bluuebunny/crossref_metadata_2025 huggingface dataset:
Consistency ofBRCA1andBRCA2Variant Classifications Among Clinical Diagnostic Laboratories
Authors: Lincoln Stephen E. , Yang Shan , Cline Melissa S. , Kobayashi Yuya , Zhang Can , Topper Scott , Haussler David , Paten Benedict , Nussbaum Robert L.
Published: July 2017

Purpose

Genetic tests of cancer predisposition genes, BRCA1 and BRCA2, inform significant clinical decisions for both physicians and patients. Most uncovered variants are benign, and determining which few are pathogenic—disease causing—is sometimes challenging and can potentially be inconsistent among laboratories. The ClinVar database makes deidentified clinical variant classifications from multiple laboratories publicly available for comparison and review, per recommendations by the American Medical Association, the American College of Medical Genetics, the National Society for Genetic Counselors, and other organizations.

Methods

Classifications of more than 2,000 BRCA1/2 variants in ClinVar that represent approximately 22,000 patients were dichotomized as clinically actionable or not actionable and compared among as many as seven laboratories. The properties of these variants and classification differences were investigated in detail.

Results

Per-variant concordance was 98.5% (CI, 97.9% to 99.0%). All discordant variants were rare; thus, per-patient concordance was estimated to be higher (99.7%). ClinVar facilitated resolution of many of the discordant variants, and concordance increased to 99.0% per variant and 99.8% per patient when reclassified, but not yet resubmitted, variants and submission errors were addressed. Most of the remaining discordances seemed to involve either legitimate differences in expert judgment regarding particular scientific evidence or were classifications that predated the availability of important scientific evidence.

Conclusion

Significant classification disagreements among professional clinical laboratories represented in ClinVar are infrequent yet important. Unrestricted sharing of clinical genetic data allows detailed interlaboratory quality control and peer review, as exemplified by this study.
Homologous Recombination Deficiency in Breast Cancer: A Clinical Review
Authors: den Brok Wendie D. , Schrader Kasmintan A. , Sun Sophie , Tinker Anna V. , Zhao Eric Yang , Aparicio Samuel , Gelmon Karen A.
Published: July 2017

BRCA1 and BRCA2 germline mutation–associated breast cancers are known to be deficient in the process of homologous recombination and often respond favorably to drugs targeting this important DNA repair pathway. There is emerging evidence that a significant proportion of patients with BRCA1/ BRCA2 wild-type breast cancer are also deficient in homologous recombination, and it is hypothesized that these patients may derive similar benefit from drugs targeting this pathway. Current research has focused on the development of a companion diagnostic to identify these sporadic BRCA-like tumors. This review outlines the various approaches that researchers have taken to predict homologous recombination deficiency as part of correlative biomarker work in various studies and clinical trials in breast cancer. As some of these tests of homologous recombination deficiency move closer to clinical use, understanding the approach and limitations of each is of relevance to clinicians who treat patients with breast cancer.
Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board
Authors: Dalton W. Brian , Forde Patrick M. , Kang Hyunseok , Connolly Roisin M. , Stearns Vered , Gocke Christopher D. , Eshleman James R. , Axilbund Jennifer , Petry Dana , Geoghegan Cindy , Wolff Antonio C. , Loeb David M. , Pratilas Christine A. , Meyer Christian F. , Christenson Eric S. , Slater Shannon A. , Ensminger Jennifer , Parsons Heather A. , Park Ben H. , Lauring Josh
Published: July 2017

Purpose

Tumor genomic profiling for personalized oncology therapy is being widely applied in clinical practice even as it is being evaluated more formally in clinical trials. Given the complexities of genomic data and its application to clinical use, molecular tumor boards with diverse expertise can provide guidance to oncologists and patients seeking to implement personalized genetically targeted therapy in practice.

Methods

A multidisciplinary molecular tumor board reviewed tumor molecular profiling reports from consecutive referrals at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins over a 3-year period. The tumor board weighed evidence for actionability of genomic alterations identified by molecular profiling and provided recommendations including US Food and Drug Administration–approved drug therapy, clinical trials of matched targeted therapy, off-label use of such therapy, and additional tumor or germline genetic testing.

Results

One hundred fifty-five patients were reviewed. Actionable genomic alterations were identified in 132 patients (85%). Off-label therapies were recommended in 37 patients (24%). Eleven patients were treated off-label, and 13 patients were enrolled onto clinical trials of matched targeted therapies. Median progression-free survival of patients treated with matched therapies was 5 months ( 95% CI, 2.9 months to not reached), and the progression-free survival probability at 6 months was 43% (95% CI, 26% to 71%). Lack of locally available clinical trials was the major limitation on clinical actionability of tumor profiling reports.

Conclusion

The molecular tumor board recommended off-label targeted therapies for a quarter of all patients reviewed. Outcomes were heterogeneous, although 43% of patients receiving genomically matched therapy derived clinical benefit lasting at least 6 months. Until more data become available from precision oncology trials, molecular tumor boards can help guide appropriate use of tumor molecular testing to direct therapy.
dot-app: a Graphviz-Cytoscape conversion plug-in
Authors: Fitts Braxton , Zhang Ziran , Maher Massoud , Demchak Barry
Published: July 2017

dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (.dot, .gv) files, also known as DOT files due to the .dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including Graphviz, Gephi, Tulip, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not have as many styling options as the Graphviz software suite. dot-app enables the interchange of networks between Cytoscape and DOT-compatible applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.
The Institutions of Innovative Development of The Region
Authors: Бахарева  , Bahareva Ol'ga , Романова  , Romanova Anna
Published: July 2017

Strengthening and dissemination of innovative forms of business organization, addressing the problems of their participation in the development of market relations becomes critical for the formation of effective demand, development of innovative entrepreneurship and stimulating business in region. Currently, there is a need to ensure the further development of innovative technologies (TIM-technology and BIM), to form a stable institutional environment, development of regional innovative infrastructure, to organize effective management towards sustainable functioning of the region.
Economic performance of sports clubs charitable status in Poland
Authors: Wyszyński Artur
Published: July 2017

The main aim of this article is to assess the financial condition and results of Polish football clubs who have the status of public benefit organizations (OPP). The analysis was conducted for clubs that were played matches in the 2013/2014 season in the men's football tournament at all levels except the highest such competitions. Ekstraklasa (no clubs having the status OPP) for levels I, II, III, IV league and class district, A , B and C. All the clubs analyzed as a function of the association. The analysis shows that clubs are in a bad financial situation. Most clubs, regardless of the grade level in which the matches were played were characterized by a low value of wealth. Average debt was close to 100%. As a result, nearly one-third of the clubs showed a negative equity value. About half of the clubs observed a negative value total return on assets and return on sales. In the structure of revenues are the primary source of public funds. Other sources of income included clubs, private funds, other and income from the 1% tax on individuals
The identification of the differences in the level of the speed abilities and the endurance-speed abilities: a case study from the second league football team
Authors: Różycki Waldemar
Published: July 2017

The use of technical-tactical abilities is to a great extent dependent on the condition preparation of the player. In order to obtain the information on the players abilities to perform locomotive tasks a collection of tests and trials is carried out. The aim of the work was to identify the differences in the level of speed abilities and endurance-speed abilities of the players of the second league football club basing on a test including multiple effort tasks of maximum intensity with short-term breaks of the active character (modified Rast Test). The analyzed parameters included: start speed, run speed, speed endurance 1, speed endurance 2. The analysis of the research data has proved that the group varies in the abilities to perform locomotive tasks. The highest level of differences was detected in the parameter of start speed, the lowest in speed endurance 1. The cluster analysis appeared to be a sufficient method of identification of relatively homogenous groups of players.
The quality of teaching by lecturers in the evaluation of students of the Academy of Physical Education and University of Economics in Katowice
Authors: Socha Paulina
Published: July 2017

The aim of the study was to present the expectations of students towards their teachers in the teaching process . Material and methods. The study was conducted using the questionnaire method among students of Physical Education and the University of Economics in Katowice. Assessed the quality of education by using 5-points Likerts scale . Basic results. The most highly valued aspects of the work of lecturers were having practical knowledge, skill and competence of its transmission. Conclusions. The study may serve scholars to align standards and level of education relative to the requirements of the students.
University Sports Association as the way to sport activity development among Silesian students
Authors: Mędrak Anna , Rżany Michał , Otremba Barbara , Brodowska Elwira , Szynal Magdalena , Alcer Magdalena , Górecka Anna , Stefaniak Tomasz , Suszyński Krzysztof , Górka Dariusz
Published: July 2017

Introduction. There are two fundaments of healthy lifestyle philosophy: regular physical activity and proper diet. The development of physical activity among students is determined by many complex factors. We can distinguish certain aspects such as university profile, access to the sport facilities and the opportunity to participate in sport activities which are organized by sport clubs or University Sports Association. The aim of the study. The aim of the study was to analyze the factors that affect self-assessment of students physical activity. The following questions have been asked: 1.Is the choice of the university related to the access to sport activities which are organized by University Sport Association?2.Does the participating in activities, which are organized by University Sport Association, help in physical development?3.Is there any relation between the location, time, type, the way of sport activities which are offered by University Sport Association and participating in them?Material and methods. 395 students took part in research: 257 women (18-27 years old) (x=20,7 ; SD=1,4) and 108 men (18-26 years old) (x=21; SD=1,45). All the students are from five Silesian universities. Method used for the research was the anonymous questionnaire consisting of 37 questions which concerned: the way of the physical activity taken by students, the issue of University Sport Association and the influence of the university profile on physical activity development. The Likert scale was used in 21 questions. Statistical description included descriptive statistics. Degree of difference was defined by ANOVA analysis. Results. Descriptive analysis showed significant dependence between the type of the university and the location of sport facilities (p=0,04). The type of the university has no influence on the factors like: time (p=0,07) and type of sport activities offered by University Sport Association (p=0,39). There is also an important connection between the type of the university and resignation from doing sport (p=0,0002). Mostly – Medical University of Silesia students, least frequently – University of Silesia students. There is dependence between approach to doing sport among students and the type of university (p=0,01). The university which helps the most in sport career is University of Economics in Katowice.Conclusions:1.Taking the physical activity by student depends on location of the university and sport facilities.2.The factors such as time and type of sport activities are not related to the type of the university.3.The type of the university influence the resignation from doing sport by students.
Exclusion of criminal liability of sports participants for sport injuries
Authors: Cegliński Paweł
Published: July 2017

This paper deals with one of the criminal law problems, which is criminal liability of sports participants for injuries occuring during the practice of a sport. This article aims to provide a brief summarization of the most important conception explaining this problem in Polish law – sport risk as a circumstance excluding criminal liability. The research is supported by the analysis of Polish literature. There are also some empirical examples involved.
The Fusion of Fascia-Oriented Exercise and Pilates in Rollpilates Course at Masaryk University
Authors: Vychodilová Renata , Pokorná Alena , Vrtělová Hana
Published: July 2017

The aim of this paper is to analyse Pilates and fasia-oriented exercise in terms of their possible interconnection. We intend to introduce the fusion of Pilates and fascia-oriented exercise in the form of a new sports course Rollpilates lectured at the Faculty of Sports studies, Masaryk University, Brno. The course was formed in the project approved as part of the Masaryk University Development Fund and involves a nouveau approach towards the interconnection of two types of exercise.                The methods include an analysis of scientific publications and educational materials dealing with Pilates and fascia-oriented exercise. In order to comprehend the theory and principles of fascia-oriented exercise and its interconnection with Pilates and to study new trends in Pilates, the work incorporates a bibliographic search, a research probe, the participation in several educational courses and the interviewing of experienced lectures of fascia-oriented and Pilates exercise, with the support of our own practical experience. Based on the analysis, a Rollpilates course was established and its programme, content and principles were defined. In order to enhance and propagate the course, educational online material was designed and displayed in the Information system of Masaryk University.
Rating preferred predisposition personal trainer
Authors: Stefaniak Tadeusz , Harmaciński Dariusz , Groffik Bartosz , Pawlak Gabriel
Published: July 2017

Services provided by personal trainers in Poland are becoming more popular. The legal situation of this professional group in Poland is unregulated, which creates many doubts about the competence and suitability personal trainer.                The essence of the work presented in the study is to determine the changes in terms of perception of competence coach, taking place in recent years. The research was conducted in 2009 and repeated in 2015 in fitness clubs coming in Lower Silesia.                The study involved 240 respondents, including 72 women and 168 men.                Research results indicate that over the years, the number of people regularly using the services of a coach nearly doubled. The significant number of people for whom the profession of coaching combined with better and better assessment of the social and his authority continues to grow. 67.5% of respondents think that the coach should be well built and have mixed personality traits.
Towards coopetition in sport. Challenges for the market of high competition
Authors: Stosik Aneta , Leśniewska Aleksandra
Published: July 2017

One of the most important aspects of leading service organizations is searching for advantages and creative solutions. Organizations look for new qualitative assets, create new values for their clients and create processes on the basis of their key competences. That kind of approach enable to improve organizational effectiveness and economic efficiency but more important to gain competitive advantages. Sport and recreational services develops extremely dynamically. Changes of lifestyle and social norms impose on clients non-standard actions and looking for individualized services. Personal training became a response for specific client’s needs. Personal trainers help not only to shape bodies and build fitness for clients, but also provide professional and individualized services by their competency complementarity. To achieve this personal trainers need to look for support and cooperation with other specialists and trainers in the whole customer service process. Building competitive advantages by cooperation with competitors cause a situation where personal trainers have to cooperate and compete with them at the same time - this phenomenon is called co-opetition and becomes more often a standard in recreational services.
A Simple Algorithm for Predicting Bacteremia Using Food Consumption and Shaking Chills: A Prospective Observational Study
Authors: Komatsu Takayuki , Takahashi Erika , Mishima Kentaro , Toyoda Takeo , Saitoh Fumihiro , Yasuda Akari , Matsuoka Joe , Sugita Manabu , Branch Joel , Aoki Makoto , Tierney Lawrence M. , Inoue Kenji
Published: July 2017

BACKGROUND

Predicting the presence of true bacteremia based on clinical examination is unreliable.

OBJECTIVE

We aimed to construct a simple algorithm for predicting true bacteremia by using food consumption and shaking chills.

DESIGN

A prospective multicenter observational study.

SETTING

Three hospital centers in a large Japanese city.

PARTICIPANTS

In total, 1,943 hospitalized patients aged 14 to 96 years who underwent blood culture acquisitions between April 2013 and August 2014 were enrolled. Patients with anorexia‐inducing conditions were excluded.

INTERVENTIONS

We assessed the patients' oral food intake based on the meal immediately prior to the blood culture with definition as “normal food consumption” when >80% of a meal was consumed and “poor food consumption” when <80% was consumed. We also concurrently evaluated for a history of shaking chills.

MEASUREMENTS

We calculated the statistical characteristics of food consumption and shaking chills for the presence of true bacteremia, and subsequently built the algorithm by using recursive partitioning analysis.

RESULTS

Among 1,943 patients, 223 cases were true bacteremia. Among patients with normal food consumption, without shaking chills, the incidence of true bacteremia was 2.4% (13/552). Among patients with poor food consumption and shaking chills, the incidence of true bacteremia was 47.7% (51/107). The presence of poor food consumption had a sensitivity of 93.7% (95% confidence interval [CI], 89.4%‐97.9%) for true bacteremia, and the absence of poor food consumption (ie, normal food consumption) had a negative likelihood ratio (LR) of 0.18 (95% CI, 0.17‐0.19) for excluding true bacteremia, respectively. Conversely, the presence of the shaking chills had a specificity of 95.1% (95% CI, 90.7%‐99.4%) and a positive LR of 4.78 (95% CI, 4.56‐5.00) for true bacteremia.

CONCLUSION

A 2‐item screening checklist for food consumption and shaking chills had excellent statistical properties as a brief screening instrument for predicting true bacteremia.
Improving the Readability of Pediatric Hospital Medicine
Authors: Instructions Discharge , Unaka Ndidi I. , Statile Angela , Jerardi Karen , Dahale Devesh , Morris Joan , Liberio Brianna , Jenkins Ashley , Simpson Blair , Mullaney Randi , Kelley Jodi , Durling Michelle , Shafer Jennifer , Brady Patrick W.
Published: July 2017

BACKGROUND

Readable discharge instructions may help caregivers understand and implement care plans following hospitalization. Many caregivers of hospitalized children, however, have limited literacy. We aimed to increase the percentage of discharge instructions written at 7th grade level or lower for hospital medicine patients from 13% to 80% in 6 months.

METHODS

Quality improvement efforts targeted a 42‐bed unit at the community satellite of our large, urban academic hospital. A multidisciplinary team of physicians, nurses, and parents focused on key drivers: family engagement in discharge process, standardization of discharge instructions, staff engagement in discharge preparedness, and audit and feedback of data. Improvement cycles included 1) education and implementation of a general discharge instruction template in the electronic health record (EHR); 2) visible reminders and tips for writing readable discharge instructions; 3) implementation of disease‐specific discharge instruction templates in the EHR; and 4) individualized feedback to staff on readability and content of their written discharge instructions. Instructions were individually scored for readability using an online platform. An annotated control chart assessed the impact of interventions over time.

RESULTS

Through sequential interventions over 6 months, the percentage of discharge instructions written at 7th grade or lower readability level increased from 13% to 98% and has been sustained for 4 months. The reliable use of the EHR templates was associated with our largest improvements.

CONCLUSION

Use of standardized discharge instruction templates and rapid feedback to staff improved the readability of instructions. Next steps include adaptation and spread to other patient populations.
An Equilibrium Model for Spot and Forward Prices of Commodities
Authors: Anthropelos Michail , Kupper Michael , Papapantoleon Antonis
Published: July 2017

We consider a market model that consists of financial investors and producers of a commodity. Producers optionally store some production for future sale and go short on forward contracts to hedge the uncertainty of the future commodity price. Financial investors take positions in these contracts to diversify their portfolios. The spot and forward equilibrium commodity prices are endogenously derived as the outcome of the interaction between producers and investors. Assuming that both are utility maximizers, we first prove the existence of an equilibrium in an abstract setting. Then, in a framework where the consumers’ demand and the exogenously priced financial market are correlated, we provide semi-explicit expressions for the equilibrium prices and analyze their dependence on the model parameters. The model can explain why increased investors’ participation in forward commodity markets and higher correlation between the commodity and the stock market could result in higher spot prices and lower forward premia.
Examining the lived experiences of newly qualified midwives during their preceptorship
Authors: Wain Amanda
Published: July 2017

Background

Novice midwives at one NHS Trust undertook a 12-month preceptorship programme, designed to support them to consolidate their education and develop their competence. The study was commenced following concerns voiced by new midwives about levels of support during their transition, and also because of a high rate of attrition of newly qualified midwives at the Trust.

Aims

The aim of the study was to evaluate the experiences of newly qualified midwives during their preceptorship at the Trust.

Methods

A qualitative research design was applied. A sample of eight midwives provided data collected using a process of semi-structured interviews.

Findings

The findings of the research demonstrated that most of the midwives felt well-supported by their colleagues. However, although a preceptorship programme was in place at the Trust, barriers to implementing the programme included staffing levels, time for consolidation, not receiving protected time with preceptors and differences to allocated supernumerary time.

Conclusions

Recommendations were made for practice to include effective monitoring of the programme, and the provision of a specific Trust guideline for the preceptorship of newly qualified midwives. Providing individualised preceptorship pathways with supernumerary time in each clinical area was also recommended.
Learning from error: leading a culture of safety
Authors: Gibson Russell , Armstrong Alexander , Till Alex , McKimm Judy
Published: July 2017

A recent shift towards more collective leadership in the NHS can help to achieve a culture of safety, particularly through encouraging frontline staff to participate and take responsibility for improving safety through learning from error and near misses. Leaders must ensure that they provide psychological safety, organizational fairness and learning systems for staff to feel confident in raising concerns, that they have the autonomy and skills to lead continual improvement, and that they have responsibility for spreading this learning within and across organizations.
A Brief Overview of Vegetation of Pangi Valley: An High Altitude Region of Northwest Himalaya, India
Authors: Singh Harminder , Kumar Puneet
Published: July 2017

ABSTRACT: Preliminary survey was conducted in the Pangi Valley a high altitude region of Northwest Himalaya, India. Pangi Valley has been least studied for floristic studies except for few cytological and ethnobotanical studies. Pangi was excluded in Flora of Chamba District and there is not much information on the vegetation. With the ever increasing population and, stress on natural resources for human needs, Pangi is now headed to a road for development. This area which hold enormous potential of vast floral and faunal genetic diversity requires to be explored before it gets too late. The current attempt aims to present a general overview of the vegetation of this geographically important cold desert region of India.
Isolation and Identification of Pathogenic Bacteria and Fungi from Some Saudi Bank Note Currency
Authors: M. A. Saadabi Abdulmoniem , S. Alhussaini Mohammed , A. Al-Ghanayem Abdullah , Joseph Babu , S. A-l Shuriam Mohammed
Published: July 2017

ABSTRACT: Saudi Bank notes in different values were critically evaluated to show the level of contamination with pathogenic bacteria and fungi using standard techniques. The fungal genera Trichophyton sp., Microsporum sp., Epidermophyton sp., Aspergillus sp., Alternaria sp., Penicillium sp., Candida sp., Phycomyces sp., Saccharomyces sp. and Cladosporium sp. were isolated and identified. The genera of bacteria that isolated were Escherichia coli, Citrobacter sp., Klebsiella sp., Proteus sp., Streptococcus sp., Bacillus sp., Corynebacterium sp. and Staphylococcus sp. The potential of Saudi currency notes to act as environmental vehicles for transmission of pathogenic fungi & bacteria was assessed. The lower values of bank notes were highly contaminated and there is a negative correlation between bank notes value and microbial contamination. The results suggest that currency notes may be contaminated, especially with bacteria and enteric microbes and may serve as a source of contamination or infection. Personal hygiene and electronic or credit banking to reduce the risk of infection were recommended.
The abundance of prospective natural food for sea cucumber Holothuria atra at Karimunjawa Island waters, Jepara, Indonesia
Authors: HARTATI RETNO , WIDIANINGSIH WIDIANINGSIH , TRIANTO AGUS , ZAINURI MUHAMMAD , AMBARIYANTO AMBARIYANTO
Published: July 2017

Hartati R, Widianingsih, Trianto A, Zainuri M, Ambariyanto. 2017. The abundance of prospective natural food for sea cucumber Holothuria atra at Karimunjawa Island waters, Jepara, Indonesia. Biodiversitas 18: 947-953. Holothuria atra, as one of the most abundant and widely distributed sea cucumber species, is an omnivore, consuming detritus, uneaten food, and algae in the substrate. For sea ranching purpose, the objective of present works was aimed to determine potential food availability for H. atra in Karimunjawa Island of Jepara. Biotic environment factors in proposed location were assessed including seaweed and seagrass associated communities, epiphytes on the seagrass, phyto and zooplankton, benthic organism, microphytobenthic as chlorophyll-a, phaeophytin and chloropigmen as well as sediment characteristics. There were six species seagrasses and 10 species of seaweeds found in Karimunjawa waters, with Enhalus acoroides and Thalassia hemprichii provide shelter and food for H. atra. Algal epiphytes use seagrass leaves and rhizome as substrate and there were 28 genera of them belong to Chrysophyta, Chlorophyta, and Cyanophyta. The variety and abundance of phytoplankton, zooplankton the benthos enrich the location. The chlorophyll-a, phaeophytin and total chloropigment in the sediment of Karimunjawa waters could be representative of microphytobenthos. The substrate of Karimunjawa waters consisted of fine sandy-coarse sediment and the content of organic matter may be important for feeding activity of H. atra.
Genetic diversity of Tor douronensis (Pisces: Cyprinidae) in West Sumatra, Indonesia
Authors: ROESMA DEWI IMELDA , TJONG DJONG HON , MUNIR WARNETY , AGESI ANUGRAH VIONA , CHORNELIA ADA
Published: July 2017

Roesma DI, Tjong DH, Munir W, Agesi AV, Chornelia A. 2017. Genetic diversity of Tor douronensis (Pisces: Cyprinidae) in West Sumatra, Indonesia. Biodiversitas 18: 1018-1025. A random amplified polymorphic DNA-polymerase chain reaction (RAPDPCR) analysis was applied to determine the genetic diversity within and among the populations of Tor douronensis in West Sumatra river system. The results provided information for proper breeding, maintenance, and conservation of T. douronensis. The highest and the lowest values of genetic diversity were the population of Batang Matur (H = 0.1571; I = 0.2411) and Batang Malalo (H = 0.0880; I = 0.1353), respectively. The value of genetic differentiation (GST) was 0.4266 while that of heterozygosity between populations (DST) and within a population (HS) was, respectively, 0.088 and 0.1184. The value of gene flow between populations (Nm) was 0.6721. Grouping of individuals in a population based Principal Coordinates Analysis (PCO) and UPGMA was in line with the genetic distance values. Matur and Malalo were the most closely related populations (0.0174) while Batang Gumanti and Batang Sinuruik were the most distantly related populations (0.1918). The genetic variation between populations was lower than the genetic variation within the population of T. douronensis and population of Matur is recommended to be used as brood stock in the procurement of stock.
Population study of Peristylus goodyeroides (Orchidaceae) in five habitats and implication for its conservation
Authors: NURFADILAH SITI
Published: July 2017

Nurfadilah S. 2017. Population study of Peristylus goodyeroides (Orchidaceae) in five habitats and implication for its conservation. Biodiversitas 18: 1084-1091. Many orchids have experienced population decline because of natural and anthropogenic disturbances and the remaining populations occur in fragmented habitats. The present study aimed to investigate (i) population of a terrestrial orchid, Peristylus goodyeroides (D. Don) Lindl., in terms of its demography, population size, and plant size, and (ii) characteristics of vegetation surrounding P. goodyeroides and its effect on the population size of P. goodyeroides (iii) environmental factors (litter thickness and soil pH) and their effects on the plant size of P. goodyeroides in five habitats. Number of individuals, plant height and leaf area of P. goodyeroides, surrounding vegetation, litter thickness, and soil pH were recorded in each habitat. The results showed that there was variation in the demographic structure of the population of P. goodyeroides in five habitats. Furthermore, three habitats of P. goodyeroides had small population size and small plant size compared to the other two habitats that had relatively larger population size and plant size. Small population size was correlated with taller vegetation surrounding P. goodyeroides reducing light availability for P. goodyeroides, while small plant size was related to sparse and thin litter cover causing low soil moisture and lacking nutrient availability for P. goodyeroides. Soil pH between habitats was similar and did not affect P. Goodyeroides plant size. The present study has implication on the conservation of P. goodyeroides for the improvement of population performance for the increase in population size and plant size for the species survival.
Morphological and molecular identificationof fungal pathogens causing gummosis disease of Citrus spp. in Indonesia
Authors: HENUK JULINDA B.D. , SINAGA MEITY S. , HIDAYAT SRI H.
Published: July 2017

Henuk JBD, Sinaga MS, Hidayat SH. 2017. Morphological and molecular identificationof fungal pathogens causing gummosis disease of Citrus spp. in Indonesia. Biodiversitas 18: 1100-1108. Gummosis is one of the most important diseases of citrus. The disease is caused by several species of Phytophthora, i.e. P. nicotianae, P. palmivora, P. citrophthora; as well as Lasiodiplodia theobromae (synonyms: Botryodiplodia theobromae and Diplodia natalensis; teleomorph Botryosphaeria rhodina). The objective of this study was to identify the isolates of fungal pathogens, i.e. Phytophthora spp. and B. theobromae and/or D. natalensis from several different areas of citrus central production in Indonesia based on their morphological and molecular characteristics. This study included two activities, i.e. (i) collection, isolation, and identification of pathogenic fungi from infected tissues, basal stem roots, and soil surface and rhizosphere; and (ii) extraction of genomic DNA and amplification of DNA fragments using PCR technique for molecular characterization. Results of morphological characterization and DNA sequence analysis revealed that gummosis was caused by Botryodiplodia theobromae Pat. (Teleomorph Botryosphaeria rhodina (Cooke) Arx.)), and P. citrophthora.
Short Communication: Water quality improvement of Nile tilapia and catfish polyculture in aquaponics system
Authors: HASAN ZAHIDAH , DHAHIYAT YAYAT , ANDRIANI YULI , ZIDNI IRFAN
Published: July 2017

Hasan Z, Dhahiyat Y, Andriani Y, Zidni I. 2016. Water quality improvement of Nile tilapia and catfish polyculture in aquaponics system. Nusantara Bioscience 8: 83-85. Research on the improvement of polyculture water quality in aquaponics system was conducted from July 2014 to August 2014. This study aims to improve the water quality in Nile tilapia and catfish polyculture by applying the aquaponics system. The results show that several water quality parameters increase, such as dissolved oxygen, ammonia, and nitrate. Meanwhile, Orthophosphate tends to be similar both in aquaponics system and control. The study is conducted experimentally by using completely randomized design. The cultured fish are catfish and Nile tilapia while the aquatic plants are water spinach and lettuce. At the end of the study the concentration of dissolved oxygen in the aquaponics system ranges from 5.3 to 7.6 mg/L, while in the media control ranges from 4.2 to 4.3 mg/L. Average concentrations of ammonia, nitrate and orthophosphate in the aquaponics system range from 0.003 to 0.25 mg/L, 10.0 to 50.7 mg/L and 3.0 mg/L-5.0 mg/L respectively. Meanwhile, in media control, concentration of those three parameters are 0.003 to 0.35 mg/L, 10.0 to 60.0 mg/L and 3.0 to 5.0 mg/L respectively. Based on this study, it is concluded that the polyculture water quality can be improved through the application of the aquaponics system.
Anti-fertility effect of ethanol extract of lerak (Sapindus rarak DC) fruits in female Sprague Dawley Rats
Authors: FAJRIATY INARAH , H. HARIYANTO I. , HARYANTO YOUNGKY
Published: July 2017

Fajriaty I, Hariyanto I.H, Haryanto Y. 2017. Anti-fertility effect of ethanol extract of lerak (Sapindus rarak DC) fruits in female Sprague Dawley Rats. Nusantara Bioscience 9: 102-106. This research aims to observe the antifertility effect of ethanol extract of Lerak fruits (SFEE) in female sprague dawley rats. Group of rats are divided into four groups, the first group is given carboxymethyl cellulose (CMC) as negative control (KN), the second group is given ethinylestradiol as positive control (KP), the third group is given SFEE with dose 50 mg/kg BW, and the fourth group is given SFEE with dose 100 mg/kg BW. The female rats in estrus phase is mated with male rats. In plug vaginal checking and smear vaginal there is sperm that signify if female rats have experienced copulation and currently on the day of the zero pregnancy. All treatment are given orally from 0 day of pregnancy to 10th day of pregnancy. Antifertility effect on treatment in rats is shown from laparotomy in the 20th day of pregnancy. Determining of the antifertility effect that to do include pre-implantation loss effect and post implementation loss effect. The result of this research shows that SFEE with dose 50 mg/kg BW has antifertility effect that is pre-implantation loss as big as 0% and post-implantation loss as big as 10.53% and SFEE with dose 100 mg/kg BW shows antifertility effect is pre-implantation loss and post implantation loss in each of 47.50% and 28.57%. This observation shows that SFEE has antifertility effect.
Response of soybean genotypes to salinity in germination stage
Authors: PUTRI PRATANTI HAKSIWI , SUSANTO GATUT WAHYU ANGGORO , ARTARI RINA
Published: July 2017

Putri PH, Susanto GWA, Artari R. 2017. Response of soybean genotypes to salinity in germination stage. Nusantara Bioscience 9: 133-137. Salinity is one of the agricultural problem, especially in marginal land. The negative impact of salinity for plants such as delay germination time, growth inhibition, reduce nodules formation, decrease biomass accumulation, and reduce yield quantity and quality. Initial selection for salt resistance of soybean, conducted on 16 genotypes, using three levels of NaCl and three replications. Germination conducted for six days, in germinator which has been set at 25oC, with lighting. Mean Germination Time (MGT), Final Germination Percent (FGP), sprout length (root and overall) and weight (fresh and dry), seedling vigor index (length and weight) were observed. Data were analyzed using ANOVA, followed by LSD at 5%. Sixteen soybean genotypes show inhibition effect of salinity. The results showed that 125 mM NaCl does not inhibit germination but it causes abnormal growth at some genotypes. Number of normal germination decreased 20-30% at 125 mM NaCl. Sprouts total length declined by 17-58% at 75 mM and 45-78% at 125 mM NaCl. Root length decrease from 23.2-55.3% at 75 mM and 52.1-81.2% in 125 mM. Fresh weight diminish by 3.8-39.9% at 75 mM and 12.7-52.5% at 125 mM NaCl. Response of sixteen soybean genotypes into salinity stress is clearly visible at sprout length and fresh weight variable. Ichiyou was salt-sensitive based on all variable especially sprout length and fresh weight, while Baluran was salttolerant up to 125 mM NaCl based on sprout length and fresh weight.
The effect of NPK fertilizer and planting media on plant growth and saponin content of the medicinal plant Anchomanes difformis
Authors: RIVAI REZA RAMDAN , WARDANI FITRI FATMA , ZULKARNAEN RIZMOON NURUL
Published: July 2017

Rivai RR, Wardani FF, Zulkarnaen RN. 2017. The effect of NPK fertilizer and planting media on plant growth and saponin content of the medicinal plant Anchomanes difformis. Nusantara Bioscience 9: 141-145. Anchomanes difformis (Blume) Engl., belongs to the aroid family (Araceae) and has potential as a medicinal plant. A. difformis has not in the past been widely cultivated by farmers in Indonesia, so if it is to be grown as a crop for medicinally active compounds, we must first find how best to cultivate it. The objective of the research described here was to determine an effective planting media and optimum dosage of a standard NPK fertilizer for A. difformis plant growth in pots, and saponin content of its rhizomes. The research was conducted at the Treub Laboratory and Garden Nursery, Center for Plant Conservation Botanic Gardens, Indonesian Institute of Sciences (LIPI). A completely randomized design with three replications was used to test a factorial arrangement of two treatment factors, namely: planting media of three types; and dosage of a standard NPK fertilizer (15% N, 15% P2O5, 15% K2O) at four levels. Results showed that for plant growth of Anchomanes difformis, a mixed medium of soil/cocopeat (1:1) was the best of the three media evaluated, and the application of the NPK fertilizer at a dosage equivalent to 100 kg/ha was the optimum fertilizer level. There was no statistical interaction between the treatment factors. The rhizomes of A. difformis had their highest level of saponin content when planted in the mixed soil/cocopeat (1:1) medium, and with NPK fertilizers at a dose level of 100 kg/ha.
Short Communication: Acute toxicity effects of titanium nano particle TiO2 NPs on hematological indices in Goldfish (Carassius auratus, Linnaeus 1758)
Authors: HEDAYATI ALIAKBAR , DARABITABAR FATEMEH , AHMADVAND SHAYDA , AHMADVAND SHARAREH
Published: July 2017

Hedayati A, Darabitabar F, Ahmadvand S, Ahmadvand S. 2017. Short Communication: Acute toxicity effects of titanium nano particle TiO2 NPs on hematological indices in Goldfish (Carassius auratus, Linnaeus 1758). Nusantara Bioscience 9: 152-155. Metal nanoparticles which include particles manufactured from metal oxides such as zinc oxide ZnO and titanium oxide TiO2 particles are broadly used due to their inimitable attributes such as diversity level chemistries and can be prepared into a variety of figures and sizes. The aim of this study was to investigate the effect of different TiO2 NPs concentrations on hematology indices in Goldfish (Carassius auratus). 105 goldfish with average total lengths of 6.50 Â± 0.43 cm were used in this present study. Goldfish were exposed to a lethal concentration of 50% LC50 nano-titanium dioxide for a period of 0 (control), 24, 48 and 96h static toxicity examination, presented in tanks of 60L. The results of this study shows LC5096h nano titanium dioxide for goldfish is 19985Â±2.27 ppm and MAC value or the maximum allowable concentration calculated for this toxin is 1998 mg/L. No mortality observed in the control group. Fish exposed to nano-titanium dioxide for 7 days, a significant change in hematological (Hb, MCH, MCHC, MCV, RBC), and immunological (WBC) indices concentrations toward the control groups (p<0/05). The results of this study showed, however, LC50 of nano titanium dioxide was very high that means it doesnâ€™t have much mortality effect, but it has negative effect on blood indices in goldfish and reduces red blood cells and hemoglobin in fish, eventually caused the death of fish.
Morphometry and abnormality evaluation of sex-sorted sperm of spotted buffalo (Tedong bonga)
Authors: KAIIN EKAYANTI MULYAWATI , GUNAWAN MUHAMMAD , MAULANA TULUS
Published: July 2017

Kaiin EM, Gunawan M, Maulana T. 2017. Morphometry and abnormality evaluation of sex-sorted sperm of spotted buffalo (Tedong bonga). Nusantara Bioscience 9: 175-180. This research aimed to determine the morphometry and the abnormality of the spotted buffallo (Tedong bonga) sperm after the separation of X and Y-chromosome-bearing sperms. Semen was collected from the spotted buffalo bull by using an artificial vagina.The semen quality was evaluated macro- and microscopically. Semen that met the required standard were subjected to separation by using Bovine Serum Albumin (BSA) 5% and 10% column method. The quality of sex-sorted sperm was evaluated microscopically, including motility, concentration, viability, abnormality and intact plasma membrane. Smear preparation using Eosin-Nigrosin dyes was made for sperm morphometry and abnormality evaluation.The evaluation of sperm morphometry and abnormality was conducted on 200 sperm cells for each observation and repeated in triplicates of observation, by using Axiovision Imager Z microscope at objective and ocular magnifications 40x and 10x, respectively.The morphological parameters observed were including the length and the width of head sperm and the head area of sperm X or Y. The abnormality parameter consisted of primary and secondary abnormalities. The data were analyzed descriptively. The results showed that the head size of the Y sperm of spotted buffalo (27.16 Î¼m2) was smaller than that of the X sperm (29.86 Î¼m2) with the abnormality of the Y sperm (7.85%) was also lower than that of the X sperm (9.7%).
Screening of soybean genotypes for resistance to pod sucking bug, Riptortus linearis
Authors: KRISNAWATI AYDA , IKA BAYU MARIDA SANTI YUDHA , ADIE M. MUCHLISH
Published: July 2017

Krisnawati A, Bayu MSIY, Adie MM. 2017. Screening of soybean genotypes for resistance to pod sucking bug, Riptortus linearis. Nusantara Bioscience 9: 181-187. Pod sucking bug, Riptortus linearis, is potentially harmful pest of soybean in Indonesia. The development of resistant variety is one of the major goal in soybean breeding. The research aimed was to identify the resistance of soybean genotypes to pod sucking bug. The experiment was conducted in Indonesian Legumes and Tuber Crops Research Instituteâ€™s screen house from March to June 2015. The experiment was arranged in Randomized Complete Block Design using 10 soybean genotypes with three replicates. The resistance was evaluated by choice and no-choice test. Data collected on some agronomic characters, number of damaged pod/plant, and number of damaged seed/plant. The resistance criteria determined by using the method from Chiang and Talekar (1980). The results showed that the lowest percentage of pod and seed damage was found on G511H/Anjasmoro//Anjasmoro-2-8 in both no-choice and choice test. In the no-choice test, the lowest percentage of pod and seed damage were 25.83% and 19.12%, respectively. In the choice test, the lowest percentage of pod and seed damage were 25.02% and 20.02%, respectively. The grouping of resistance genotypes based on the no-choice test as well as choice test, the genotype G511H/Anjasmoro//Anjasmoro-2-8 showed a consistently resistant. This genotype could be used as a resistant donor in the soybean breeding program for resistance to pod sucking bug.