an opposing effect. Consistent with the findings of in vitro studies, adeno-associated viruses 8 (AAV8)-mediated FTO overexpression in the liver promoted hepatic steatosis in C57BL/6J mice. Mechanistically, FTO inhibited the mRNA of peroxisome proliferator-activated receptor α (PPARα) in hepatocytes. Activation of PPARα by its agonist GW7647 reversed lipid accumulation in hepatocytes induced by FTO overexpression.

Conclusions

Overall, FTO expression is increased in NAFLD, and it promotes hepatic steatosis by targeting PPARα.
Molecular identification and safety assessment of Bacillus strains isolated from Burkinabe traditional condiment “soumbala”
Authors: Dabiré Yérobessor , Somda Namwin Siourimè , Somda Marius K. , Mogmenga Iliassou , Traoré Abdoulaye K. , Ezeogu Lewis I. , Traoré Alfred S. , Ugwuanyi Jerry O. , Dicko Mamoudou H.
Published: March 2022

Purpose

Alkaline-fermented foods (AFFs) play an essential role in the diet of millions of Africans particularly in the fight against hidden hunger. Among AFFs, soumbala is a very popular condiment in Burkina Faso, available and affordable, rich in macronutrients (proteins, lipids, carbohydrates, essential amino acids, and fatty acids), micronutriments (minerals, B group vitamins), and fibers. Bacillus spp. are known to be the predominant microbial species in AFFs and thus have elicited enhanced interest as starter cultures or probiotics. However, few data exist on identification and safety attributes of relevant Bacillus species from African AFFs, particularly from Burkinabe soumbala.

Methods

This study aimed to genotypically characterize 20 Bacillus strains previously isolated from soumbala, using PCR and sequencing of the 16S rRNA genes, and to evaluate their safety attributes.

Results

Phylogenetic analysis revealed that the strains were most closely related by decreasing numbers to B. cereus, B. subtilis, Bacillus sp., B. tropicus, B. toyonensis, B. nealsonii, B. amyloliquefaciens, Brevibacillus parabrevis, and B. altitudinis. Among the isolates, 10 were β-hemolytic and 6 were γ-hemolytic while 4 were of indeterminate hemolysis. The 6 γ-hemolytic (presumptively non-pathogenic) strains were susceptible to all tested antibiotics except bacitracin. Strains F20, and F21 were the most sensitive to imipenem (38.04 ± 1.73 mm and 38.80 ± 1.57 mm, respectively) while strain B54 showed the weakest sensitivity to bacitracin (11.00 ± 0.63 mm) with high significant differences (p < 0.0001).

Conclusion

The findings highlight identification and safety quality of Bacillus strains which could be further characterized as probiotic-starter cultures for high-quality soumbala production.
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data
Authors: Kaliyaperumal Rajaram , Wilkinson Mark D. , Moreno Pablo Alarcón , Benis Nirupama , Cornet Ronald , dos Santos Vieira Bruna , Dumontier Michel , Bernabé César Henrique , Jacobsen Annika , Le Cornec Clémence M. A. , Godoy Mario Prieto , Queralt-Rosinach Núria , Schultze Kool Leo J. , Swertz Morris A. , van Damme Philip , van der Velde K. Joeri , Lalout Nawel , Zhang Shuxin , Roos Marco
Published: March 2022

Background

The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles.

Results

Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR.

Conclusions

Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.
Effects of sustainable agricultural practices on farm income and food security in northern Ghana
Authors: Setsoafia Edinam Dope , Ma Wanglin , Renwick Alan
Published: March 2022

The adoption of sustainable agricultural practices (SAPs) has been recommended by many experts and international institutions to address food security and climate change problems. Global support for the Sustainable Development Goals has focused attention on efforts to up-scale the adoption of SAPs in developing countries where growth in populations and incomes compromises the resilience of natural resources. This study investigates the factors affecting smallholder farmers’ decisions to adopt SAPs (improved seed, fertilizer, and soil and water conservation) and the impacts of the adoption on farm income and food security, using data collected from Ghana. Food security is captured by the reduced coping strategy index and household dietary diversity. The multinomial endogenous switching regression model is utilized to address selection bias issues. Results show that farmers’ decisions to adopt SAPs are influenced by the social demographics of the households, plot-level characteristics, extension services and locations. Adopting all three SAPs has larger positive impacts on farm income and food security than adopting single or two SAPs. Our findings advocate for policies that enhance the quality of extension service and strengthen farmer-based organizations for the wider dissemination of adequate SAP information. Farmers should be encouraged to adopt SAPs as a comprehensive package for increasing farm income and ensuring food security.
Life in the hole: practices and emotions in the cultural political economy of mitigation deterrence
Authors: Markusson Nils , McLaren Duncan , Szerszynski Bronislaw , Tyfield David , Willis Rebecca
Published: March 2022

Negative emissions techniques (NETs) promise to capture greenhouse gases from the atmosphere and sequester them. Since decarbonisation efforts have been slow, and the climate crisis is intensifying, it is increasingly likely that removing greenhouse gases from the atmosphere will be necessary to meet internationally-agreed targets. Yet there are fears that pursuing NETs might undermine other mitigation efforts, primarily the reduction (rather than removal) of greenhouse gas emissions. This paper discusses the risk of this phenomenon, named ‘mitigation deterrence’. Some of us have previously argued that a cultural political economy framework is needed for analysing NETs. Such a framework explains how promises of future NETs deployment, understood as defensive spatio-temporal fixes, are depoliticised and help defend an existing neoliberal political regime, and its inadequate climate policy. Thus they risk deterring necessary emissions reductions. Here we build on that framework, arguing that to understand such risks, we need to understand them as the result of historically situated, evolving, lived practices. We identify key contributing practices, focussing in particular but not exclusively on climate modelling, and discuss how they have been reproduced and co-evolved, here likened to having dug a hole for ourselves as a society. We argue that understanding and reducing deterrence risks requires phronetic knowledge practices, involving not just disembodied, dispassionate technoeconomic knowledge-making, but also strategic attention to political and normative issues, as well as emotional labour. Reflecting on life in the hole hurts.
A review of academic literacy research development: from 2002 to 2019
Authors: Li Dongying
Published: March 2022

Academic literacy as an embodiment of higher-order language and thinking skills within the academic community bears huge significance for language socialization, resource distribution and even power disposition within the larger sociocultural context. However, although the notion of academic literacy has been initiated for more than twenty years, there still lacks a clear definition and operationalization of the construct. The study conducted a systematic review of academic literacy research based on 94 systematically selected research papers on academic literacy from 2002 to 2019 from multiple databases. These papers were then coded respectively in terms of their research methods, types (interventionistic or descriptive), settings and research focus. Findings demonstrate (1) the multidimensionality of academic literacy construct; (2) a growing number of mixed methods interventionistic studies in recent years; and (3) a gradual expansion of academic literacy research in ESL and EFL settings. These findings can inform the design and implementation of future academic literacy research and practices.
Estradiol Valerate vs Ethinylestradiol in Combined Oral Contraceptives: Effects on the Pituitary-Ovarian Axis
Authors: Haverinen Annina , Luiro Kaisu , Kangasniemi Marika H , Piltonen Terhi T , Hustad Steinar , Heikinheimo Oskari , Tapanainen Juha S
Published: March 2022

Context

Limited studies have compared the effects of combined oral contraceptives (COCs) containing natural estrogens and synthetic ethinylestradiol (EE) on reproductive hormones.

Objective

To compare estradiol valerate (EV) + dienogest (DNG), EE + DNG, and DNG alone (active control) on levels of follicle stimulating hormone (FSH), luteinizing hormone, anti-Müllerian hormone (AMH), ovarian steroids, sex hormone binding globulin (SHBG), and the free androgen index (FAI).

Methods

This spin-off study from a randomized trial enrolled 59 healthy, 18 to 35-year-old ovulatory women, outpatients at Helsinki and Oulu University Hospitals, Finland, who were randomized to EV 2 mg + DNG 2-3 mg (n = 20); EE 0.03 mg + DNG 2 mg (n = 20); and DNG 2 mg (n = 19) for 9 weeks. Blood samples were drawn at baseline, and at 5 and 9 weeks. Age and BMI were comparable between groups; 3 women discontinued.

Results

EV + DNG suppressed FSH by −27% (−51% to −3%) (median [95% CI]) vs EE + DNG, −64% (−78 to −51), P = 0.04, but AMH levels decreased similarly by −9% (−18 to −0.1) vs −13% (−28 to 0.2), P = 0.38, respectively. EV + DNG increased SHBG levels by 56% (30% to 82%) and EE + DNG by 385% (313% to 423%), P < 0.001. Total testosterone decreased by 16% (−27% to −5%) in the EV + DNG group but it did not decrease in the EE + DNG group, whereas the FAI decreased by −39% (−54% to −25%) vs −72% (−78% to −67%), P < 0.001. DNG alone did not induce changes in any of these parameters.

Conclusion

Compared with EE + DNG, treatment with EV + DNG resulted in milder pituitary downregulation and reduced induction of hepatic SHBG synthesis—potentially carrying more beneficial health effects.
Developing leadership skills in children
Authors: Καραγιάννη Δέσποινα
Published: March 2022

Αυτή η διατριβή εξέτασε πώς οι έφηβοι και οι νέοι αντιλαμβάνονται την ηγεσία. Πιο συγκεκριμένα, η διατριβή εξέτασε τις πεποιθήσεις και τις αντιλήψεις τους για το τι σημαίνει να είσαι ηγέτης στην Ελλάδα και κατανοήθηκαν οι παράγοντες που συμβάλλουν στις ιδέες και τις αντιλήψεις τους για την ηγεσία. Η διατριβή στόχευε να απαντήσει στα ακόλουθα ερευνητικά ερωτήματα: με ποιους τρόπους τα προγράμματα ηγεσίας επηρεάζουν τις σκέψεις και τις συμπεριφορές των εφήβων και των νέων σε σχέση με τις ιδέες τους για την ηγεσία, ποιοι παράγοντες επηρεάζουν τις σκέψεις και τις συμπεριφορές των εφήβων σε σχέση με τις ιδέες τους για την ηγεσία, ποια περιστατικά εντοπίζουν οι έφηβοι ότι επηρεάζουν τις σκέψεις και τις συμπεριφορές τους όσον αφορά την ηγεσία. Η διατριβή παρουσιάζει τα αποτελέσματα μιας συστηματικής ανασκόπησης και δύο ποιοτικών μελετών. Στην ενότητα συζήτησης, η διατριβή αντικατοπτρίζει τη συμβολή της έρευνας στη μελέτη της ανάπτυξης ηγεσίας μεταξύ των εφήβων. Περιορισμοί και θέματα αναστοχαστικότητας συζητούνται λεπτομερώς. Η διατριβή κάνει συστάσεις σχετικά με το πώς το ελληνικό εκπαιδευτικό σύστημα μπορεί να ενσωματώσει τα ευρήματα στο ελληνικό αναλυτικό πρόγραμμα σπουδών. Τα θέματα της διατριβής είναι σημαντικά για τους υπεύθυνους χάραξης πολιτικής στα σχολεία. Τέλος, συζητούνται μελλοντικές κατευθύνσεις για έρευνα.
The genome sequence of the orange-striped anemone, Diadumene lineata (Verrill, 1869)
Authors: Wood Christine , Bishop John , Harley Joanna , Mrowicki Robert ,   Marine Biological Association Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life programme,   Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: March 2022

We present a genome assembly from an individual Diadumene lineata (the orange-striped anemone; Cnidaria; Anthozoa; Actiniaria; Diadumenidae). The genome sequence is 313 megabases in span. The majority of the assembly (96.03%) is scaffolded into 16 chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 17.6 kilobases in length.
Zespół rakowiaka: kliniczny opis przypadku rakowiaka: opuszki dwunastnicy, płuca, raka jasnokomórkowego nerki.
Authors: Adamczyk-Gruszka Olga , Gruszka Jakub , Świercz Grzegorz , Zwierzyńska Anna
Published: March 2022

Chirurgia bariatryczna w ostatnich latach jest najbardziej rozpowszechnioną, a zarazem najskuteczniejszą metodą w leczeniu otyłości. Jest najskuteczniejszą opcją terapeutyczną dla pacjentów otyłych, wiąże się jednak z dużym ryzykiem zabiegu operacyjnego, oraz powikłaniami późnymi związanymi z zaburzeniami hormonalnymi, hipoglikemią, osteoporozą, zespołem złego wchłaniania. W ostatnich latach zwiększa się liczba operacji bariatrycznych z udziałem niezależnych procedur medycznych. Pacjent oraz lekarze biorący udział w planowanej operacji i dalszym leczeniu powinni być świadomi możliwych zagrożeń i powikłań związanych z otyłością patologiczną i zastosowanym leczeniem. Rakowiak żołądka (GC) zwany guzem neuroendokrynny żołądka jest rzadkim nowotworem wywodzącym się z komórek enterochromafinopodobnych żołądka. Ponad 75% GC to widoczne zmiany w endoskopii, pozostała część znajduje się w błonie śluzowej i nie jest identyfikowana w badaniu endoskopowym. Dlatego wymagana jest mapa żołądka z biopsjami odbytu  i dna żołądka, aby potwierdzić jego obecność. W aktualnych klasyfikacjach NET zaleca się, aby guzy neuroendokrynne (pNET) guzy trzustki oraz guzy NET w innych lokalizacjach, były klasyfikowane jako guzy neuroendokrynne (NET)
First record of leucism in the volcano rabbit (Romerolagus diazi), endemic to México
Authors: Guerrero José Antonio , Montes-Carreto Leslie M. , Uriostegui-Velarde Juan Manuel , Teporingos 1 Brigada Comunitaria
Published: March 2022

El leucismo es la pérdida total o parcial de la pigmentación del pelaje o plumaje sin afectar el color de los ojos, la piel y las uñas.  Durante uno de los recorridos diarios de vigilancia y protección que realiza la brigada comunitaria Teporingos 1 realizó el registro de un zacatuche juvenil leucístico en los terrenos de la Reserva Ecológica Comunal de San Miguel Topilejo de la Ciudad de México, México.  En esta nota, reportamos este primer registro de leucismo en la especie y discutimos la relevancia de este hallazgo.
Türkiye’de müzik sosyolojisinde önemli bir unsur olan düğünde çalan müzisyenlerin sosyo-ekonomik durumları ve pandeminin etkisi hakkında bir durum çalışması: Safranbolu örneği
Authors: Ertan Hacısüleymanoğlu Gülcan , Sağer Turan
Published: March 2022

Bu araştırma pandemi döneminde Safranbolu ilçesinde düğünde çalan müzisyenlerin, sosyo ekonomik durumları ve pandeminin etkisine ilişkin görüşlerinin belirlenmesini amaçlamıştır. Safranbolu, Türk folklorik unsurlarından düğün ve düğünde çalan müzisyenlerin araştırılmasında önemli bir bölgedir. Araştırma, nitel araştırma yöntemlerinden durum çalışması yöntemine göre yapılmıştır. Düğünde çalan müzisyenlerininin deneyimlerin objektif bir şekilde betimlenmesinin amaçlanması açısından da fenomonolojik yaklaşım araştırmanın yöntemleri arasında yer alabilir. Araştırmada katılımcıların seçimi için bazı ölçütler belirlenmiştir. Bunlar; düğünde çalan müzisyen olmaları, zengin deneyim ve bilgi içeriğine sahip olmalarıdır. Bu ölçütlere uyan beş düğünde çalan müzisyen katılımcı olarak belirlenmiştir. Araştırmacı, Karabük Üniversitesi’nde çalışmakta olup Safranbolu ilçesine yani verilerin toplandığı yere oldukça yakındır. Araştırmada kullanılan örnekleme yöntemleri; zengin ve derinlemesine verilerin alınması ve belli ölçütlerin katılımcılarda aranması açısından ölçüt örnekleme, verilerin kolay ve ekonomiklikle toplanmasında Safranbolu’nun seçilmesi açısından kolayda örnekleme, araştırmanın amaçlarına hizmet edecek özellikteki katılımcı grubunun belirlenmesi açısından amaçlı örnekleme metodu şeklindedir. Verilerin analizinde, veriler içerik analizi yöntemi kullanılmıştır. Araştırma bulgularına göre görüşler Gelir Durumu, Başka Meslek İcra Etme, Başka Meslek İcra Etme Nedenleri ve Pandemi Dönemi Sorunlar olmak üzere dört tema ve on yedi alttema altında toplanmıştır. Sonuç olarak Safranbolu’daki düğünde çalan müzisyenler; pandemi dönemi öncesi gelir durumlarını yeterli görmekte, ancak bir çoğu farklı meslekleri de icra etmekte olduklarını ve nunun nedeni olarak yapılan işin sezonluk olduğunu belirttikleri görülmektedir. Düğünde çalan müzisyenler, sosyal güvence ve devlet desteklerinin artırılmasını etmektedirler.
Capturing the magic of pianistic sound and touch: toward a synergy of ear and fingers in the creation of the artistic image
Authors: Valjarevic Vladimir
Published: March 2022

“To learn how to hear, to educate the ear, to develop a student’s sense of voicing and timbre in nuanced hearing – this is the first task of a pedagogue-musician, a defining pillar of his work.” These words of the great Russian musician, Grigory Kogan, shine light on the inspiring path of what it means for a teacher to simultaneously develop student’s ears and fingers with the aim of building the artistic image of a composition. Of course, such instruction requires a holistic approach and, yet some approaches from the past were anything but that. Indeed, the 19th century saw a rise in mechanical finger training, which often resulted in injuries and stultified the ear. This article analyzes these and other past trends in piano teaching and performance and their influence on the training of fingers, ears--or both. In addition, it offers practical advice on how best to foster the simultaneous schooling of ears and fingers, with the goal of nurturing a complete musician.
Revealing Spanish mackerel’s diversity in Indonesian through local commodities in the fish market
Authors: WIDAYANTI RINI , NUGROHO HERJUNO ARI , MEGARANI DOROTHEA VERA , WIDIASIH DYAH AYU , PAKPAHAN SUHENDRA
Published: March 2022

Abstract. Widayanti R, Nugroho HA, Megarani DV, Widiasih DA, Pakpahan S. 2021. Revealing Spanish mackerel’s diversity in Indonesian through local commodities in the fish market. Biodiversitas 23: 624-630. The objective of this study was to explore the diversity of Spanish mackerel in Indonesian Archipelago based on commodities offered in local fish markets. Eighteen specimens were collected from six different fish markets around the Indonesian archipelago. According to Wallace Line, the cytochrome B sequence was used as a genetic marker to reveal diversity from West Indonesia to East Indonesia. Gene amplification was performed using the polymerase chain reaction followed by Sanger sequencing. Based on DNA sequence analysis, we identified three species of Spanish Mackerel available at various fish markets around the region. The first group is related to Scomberomorus commerson, which was sold in both Western and Eastern Indonesian fish markets; the second group is related to Scomberomorus semifasciatus, which was sold in Eastern Indonesian fish markets; and the third group is related to Scomberomorus koreanus, which was sold in Western Indonesian fish markets. The genetic differences amongst Spanish Mackerel populations ranged from 0 to 17% and the average evolutionary divergence in the overall populations was determined to be 4%. The data collected can be utilized to initiate map mackerel diversity based on CYT B sequence throughout the Indonesian Archipelago, as well as for further study and application in the identification of foods produced from mackerel.
Mangrove species diversity and carbon stock in silvofishery ponds in Deli Serdang District, North Sumatra, Indonesia
Authors: HAREFA MEILINDA SURIANI , NASUTION ZULKIFLI , MULYA MISWAR BUDI , MAKSUM AZHAR
Published: March 2022

Abstract. Harefa MS, Nasution Z, Mulya MB, Maksum A. 2021. Mangrove species diversity and carbon stock in silvofishery ponds in Deli Serdang District, North Sumatra, Indonesia. Biodiversitas 23: 655-662. Mangrove-based silvofishery ponds are promoted as a win-win solution for biodiversity conservation, climate change mitigation as well as income generation for coastal communities. This study aimed to analyze the species diversity and carbon stock of mangrove vegetation in silvofishery ponds in Tanjung Rejo Village, Percut Seituan Sub-district, Deli Serdang District, North Sumatra, Indonesia. Data of the mangrove species were obtained using vegetation analysis, and the potential carbon stock was estimated based on allometric equations of both above- and below-ground tree biomass. For this purpose, plot samples from 22 silvofishery ponds were taken by establishing 5 aligned circular plots, each with a radius of 5.64 m, perpendicular to the coastline and with a distance of 15 meters between their perimeters. The results show that the mangrove species with the highest Importance Value Index (IVI) was Rhizophora apiculata (122.05%), followed by Excoecaria agallocha (42.29%) and Avicennia marina (36.84%), and the lowest IVI was Sonneratia caseolaris (1.48%). Higher IVI values indicate a larger carbon deposit from mangrove vegetation in silvofishery ponds. Our results indicate that mangrove area coverage of 44-80% per hectare in silvofishery ponds can deposit 40-50 tonnes of carbon per hectare and have greater potential carbon stock compared to coverage below 40%. The mangrove management activities with the sylvofishery scheme have a good impact on the community's economy and also maintain the existence of mangroves as carbon storage.
Morphological and molecular identification of multi-antibiotic resistant bacteria in the wound site of diabetic ulcers
Authors: RISQIYAH WIDAYANTI , NARULITA ERLIA , ROFIQOH AFIFATUR , LUDFI ACHMAD SYAIFUL , IQBAL MOCHAMMAD
Published: March 2022

Abstract. Risqiyah W, Narulita E, Rofiqoh A, Ludfi AS, Iqbal M. 2021. Morphological and molecular identification of multi-antibiotic resistant bacteria in the wound site of diabetic ulcers. Biodiversitas 23: 663-670. The study aimed to determine the characteristics of diverse species of bacteria found in diabetic ulcers and the inhibition of antibiotics against these bacteria. The method used is Gram staining for morphological characterization, identification using 16S rRNA gene, and pour plate for antibiotic resistance test. The morphological characterization result showed that the colonies had white color, circular shape, flat elevation, entire edge, small size, and basil shape with Gram negative type of bacteria. Another result showed yellow, greenish, pellucid, and green color, irregular shape, raised elevation, undulate and lobate edge, medium size, coccus and Gram positive type of bacteria. Query cover of molecular identification showed 73-100% and 77.61-96.77% for the result of similarity identification with Alcaligenes faecalis, Shigella flexneri, Enterococcus faecalis, Proteus mirabilis, and Acinetobacter seohaensis. The identification and antibiotic resistance testing showed that the bacterial species found in diabetic ulcers was A. faecalis strain NRBC 13111, which was resistant to all tested antibiotics, except A. faecalis strain NRBC 13111 from the UB 2.3K and A. faecalis strain NRBC 13111 from the sample UB 3.4M. Enterococcus faecalis strain ATCC 19433 was resistant to ceftriaxone, ceftazidime, clindamycin and metronidazole, intermediates to cefoperazone, and sensitive to ciprofloxacin. Proteus mirabilis strain JCM 1669 was resistant to clindamycin and metronidazole, sensitive to ceftriaxone and ciprofloxacin, intermediates to ceftazidime and cefoperazone. Proteus mirabilis strain ATCC 29906, A. seohaensis strain SW-100 and S. flexneri strain ATCC 29903 were resistant to all tested antibiotics.
Distribution, occurrence and molecular characterization of Bacillus related species isolated from different soil in Basrah Province, Iraq
Authors: ALYOUSIF NASSIR ABDULLAH
Published: March 2022

Abstract. Alyousif NA. 2021. Distribution, occurrence and molecular characterization of Bacillus related species isolated from different soil in Basrah Province, Iraq. Biodiversitas 23: 679-686. Bacillus related species are widely predominant in various environments such as soil with diverse environmental conditions. These bacteria are one of the most explored groups of bacteria in industrial biotechnology due to their enzymes. The present study was aimed to isolate, screen and determine the distribution of Bacillus related species from soil samples. The total Bacillus related species counts in one gram of each soil sample ranged between 3.2 X 103 cfu/g and 4 X 103 cfu/g. A total of 43 isolates with different morphologies were isolated from the soil samples out of ten different habitats and the number of morphotypes recovered from each habitat varied from 2 to 7. The molecular identification of isolates by PCR technique and sequencing of 16S rDNA gene indicated that 43 isolates belonged to the genera Bacillus, Cytobacillus, Priestia and Peribacillus. The species Bacillus licheniformis and Bacillus subtilis were the most distributed species in the habitats. The bacterial isolates were showed 100% similarity, except 8 isolates were showed 99% similarity were identified as new strains and their sequences were deposited at the National Center for Biotechnical Information (NCBI). The phylogenetic tree was constructed by MEGA X software based on 16S rDNA gene sequences of Bacillus related species to evaluate their close relationship and evolution. The study revealed the higher diversity and distribution of Bacillus related species in the soil samples and the molecular technique was the best method for identifying Bacillus related species.
Structure and composition of tree community in the upstream area of Batang Mahat Watershed, Lima Puluh Kota District, West Sumatra, Indonesia
Authors: EKAWATY RENI , YONARIZA YONARIZA , EKAPUTRA ERI GAS , ARBAIN ARDINIS
Published: March 2022

Abstract. Ekawaty E, Yonariza, Ekaputra EG, Arbain A. 2021. Structure and composition of tree community in the upstream area of Batang Mahat Watershed, Lima Puluh Kota District, West Sumatra, Indonesia. Biodiversitas 23: 687-696. Land-use change at the upstream area of Batang Mahat Watershed is assumed to cause flood during the rainy season and is related to vegetation community which has been heavily exploited. Information regarding the current vegetation condition in this area has never been studied; therefore, this study aims to investigate the structure and composition of the tree community in the upstream area of Batang Mahat at Jorong Kubu Baru Nagari, Baruh Gunung, Bukit Barisan District. Furthermore, sampling was implemented using three 20x50 m belt-transects with 10 m intervals between each sample. The results showed 1) 116 identified and three unidentified tree samples belonging to 40 families; 2) The trees with the highest important value index (IVI) in transect 1 were Rhodoleia championii (63.339%) and Calophylum soulatteri (23.697%), in transect 2 Voacanga foetida (48.568%) and Schima wallichii (32.756%), and in transect 3 Schima wallichii (42.964%) and Voacanga foetida (40.713%); 3) The saplings with the highest IVI in transect 1 were Timonius sp. (33.111%) and Alstonia sp. (21.345%), in transect 2 Hancea pengangensis (24.551%) and Sterculia sp. (21.199%), as well as transect 3 Voacanga foetida (42.862%), and Macaranga lowii (30.844%); 4) Both vegetation categories have considerably high diversity (H’ tree 3.13-3.2, H’ saplings 3.04-3.36), and were moderately distributed across studied transects (E1 = 2.025, E2 = 2.089, E3 = 2.016). From the results, it can be concluded that the forest in the upstream area of the Batang Mahat watershed, which was located in Jorong Kubu Baru, Nagari Baruh Gunung, was still in the good category.
The potential of copper-resistant bacteria Acinetobacter sp. strain CN5 in decolorizing dyes
Authors: IRAWATI WAHYU , PINONTOAN REINHARD , MOURETTA BELLEN , YUWONO TRIWIBOWO
Published: March 2022

Abstract. Irawati W, Pinontoan R, Mouretta B, Yuwono T. 2021. The potential of copper-resistant bacteria Acinetobacter sp. strain CN5 in decolorizing dyes. Biodiversitas 23: 680-686. Bacteria with multi-resistance to copper and dyes may be employed in bioremediation of copper and dye waste more effectively than physical or chemical remediation. This study aims at determining the effect of the addition of various textile dyes and copper on the growth of Acinetobacter sp. CN5 and its ability to decolorize dyes. The dye resistance test was carried out by inoculating bacterial isolates into Luria Bertani media containing 50, 100, 150, 200, 250, 300, 350, 400, 450, and 500 ppm dyes. The twelve dyes used in the test were methylene blue, malachite green, congo red, mordant orange, reactive black, direct yellow, basic fuchsine, reactive orange, dispersion orange, remazol red, wantex yellow, and wantex red. The decolorization activity was analyzed by spectrophotometry at a 300-900 nm wavelength. The study results demonstrated that bacteria thrived in media containing 50 ppm of all dyes, except malachite green dye. Acinetobacter sp. CN5 was found to be resistant to up to 500 ppm methylene blue, basic fuchsine, and wantex red and resistant to congo red at 450 ppm. Acinetobacter sp. CN5 was also able to decolorize methylene blue, congo red, basic fuchsine, and red wantex by 57.64%, 53.17%, 91.37%, and 67.50%, respectively. The addition of 5 mM CuSO4 to the medium increased the ability of Acinetobacter sp. CN5 to decolorize the congo red from 57.64% to 82.58%.
Survival and growth rates of mangroves planted in vertical and horizontal aquaponic systems in North Jakarta, Indonesia
Authors: HILMI ENDANG , SARI LILIK KARTIKA , CAHYO TRI NUR , MAHDIANA ARIF , SOEDIBJA PETRUS HARY TJAHJA , SUDIANA EMING
Published: March 2022

Abstract. Hilmi E, Sari LK, Cahyo NT, Mahdiana A, Soedibja PHT, Sudiana E. 2021. Survival and growth rates of mangroves planted in vertical and horizontal aquaponic systems in North Jakarta, Indonesia. Biodiversitas 23: 687-694. Mangrove rehabilitation is aimed to reverse mangrove deforestation and degradation. Various efforts have been conducted to rehabilitate the degraded mangroves, yet problems arise when planting mangroves in the high and permanently water-logged areas in coastline. The aquaponic system is a mangrove planting method introduced to reduce the impact of permanent and high water inundation. This research aims to analyze the survival rate of mangroves planted using vertical and horizontal aquaponic systems in Jakarta's north coast and investigate the correlation between physico-chemical environmental parameters and the survival and growth rates of the planted mangroves. The results showed that the survival rate of mangroves planted in the vertical aquaponic system reached 55.4-96.9%. On the other hand, the highest survival rate in the horizontal aquaponic system was obtained in mangrove planting at 80-100 cm from the bottom with survived plants between 70-90%. The height growth rate of mangroves planted in the aquaponic system was between 0.95-2.33 cm/month. The correlation analysis showed that soil salinity, soil pH and water salinity had a high correlation to support living trees of mangrove seedlings. Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa had highest survival and adaptation in this planting system.