bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterizing Accuracy and Precision of Glucose Sensors and Meters
Authors: Rodbard David
Published: July 2014

Background:

There is need for a method to describe precision and accuracy of glucose measurement as a smooth continuous function of glucose level rather than as a step function for a few discrete ranges of glucose. We propose and illustrate a method to generate a “Glucose Precision Profile” showing absolute relative deviation (ARD) and /or %CV versus glucose level to better characterize measurement errors at any glucose level.

Method:

We examine the relationship between glucose measured by test and comparator methods using linear regression. We examine bias by plotting deviation = (test – comparator method) versus glucose level. We compute the deviation, absolute deviation (AD), ARD, and standard deviation (SD) for each data pair. We utilize curve smoothing procedures to minimize the effects of random sampling variability to facilitate identification and display of the underlying relationships between ARD or %CV and glucose level.

Results:

AD, ARD, SD, and %CV display smooth continuous relationships versus glucose level. Estimates of MARD and %CV are subject to relatively large errors in the hypoglycemic range due in part to a markedly nonlinear relationship with glucose level and in part to the limited number of observations in the hypoglycemic range.

Conclusions:

The curvilinear relationships of ARD and %CV versus glucose level are helpful when characterizing and comparing the precision and accuracy of glucose sensors and meters.
Raman Spectroscopy as a Promising Tool for Noninvasive Point-of-Care Glucose Monitoring
Authors: Scholtes-Timmerman Maarten J. , Bijlsma Sabina , Fokkert Marion J. , Slingerland Robbert , van Veen Sjaak J. F.
Published: July 2014

Background:

Self-monitoring of glucose is important for managing diabetes. Noninvasive glucose monitors are not yet available, but patients would benefit highly from such a device.

Methods:

We present results that may lead to a novel, point-of-care noninvasive system to measure blood glucose based on Raman spectroscopy. A hospitalized cohort of 111 subjects was measured using a custom-made Raman spectrometer system. Blood glucose reference samples were used to correlate Raman data to glucose levels, using advanced preprocessing and analysis algorithms.

Results:

A correlation coefficient ( R2) of .83 was found correlating independent Raman-based predictions on reference blood glucose for the full cohort. Stratification of the cohort in gender-specific groups raised correlation levels to .88 (females) and .94 (males). Glucose could be measured noninvasively with average errors as low as 0.9 mM.

Conclusion:

We conclude that this novel system shows promising results for the advance of noninvasive, point-of-care glucose monitoring.
Osteochondral Lesions of the Ankle Joint in Professional Soccer Players
Authors: Valderrabano Victor , Barg Alexej , Alattar Abdulhameed , Wiewiorski Martin
Published: July 2014

Acute and recurrent ankle sprains and other trauma to the ankle joint are common injuries in soccer and can be accompanied by or result in osteochondral lesions of the ankle joint, majorly of the talus. Conservative treatment frequently fails. Several operative treatment techniques exist; however, the choice of the right procedure is difficult due to lack of literature with a high level of evidence. We present our treatment method for acute and chronic ankle osteochondral lesions with cystic formation approached by a new surgical technique combining bone plasty and a collagen matrix (autologous matrix-induced chondrogenesis).

Levels of Evidence: Therapeutic, Level IV: Case series
Joint Salvage After Neglected Intra-Articular Physeal Fracture of the Hallux in High-Level Gymnasts
Authors: Bariteau Jason T. , Murillo Diana Montoya , Tenenbaum Shay A. , Brodsky James W.
Published: July 2014

Chronic sports-related injuries involving the hallux are well known in adult populations. However, they are less frequently described in adolescents. We present 2 cases of elite-level gymnasts with neglected Salter–Harris IV fractures involving the proximal phalanx of the great toe following a severe hyperextension injury to the metatarsophalangeal joint. Both were successfully treated with open reduction and internal fixation with return to pre-injury level of activity, improvement in outcome scores, and demonstration of no disability from injury 2 years after surgical intervention.

Levels of Evidence: Therapeutic, Level IV: Case Series
Autologous apoptotic cells preceding transplantation enhance survival in lethal murine graft-versus-host models
Authors: Florek Mareike , Sega Emanuela I. , Leveson-Gower Dennis B. , Baker Jeanette , Müller Antonia M. S. , Schneidawind Dominik , Meyer Everett , Negrin Robert S.
Published: July 2014

Key Points

Prophylactic ECP protects against GVHD in a murine BMT model. ECP provides apoptotic signals that promote tolerance through dendritic cells and Tregs.
Enhancement of catecholamine release from PC12 cells by the traditional Japanese medicine, rikkunshito
Authors: Nagamura Yuko , Terawaki Kiyoshi , Uezono Yasuhito , Tsukada Toshihiko
Published: July 2014

Background

Rikkunshito is a traditional Japanese herbal medicine that is used to treat appetite loss associated with cancer and other disorders. The formulation contains various constituents that influence cell signaling, and rikkunshito may accordingly affect human homeostasis through multiple regulatory pathways, including those governed by the endocrine system. We investigated the actions of rikkunshito on catecholamine release from PC12 cells, an adrenal chromaffin cell line.

Methods

The actions of rikkunshito on PC12 cells were evaluated by measuring intracellular cAMP levels, tyrosine hydroxylase (TH) and vasoactive intestinal peptide (VIP) mRNA expression levels, and catecholamine levels in the culture medium. The transcriptional activation of VIP gene by rikkunshito was assessed by using a VIP promoter-driven reporter gene assay.

Results

Rikkunshito dose-dependently enhanced forskolin-induced elevations in cAMP in PC12 cells, and also increased the gene expression of TH and VIP. The transcriptional activation of VIP gene by rikkunshito was confirmed. Norepinephrine and dopamine secretion into the culture medium of PC12 cells were also dose-dependently augmented by rikkunshito and/or forskolin, but experiments with a protein kinase C (PKC) activator and a phosphodiesterase inhibitor revealed that the effects of rikkunshito were not simply due to the modulation of PKC or phosphodiesterase activity.

Conclusions

These findings suggest that rikkunshito enhances the release of catecholamines by a novel mechanism involving cAMP.
Expression Profiling of Genes Modulated by Minocycline in a Rat Model of Neuropathic Pain
Authors: Rojewska Ewelina , Korostynski Michal , Przewlocki Ryszard , Przewlocka Barbara , Mika Joanna
Published: July 2014

Background:

The molecular mechanisms underlying neuropathic pain are constantly being studied to create new opportunities to prevent or alleviate neuropathic pain. The aim of our study was to determine the gene expression changes induced by sciatic nerve chronic constriction injury (CCI) that are modulated by minocycline, which can effectively diminish neuropathic pain in animal studies. The genes associated with minocycline efficacy in neuropathic pain should provide insight into the etiology of neuropathic pain and identify novel therapeutic targets.

Results:

We screened the ipsilateral dorsal part of the lumbar spinal cord of the rat CCI model for differentially expressed genes. Out of 22,500 studied transcripts, the abundance levels of 93 transcripts were altered following sciatic nerve ligation. Percentage analysis revealed that 54 transcripts were not affected by the repeated administration of minocycline (30 mg/kg, i.p.), but the levels of 39 transcripts were modulated following minocycline treatment. We then selected two gene expression patterns, B1 and B2. The first transcription pattern, B1, consisted of 10 mRNA transcripts that increased in abundance after injury, and minocycline treatment reversed or inhibited the effect of the injury; the B2 transcription pattern consisted of 7 mRNA transcripts whose abundance decreased following sciatic nerve ligation, and minocycline treatment reversed the effect of the injury. Based on the literature, we selected seven genes for further analysis: Cd40, Clec7a, Apobec3b, Slc7a7, and Fam22f from pattern B1 and Rwdd3 and Gimap5 from pattern B2. Additionally, these genes were analyzed using quantitative PCR to determine the transcriptional changes strongly related to the development of neuropathic pain; the ipsilateral DRGs (L4-L6) were also collected and analyzed in these rats using qPCR.

Conclusion:

In this work, we confirmed gene expression alterations previously identified by microarray analysis in the spinal cord and analyzed the expression of selected genes in the DRG. Moreover, we reviewed the literature to illustrate the relevance of these findings for neuropathic pain development and therapy. Further studies are needed to elucidate the roles of the individual genes in neuropathic pain and to determine the therapeutic role of minocycline in the rat neuropathic pain model.
Stem cell delivery of therapies for brain disorders
Authors: Aleynik Alexander , Gernavage Kevin M , Mourad Yasmine SH , Sherman Lauren S , Liu Katherine , Gubenko Yuriy A , Rameshwar Pranela
Published: July 2014

The blood brain barrier (BBB) poses a problem to deliver drugs for brain malignancies and neurodegenerative disorders. Stem cells such as neural stem cells (NSCs) and mesenchymal stem cells (MSCs) can be used to delivery drugs or RNA to the brain. This use of methods to bypass the hurdles of delivering drugs across the BBB is particularly important for diseases with poor prognosis such as glioblastoma multiforme (GBM). Stem cell treatment to deliver drugs to neural tumors is currently in clinical trial. This method, albeit in the early phase, could be an advantage because stem cells can cross the BBB into the brain. MSCs are particularly interesting because to date, the experimental and clinical evidence showed ‘no alarm signal’ with regards to safety. Additionally, MSCs do not form tumors as other more primitive stem cells such as embryonic stem cells. More importantly, MSCs showed pathotropism by migrating to sites of tissue insult. Due to the ability of MSCs to be transplanted across allogeneic barrier, drug‐engineered MSCs can be available as off‐the‐shelf cells for rapid transplantation. This review discusses the advantages and disadvantages of stem cells to deliver prodrugs, genes and RNA to treat neural disorders.
Antenatally detected cystic biliary atresia: differential diagnoses of a double bubble
Authors: Adewole Victoria A , Wright Naomi J , Hallows Ruth , Davenport Mark
Published: July 2014

The ‘double bubble’ sign on antenatal ultrasound is often associated with duodenal atresia although there are numerous causes. We present a case of cystic biliary atresia presenting with a “double bubble” at 36-weeks gestation. Postnatal ultrasound and MRCP confirmed a cystic lesion at the porta hepatis, mandating early laparotomy and a successful Kasai portoenterostomy.

Although diagnosis of such lesions may be imprecise antenatally, awareness and detection does allow early postnatal investigation and management, which is vital to optimise outcome.

This case highlights the need to be mindful of other important anomalies that can give this appearance and that may require early intervention.
The TGF-β-inducible miR-23a cluster attenuates IFN-γ levels and antigen-specific cytotoxicity in human CD8+ T cells
Authors: Chandran P Anoop , Keller Andreas , Weinmann Lasse , Adel Seida Ahmed , Braun Matthias , Andreev Katerina , Fischer Birgitt , Horn Evi , Schwinn Stefanie , Junker Markus , Houben Roland , Dombrowski Yvonne , Dietl Johannes , Finotto Susetta , Wölfl Matthias , Meister Gunter , Wischhusen Jörg
Published: July 2014

Cytokine secretion and degranulation represent key components of CD8+ T-cell cytotoxicity. While transcriptional blockade of IFN-γ and inhibition of degranulation by TGF-β are well established, we wondered whether TGF-β could also induce immune-regulatory miRNAs in human CD8+ T cells. We used miRNA microarrays and high-throughput sequencing in combination with qRT-PCR and found that TGF-β promotes expression of the miR-23a cluster in human CD8+ T cells. Likewise, TGF-β up-regulated expression of the cluster in CD8+ T cells from wild-type mice, but not in cells from mice with tissue-specific expression of a dominant-negative TGF-β type II receptor. Reporter gene assays including site mutations confirmed that miR-23a specifically targets the 3′UTR of CD107a/LAMP1 mRNA, whereas the further miRNAs expressed in this cluster—namely, miR-27a and -24—target the 3′UTR of IFN-γ mRNA. Upon modulation of the miR-23a cluster by the respective miRNA antagomirs and mimics, we observed significant changes in IFN-γ expression, but only slight effects on CD107a/LAMP1 expression. Still, overexpression of the cluster attenuated the cytotoxic activity of antigen-specific CD8+ T cells. These functional data thus reveal that the miR-23a cluster not only is induced by TGF-β, but also exerts a suppressive effect on CD8+ T-cell effector functions, even in the absence of TGF-β signaling.
Using Reporting Requirements to Improve Employer Wellness Incentives and Their Regulation
Authors: Madison Kristin , Schmidt Harald , Volpp Kevin G.
Published: July 2014

Employer interest in offering financial incentives for healthy behaviors has been increasing. Some employers have begun to tie health plan–based rewards or penalties to standards involving tobacco use or biometric measures such as body mass index. The Patient Protection and Affordable Care Act attempts to strike a balance between the potential benefits and risks of wellness incentive programs by permitting these incentives but simultaneously limiting their use. Evidence about the implications of the newest generation of incentive programs for health, health costs, and burdens on individual employees will be critical for informing both private and public decision makers. After describing the many pieces of information that would be valuable for assessing these programs, this article proposes more narrowly targeted reporting requirements that could facilitate incentive program development, evaluation, and oversight.
Arkansas's Alternative to Medicaid Expansion Raises Important Questions about How HHS Will Implement New ACA Waiver Authority in 2017
Authors: Allison Andrew
Published: July 2014

This essay presents Arkansas's alternative to Medicaid expansion as a case study motivating John McDonough's assessment of the recommendations states may want to make to the Department of Health and Human Services regarding the implementation of statewide Patient Protection and Affordable Care Act–alternative waivers scheduled to begin in 2017. Arkansas's private option uses federal funds to purchase marketplace silver-level qualified health plans for low-income, low-risk participants, while “medically frail” adults are covered through Medicaid. By improving the size and risk profile of Arkansas's health insurance marketplace, the private option will also encourage entry of and competition among private carriers. If it succeeds in keeping insurance premiums below the level they would otherwise be in the marketplace, Arkansas's private option could reduce subsidy costs for the federal government. Under the broadened scope of section 1332 waivers, states will be able to capture such savings and use them to support innovation across both Medicaid-funded and Treasury-subsidized programs and populations.
Kremen1 restricts Dkk activity during posterior lateral line development in zebrafish
Authors: McGraw Hillary F. , Culbertson Maya D. , Nechiporuk Alex V.
Published: July 2014

Canonical Wnt signaling plays crucial roles during development and disease. How Wnt signaling is modulated in different in vivo contexts is currently not well understood. Here, we investigate the modulation of Wnt signaling in the posterior lateral line primordium (pLLP), a cohort of ∼100 cells that collectively migrate along the trunk of the zebrafish embryo. The pLLP comprises proliferative progenitor cells and organized epithelial cells that will form the mechanosensory organs of the posterior lateral line. Wnt signaling is active in the leading progenitor zone of the pLLP and restricted from the trailing zone through expression of the secreted Wnt inhibitors dkk1b and dkk2. We have identified a zebrafish strain, krm1nl10, which carries a mutation in the kremen1 gene, a non-obligate co-receptor for the Dkk family of proteins. Previous studies have shown that Kremen1 inhibits Wnt signaling by facilitating internalization of the Kremen1-Dkk-Lrp5/6 complex. Surprisingly, we found that disruption of Kremen1 in the pLLP exhibited molecular and cellular phenotypes associated with a decrease rather than overactivation of Wnt signaling. Transplantation of wild-type cells into the mutant primordia failed to rescue the krm1nl10 phenotype, thus revealing that the effects of Kremen1 loss are non-cell-autonomous. Finally, ectopic expression of Dkk1b-mTangerine protein revealed larger spread of the fusion protein in the mutant primordia compared with the wild type. Based on our data, we propose a novel mechanism in which Kremen1 modulates Wnt activity by restricting the range of secreted Dkk proteins during collective cell migration in the pLLP.
Hand2 elevates cardiomyocyte production during zebrafish heart development and regeneration
Authors: Schindler Yocheved L. , Garske Kristina M. , Wang Jinhu , Firulli Beth A. , Firulli Anthony B. , Poss Kenneth D. , Yelon Deborah
Published: July 2014

Embryonic heart formation requires the production of an appropriate number of cardiomyocytes; likewise, cardiac regeneration following injury relies upon the recovery of lost cardiomyocytes. The basic helix-loop-helix (bHLH) transcription factor Hand2 has been implicated in promoting cardiomyocyte formation. It is unclear, however, whether Hand2 plays an instructive or permissive role during this process. Here, we find that overexpression of hand2 in the early zebrafish embryo is able to enhance cardiomyocyte production, resulting in an enlarged heart with a striking increase in the size of the outflow tract. Our evidence indicates that these increases are dependent on the interactions of Hand2 in multimeric complexes and are independent of direct DNA binding by Hand2. Proliferation assays reveal that hand2 can impact cardiomyocyte production by promoting division of late-differentiating cardiac progenitors within the second heart field. Additionally, our data suggest that hand2 can influence cardiomyocyte production by altering the patterning of the anterior lateral plate mesoderm, potentially favoring formation of the first heart field at the expense of hematopoietic and vascular lineages. The potency of hand2 during embryonic cardiogenesis suggested that hand2 could also impact cardiac regeneration in adult zebrafish; indeed, we find that overexpression of hand2 can augment the regenerative proliferation of cardiomyocytes in response to injury. Together, our studies demonstrate that hand2 can drive cardiomyocyte production in multiple contexts and through multiple mechanisms. These results contribute to our understanding of the potential origins of congenital heart disease and inform future strategies in regenerative medicine.
p120-catenin-dependent junctional recruitment of Shroom3 is required for apical constriction during lens pit morphogenesis
Authors: Lang Richard A. , Herman Ken , Reynolds Albert B. , Hildebrand Jeffrey D. , Plageman Timothy F.
Published: July 2014

Apical constriction (AC) is a widely utilized mechanism of cell shape change whereby epithelial cells transform from a cylindrical to conical shape, which can facilitate morphogenetic movements during embryonic development. Invertebrate epithelial cells undergoing AC depend on the contraction of apical cortex-spanning actomyosin filaments that generate force on the apical junctions and pull them toward the middle of the cell, effectively reducing the apical circumference. A current challenge is to determine whether these mechanisms are conserved in vertebrates and to identify the molecules responsible for linking apical junctions with the AC machinery. Utilizing the developing mouse eye as a model, we have uncovered evidence that lens placode AC may be partially dependent on apically positioned myosin-containing filaments associated with the zonula adherens. In addition we found that, among several junctional components, p120-catenin genetically interacts with Shroom3, a protein required for AC during embryonic morphogenesis. Further analysis revealed that, similar to Shroom3, p120-catenin is required for AC of lens cells. Finally, we determined that p120-catenin functions by recruiting Shroom3 to adherens junctions. Together, these data identify a novel role for p120-catenin during AC and further define the mechanisms required for vertebrate AC.
Vangl-dependent planar cell polarity signalling is not required for neural crest migration in mammals
Authors: Pryor Sophie E. , Massa Valentina , Savery Dawn , Andre Philipp , Yang Yingzi , Greene Nicholas D. E. , Copp Andrew J.
Published: July 2014

The role of planar cell polarity (PCP) signalling in neural crest (NC) development is unclear. The PCP dependence of NC cell migration has been reported in Xenopus and zebrafish, but NC migration has not been studied in mammalian PCP mutants. Vangl2Lp/Lp mouse embryos lack PCP signalling and undergo almost complete failure of neural tube closure. Here we show, however, that NC specification, migration and derivative formation occur normally in Vangl2Lp/Lp embryos. The gene family member Vangl1 was not expressed in NC nor ectopically expressed in Vangl2Lp/Lp embryos, and doubly homozygous Vangl1/Vangl2 mutants exhibited normal NC migration. Acute downregulation of Vangl2 in the NC lineage did not prevent NC migration. In vitro, Vangl2Lp/Lp neural tube explants generated emigrating NC cells, as in wild type. Hence, PCP signalling is not essential for NC migration in mammals, in contrast to its essential role in neural tube closure. PCP mutations are thus unlikely to mediate NC-related birth defects in humans.
Sortilin mediates the release and transfer of exosomes in concert with two tyrosine kinase receptors
Authors: Wilson Cornelia M. , Naves Thomas , Vincent François , Melloni Boris , Bonnaud François , Lalloué Fabrice , Jauberteau Marie-Odile
Published: July 2014

The transfer of exosomes containing both genetic and protein materials is necessary for the control of cancer cell microenvironment to promote tumor angiogenesis. The nature and function of proteins found in the exosomal cargo, their mechanisms in membrane transport and related signaling events are not clearly understood. In this study, we demonstrate in human lung cancer A549 cells, that the exosome release mechanism is closely linked to a multifaceted receptor, neurotensin (NT) receptor-3 also called sortilin. Sortilin is already known to be important for cancer cell function. Here, we report for the first time its role in the assembly of a tyrosine kinase complex and subsequent exosome release. This novel complex (TES complex) found in exosomes results in the linkage of two tyrosine kinase receptors, TrkB and EGFR with sortilin. Using in vitro models, we demonstrate that this complex containing sortilin exhibits a control on endothelial cells and angiogenesis activation through exosome transfer.
Differential effects of Akt isoforms on somatic cell reprogramming
Authors: Tang Yong , Jiang Zongliang , Luo Yan , Zhao Xueming , Wang Ling , Norris Carol , Tian Xiuchun Cindy
Published: July 2014

Akt plays an important role in cell growth, proliferation, and survival. The specific roles of the three Akt isoforms in somatic cell reprogramming have not been investigated. Here we report that during iPSC generation, enhanced Akt1 activity promotes complete reprogramming mainly through increased activation of Stat3 in concert with LIF, and to a lesser extent, through promotion of colony formation. Akt1 augments Stat3 activity through activation of mTOR and upregulation of LIF receptor expression. Similarly, enhanced Akt2 or Akt3 activation also promotes reprogramming, and coordinates with LIF to activate Stat3. Blocking Akt1 or Akt3, but not Akt2 expression, prohibits cell proliferation and reprogramming. Furthermore, the halt in cell proliferation and reprogramming caused by mTOR and Akt inhibitors can be reversed by inhibition of GSK3. Finally, we found that expressing the GSK3β target, Esrrb, overcomes inhibition of Akt and restores reprogramming. Our data demonstrated that during reprogramming, Akt promotes establishment of pluripotency through co-stimulation of Stat3 activity with LIF; Akt1 and Akt3 are essential for the proliferation of reprogrammed cells; and Esrrb supports cell proliferation and complete reprogramming under Akt signaling.
THREE-DIMENSIONAL CONTACT PROBLEM FOR A TRANSVERSELY ISOTROPIC SOLID
Authors: Pozharskiy Dmitry Alexandrovich , Davtyan David Borisovich
Published: July 2014

The spatial contact problem with an unknown contact domain is investigated for a transversely isotropic elastic half-space the boundary of which is perpendicular to the planes of isotropy. For a circular punch, the contact zone, as a rule, is not a circle because the stiffness of the elastic solid boundary depends on the direction. The problem is reduced to an integral equation (IE) with respect to the contact pressure the kernel of which does not include quadratures. Galanov’s numerical method which makes it possible to determine simultaneously the contact zone and the contact pressure is used to solve the IE. The simple form of the IE kernel allows regularizing it by using a parameter which depends on mesh intervals as well as on anisotropy parameters. A well-known exact solution to a punch in the form of an elliptical paraboloid is used to verify the computer program. The numerical analysis has been made for different transversely isotropic materials contacting with conical and pyramidal punches.
INCREASE OF AIR DEDUSTING EFFECTIVENESS IN FUNCTIONAL ZONES OF METAL- AND WOODWORKING PRODUCTIONS
Authors: Bulygin Yury Igorevich , Romanov Valery Anatolyevich , Panchenko Olga Sergeyevna , Denisov Oleg Victorovich
Published: July 2014

A new cyclone apparatus enable to control the part specifications depending on the dust environment properties and characteristics is designed. This leads to the increase of the processing off-gas collection efficiency. The experimental study is resulted, and the geometrics of the diversiform cyclonic devices is related to the dedusting effectiveness. It is shown that the dedusting efficiency is higher in the inverted-cone cyclones (ICC) than in the cylinder devices. The ICC optimal design factors (the immersion depth of an exhaust branch pipe, and the cyclone working part/bunker volume ratio) raising the dust cleaning degree are found. The ICC with controlled parameters and with the gravity-discharge bin is offered. The developed ICC allows the considerable efficiency increase of the preliminary air cleaning from the metal- and woodworking production dust.
Species identification and selection to develop agroforestry at Lake Toba Catchment Area (LTCA)
Authors: WIJAYANTO NURHENI
Published: July 2014

Wijayanto N (2011) Species identification and selection to develop agroforestry at Lake Toba Catchment Area (LTCA). Biodiversitas 12: 52-58. In order to improve land productivity surrounding the LTCA, the existing ITTO project tries to establish agroforestry system. The system will be designed to meet consideration of both sides. on one side is to generate the people awareness of the forest and land rehabilitation, and on the other side is to support the poverty reduction. The aims of this research are: species identification and selection to develop agroforestry at LTCA. Data collecting was carried out with: interview, group discussion, field observation, divining manual study, and PRA. The diversity of the available crop kind shows the number of choices to be developed by the farmer. The farmers generally have the economic objective to develop agroforestry, including increase in net income, risk reduction, increase in environmental service, and the wealth and savings accumulation. Various types of agricultural crops, plantations and forest trees were found in LTCA. They can be the basis for building a wide variety of agroforestry systems.Key words: catchment area, agroforestry system, sequential, integrated.
Coral diversity indices along the Gulf of Aqaba and Ras Mohammed, Red Sea, Egypt
Authors: AMMAR MOHAMMED SHOKRY AHMED
Published: July 2014

Ammar MSA (2011) Coral diversity indices along the Gulf of Aqaba and Ras Mohammed, Red Sea, Egypt. Biodiversitas 12: 92-98. Eight sites extending from Ras Mohammed to the northern tip of the Gulf of Aqaba were surveyed for seven different indices of diversity. These sites are: Ras Ghozlani, Marsa Breika, Temple, Katy, Islands, Canyon, South Nuweiba and Marsa Muqabela. The study proved that the healthy condition can be expressed either by a high value of Shannon index or low value of these other indices. Canyon, having effective management, is considered as the healthiest site (based on Shannon species diversity H`) while South Nuweiba is the least healthiest of all sites because of the illegal destructive fishery overexploitation. Sites having old damage with improved values of richness indices and low values of dominance indices (healthy conditions) like Ras Ghozlani and Marsa Breika had enough time and effective management to improve their diversity, while sites with non improved diversity like Temple and Katy are characterized by sponge and ascidian domination representing potent competitors with corals beside the increased nutrients in those sites. Islands and Marsa Muqabela have low values of richness indices because Marsa Muqabela has the highest value of boring worms and considerable sediments.
Genetic variations of Lansium domesticum Corr. accessions from Java, Sumatra and Ceram based on Random Amplified Polymorphic DNA fingerprints
Authors: YULITA KUSUMADEWI SRI
Published: July 2014

Yulita KS (2011) Genetic variations of Lansium domesticum Corr. accessions from Java, Bengkulu and Ceram based on Random Amplified Polymorphic DNA fingerprints. Biodiversitas 12: 125-130. Duku (Lansium domesticum Corr.) is one of popular tropical fruits in SE Asia. The species has three varieties, known as duku, langsat and kokosan; and duku is the most popular one for being the sweeties fruit. Indonesia has several local varieties of duku, such as duku Condet, duku Sumber and duku Palembang. This present study aimed toassess genetic diversity of 47 accessions of duku from Java, Sumatra, and Ceram based on RAPD fingerprints. Ten RAPDâ€™s primers were initially screened and five were selected for the analysis. These five primers (OPA 7, 13, 18, OPB 7, and OPN 12) generated 53 scorable bands with an average of 10.6 polymorphic fragments per primer. Percentage of polymorphism ranged from 16.89% (OPA 7 and OPN 12) to 24.54% (OPB 7) with an average of 20.16% polymorphism. OPB 7 at 450 bp was exclusively possessed by accession 20 (Java), OPA 18 at 500 bp was by accession 6 (Java), 550 bp by 3 clones from Bengkulu. While OPN 12 at 300 bp and OPA 13 at 450 bp were shared among the accessions. Clustering analysis was performed based on RAPD profiles using the UPGMA method. The range of genetic similarity value among accessions was 0.02-0.65 suggesting high variation of gene pool existed among accessions.
First record of Odontanthias unimaculatus (Tanaka 1917) (Perciformes: Serranidae) from Indonesia
Authors: PERISTIWADY TEGUH
Published: July 2014

Peristiwady T (2011) First record of Odontanthias unimaculatus (Tanaka 1917) (Perciformes: Serranidae) from Indonesia. Biodiversitas 12: 136-140. Seven specimens of O. unimaculatus were collected from Bitung, North Sulawesi between 7 January and 18 August 2009. They were caught from depths of about 100 m in association with other deep water fishes as Epinephelus, Pristipomoides and Etelis. O. unimaculatus was most similar to O. grahami, in sharing the following characters: dorsal fin soft rays 14, anal fin soft rays 7, scales on lateral line 36-37 and gill rakers on upper limb 13-14. If caudal fin shape and coloration were ignored, O. unimaculatus would seem most closely related to O. tapui and O. chrysostictus. Their body proportions were nearly the same. However the laterspecies had longer body width, third dorsal and second anal spine but had shorter longest dorsal ray length, longest anal rays, caudal-fin length and caudal concavity. Other little different characters of O. unimaculatus with other seven species were the proportion of upper jaws length and proportion of body depth. Initially this species was described as new species from Tanabe, Wakayama Prefecture, Japan. Other specimens were reported from Suruga Bay, Japan, Keelung and Kaohsiun, Taiwan and Lubang Island, Philippines and now recorded also in Bitung, North Sulawesi, Indonesia.
Morphological divergences among three sympatric populations of Silver Sharkminnow (Cyprinidae: Osteochilus hasseltii C.V.) in West Sumatra
Authors: ROESMA DEWI IMELDA , SANTOSO PUTRA
Published: July 2014

Roesma DI, Santoso P. 2011. Morphological divergences among three sympatric populations of Silver Sharkminnow (Cyprinidae: Osteochilus hasseltii C.V.) in West Sumatra. Biodiversitas 12: 141-145. Silver sharkminnow (Osteochilus hasseltii C.V.) named by local people as Asang is one of potential Cyprinid fishes species found in several different ecosystems in West Sumatra. The differences of habitat types and another ecological factor among populations may have significant influences on variation and differentiation of morphological characters of this species. In order to elucidate the pattern of morphological divergence, meristic and morphometric characters of O. hasseltii in Singkarak and Dibawah Lake and adjoining river were compared. Phenogram based on cluster analysis showed specific morphological divergence among populations. There were 23 characters significantly different among all comparedpopulations, the highest degree of differentiation was found between Singkarak and Dibawah Lake population (22 characterssignificantly different) and the most similar population were Singkarak Lake and Ombilin an outlet river of lake (only six characters significantly different).
Inventorying the tree fern Genus Cibotium of Sumatra: Ecology, population size and distribution in North Sumatra
Authors: PRAPTOSUWIRYO TITIEN NGATINEM , PRIBADI DIDIT OKTA , PUSPITANINGTYAS DWI MURTI , HARTINI SRI
Published: July 2014

Praptosuwiryo TNg, Pribadi DO, Puspitaningtyas DM, Hartini S (2011) Inventorying the tree fern Genus Cibotium of Sumatra: Ecology, population size and distribution in North Sumatra. Biodiversitas 12: 204-211. Cibotium is one tree fern belongs to the family Cibotiaceae which is easily differentiated from the other genus by the long slender golden yellowish-brown smooth hairs covered its rhizome and basal stipe with marginal sori at the ends of veins protected by two indusia forming a small cup round the receptacle of the sorus. It has been recognized as material for both traditional and modern medicines in China, Europe, Japan and Southeast Asia. Population of Cibotium species in several countries has decreased rapidly because of over exploitation and there is no artificial cultivation until now. The aims of this study were: (i) To re-inventory the species of Cibotiun in North Sumatra, (ii) to record the ecology and distribution of each species, and (iii) to assess the population size of each species. Field study was carried out by using random search with belt transect. Two species were recorded, namely C. arachnoideum dan C. barometz. The geographical distribution of the two species in North Sumatra is presented. Cibotium is commonly growing terrestrially on opened or rather opened areas in secondary forest and primary forest at hills or lower mountains with a relatively high humidity at 30-90Âº slopes. C. arachnoideum has a strict distribution and only found at 1740-1770 m a.s.l. in primary forest, whereas C. barometz has a broad distribution in secondary forest at elevation range from 650-1200 m.
Species composition and interspecific association of plants in primary succession of Mount Merapi, Indonesia
Authors: SUTOMO SUTOMO , FARDILA DINI , PUTRI LILY SURAYYA EKA
Published: July 2014

Sutomo, Faradila D, Putri LSE (2011) Species composition and interspecific association of plants in primary succession of Mount Merapi, Indonesia. Biodiversitas 12: 212-217. Primary succession refers to the establishment of plant species and subsequent changes in composition following major disturbance such as volcanic activity. The study of succession may assist in recognizing the possible effects of species interactions (i.e. facilitation or inhibition). The barren landscapes created by volcanic disturbance on Mount Merapi, Java, Indonesia, provide excellent opportunities to study primary succession. Fifty-six species belonging to 26 families were recorded in the five nuÃ©es ardentes deposits. The highest number of species belonged to the Asteraceae, then Poaceae, followed by Fabaceae andRubiaceae. In Mount Merapi primary succession, the ecosystem may be developing with time as indicated by the increase in the number of species associations. The number of positive associations was generally higher than the number of negative associations, except in the 2001 deposit where it was equal. Native and alien invasive species had different patterns of interspecific associations. This research demonstrates that in primary succession sites on Mount Merapi, positive interspecific association increased as time progressed, which may support the view that facilitation is more prominent in a severely disturbed habitat as compared to competition.
Valuing quality of vegetation in recharge area of Seruk Spring, Pesanggrahan Valley, Batu City, East Java
Authors: YULISTYARINI TITUT , SOFIAH SITI
Published: July 2014

Yulistyarini T, Sofiah S (2011) Valuing quality of vegetation in recharge area of Seruk Spring, Pesanggrahan Valley, Batu City, East Java. Biodiversitas 12: 229-234. A Seruk spring is one of the springs in Batu city which has water debit less than 1 liter per second. Land use changes of Seruk spring recharge area was occurred in 2001. Recharge area of Seruk Spring consists of anthropogenic forest, eucalypts plantation, bamboo forest, pines plantation, horticulture and housing. The aim of this research was to valuing the quality of vegetation which supported ground water recharge in Seruk spring. Quality of vegetation was determined by vegetation structure, diversity, the thickness of litter and C-stock of each land use systems. Forests, eucalypts plantation and bamboo forests had almost same quality of vegetation.
Population density and distribution of Javan gibbon (Hylobates moloch) in Central Java, Indonesia
Authors: SETIAWAN ARIF , NUGROHO TEJO SURYO , WIBISONO YOHANNES , IKAWATI VERA , SUGARDJITO JITO
Published: July 2014

Setiawan A, Nugroho TS, Wibisono Y, Ikawati V, Sugardjito J. 2012. Population density and distribution of Javan gibbon (Hylobates moloch) in Central Java, Indonesia. Biodiversitas 13: 23-27. A survey of Javan gibbon (Hylobates moloch) was conducted from July 2009 to November 2010 in the Dieng Mountains and Mount Slamet, Central Java, Indonesia. The purpose of the survey is to assess current population status and its distribution, including factors threatening the species. We used line transect method to estimate gibbon densities. We detected a total of 144 individuals in 56 groups on a 212.7 km length trail. Average group size was calculated as 2.57 (ranging between 2 and 7) individuals. We compared the population density between Mount Slamet and Dieng Mountains. It was found that the density in Mount Slamet was lower than in the Dieng Mountains with 1.7 ind./km2 compare to 2.5-7.57 ind/km2 respectively. In total, there are about 1,034 individuals of gibbon in Central Java which is divided in two sub populations. The one in Mount Slamet is about 175 individuals whereas in the range of Dieng Mountains is 881 individuals. Establishing a protected area and enhancing conservation awareness are critically important for survival of this endangered ape. Conservation awareness should consider human needs of local people surrounding the forest habitat.
Frequency of endophytic fungi isolated from Dendrobium crumenatum Sw. (Pigeon orchid) and antimicrobial activity
Authors: MANGUNWARDOYO WIBOWO , SUCIATMIH SUCIATMIH , GANDJAR INDRAWATI
Published: July 2014

Mangunwardoyo W, Suciatmih, Gandjar I. 2012. Frequency of endophytic fungi isolated from Dendrobium crumenatum Sw. (Pigeon orchid) and antimicrobial activity. Biodiversitas 13: 34-39. Endophytic microorganisms were found in orchid such as Dendrobium crumenatum Sw. (pigeon orchid), an orchid that sometimes used in traditional medicine. The fungi were isolated from roots, bulbouses, stems, and leaves of D. crumenatum collected from Tanah Baru Housing area, Botanical Garden Bogor, and Herbarium Bogoriense, respectively. Twelve species were identified from 60 samples obtained. Guignardia endophyllicola Okane, Nakagiri, and Ito (anamorph:Phyllosticta capitalensis P. Herm.) were the dominant endophytic mould. Screening of the anti-microorganism activity of the samples revealed that Fusarium nivale (Fr.) Ces. inhibited Candida albicans ATCC 2091 and Candida tropicalis LIPIMC 203. All specimens did not inhibit the growth of Bacillus subtilis ATCC 6633, Escherichia coli ATCC 25022, and Staphylococcus aureus ATCC 25023.
The conservation of mitochondrial genome sequence in Leucadendron (Proteaceae)
Authors: PHARMAWATI MADE , YAN GUIJUN , FINNEGAN PATRICK M.
Published: July 2014

Pharmawati M, Yan G, Finnegan PM. 2012. The conservation of mitochondrial genome sequence in Leucadendron (Proteaceae). Biodiversitas 13: 53-58. Mitochondrial DNA (mtDNA) is useful for developing molecular markers and for studying plant phylogeny.However, its usefulness depends on the degree of detectable sequence variation. In seven species of the genus Leucadendron, PCRRFLP failed to reveal any polymorphisms in seven separate regions of the mtDNA. Sixty-two primer pair - enzyme combinations were used to assay at least 248 restriction sites, resulting in the direct sampling of a minimum of 992 bp across 17,500 bp of mt DNA. The highly conserved nature of the mtDNA sequence in the genus Leucadendron was confirmed by the absence of sequence variation in the 1434 bp mtDNA nad1/B-C intron across these species. Mitochondrial DNA sequences are more highly conserved than the chloroplastDNA sequences in Leucadendron and the mtDNA sequences in many other plant genera. Phylogenetic analysis using this intronsequence was consistent with other phylogenetic analyses in regard to the position of Proteaceae.
The wild plants used as traditional medicines by indigenous people of Manokwari, West Papua
Authors: LENSE OBED  ï€ 
Published: July 2014

Lense O. 2012. The wild plants used as traditional medicines by indigenous people of Manokwari, West Papua. Biodiversitas 13: 98- 106. The aims of the research were to identify the main plant species which are used as traditional medicines by native people in Manokwari District, West Papua Province and also to describe the method of preparation and uses of some of the medicinal plants. This research was conducted in seven sub-districts, ie. Manokwari, Ransiki, Kebar, Wasior, Mimyambouw, Merdey and Anggi-Sururey sub- District. Information recorded including methods of diagnosis and treatment of diseases, tribal name of a plant they used for treating disease (s), part of the plant used, preparation and mode of application, and whether the plant is used alone or in combination with other plants. Results indicate that the indigenous people in Manokwari District have been using at least 99 plant species (93 genera and 59 families) as sources of medicines. Most of these traditional medicinal plants are commonly gathered from the local tropical rainforest communities. At least 40 kinds of sickness and injuries such as malaria, fever, and wounds can be treated by using traditional medicinal plants from Manokwari District. Research also found that all parts of plants used, but leaf extracts are the most common part of the plant used for treating medical condition.
A comparative phylogenetic analysis of medicinal plant Tribulus terrestris in Northwest India revealed by RAPD and ISSR markers
Authors: KUMAR ASHWANI , VERMA NEELAM
Published: July 2014

Kumar A, Verma N. 2012. A comparative phylogenetic analysis of medicinal plant Tribulus terrestris in Northwest India revealed by RAPD and ISSR markers. Biodiversitas 13: 107-113. Several DNA marker systems and associated techniques are available today for fingerprinting of plant varieties. A total of 5 RAPD and 8 ISSR primers were used. Amplification of genomic DNA of the 6 genotypes, using RAPD analysis, yielded 164 fragments that could be scored, of which 47 were polymorphic, with an average of 9.4 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from 6 (AKR-1) to 10 (AKR-4) and varied in size from 200 bp to 2,500 bp. Percentage polymorphism ranged from 16% (AKR-4) to a maximum of 41% (AKR-4), with an average of 29.6%. The 8 ISSR primers used in the study produced 327 bands across 6 genotypes, of which 114 were polymorphic. The number of amplified bands varied from 7 (ISSR 7) to 12 (ISSR 1&3), with a size range of 250-2,800 bp. The average numbers of bands per primer and polymorphic bands per primer were 40.87 and 14.25, respectively. Percentage polymorphism ranged from 24% (ISSR 4) to 53.84% (ISSR 2), with an average percentage polymorphism of 35.59% across all the genotypes. The 3â€²-anchored primers based on poly (AC) and poly (AT) motifs produced high average polymorphisms of 53.84% and 40.81%, respectively. ISSR markers were more efficient than the RAPD assay, as they detected 35.59% polymorphic DNA markers in Tribulus terrestris as compared to 29.6% for RAPD markers. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in ISSR and combined data of RAPD and ISSR.
The exploration and diversity of red fruit (Pandanus conoideus L.) from Papua based on its physical characteristics and chemical composition
Authors: MURTININGRUM MURTININGRUM , SARUNGALLO ZITA L. , MAWIKERE NOUKE L.
Published: July 2014

Murtiningrum, Sarungallo ZL, Mawikere NL. 2012. The exploration and diversity of red fruit (Pandanus conoideus L.) from Papua based on its physical characteristics and chemical composition. Biodiversitas 13: 124-129. The aim of this study was to determine the diversity of red fruit based on its physical characteristics and chemical composition. Exploratory survey method and laboratory research (pure experiment) were used to assess the physical character and chemical composition of crude red fruit. Physical character of each accession showed a variation on fruit color (dark red and red); the fruit and single fruit (drupa) length ranged from 21-71 cm and 1.2-1.8cm, respectively. The dried red fruit contains 2.03- 3.50% ash, 3.12-6.48% protein, 11.21-30.72% fat, 43.86-79.66% carbohydrate, 3.78- 21.88 mg/100g vitamin C, 2.00-3.14 mg/100g vitamin B1, 0.53-1.11% Ca, 8.32-123.03 ppm Fe, and 0.01-0,33% P, with total carotenoids and total tocopherol ranging from 332.65-3309.42 ppm and 964.52-11917.81 ppm. The clustering analysis result of red fruit based on its physical characteristic and chemical composition showed that the related accessions was U Saem and Tawi Magari, having a 25% similarity. The accession U Saem and Tawi Magari had the highest level of similarity in total carotenoids and total tocopherol. Furthermore, they also perform similar physical characteristics by having triangular cylinder shape, red flesh color, and fruit length category.