bluuebunny/crossref_metadata_2025 huggingface dataset:
The dynamics of the population of a steppe perennial Senecio macrophyllus M.BIEB. during xerothermic grassland overgrowing
Authors: Czarnecka Bożena
Published: April 2013

The study aimed to determine the long-term changes of the Senecio macrophyllus M.BIEB. population traits: the abundance, reproduction mode, individual fecundity, seed rain and recruitment of new genets in the course of xerothermic grassland overgrowing. The study had also the applied goal: to estimate the chances of "special care" species to survive in the changing environment without management regime for the maintenance of grassland. The model object was the island population of large-leaved ragwort on Biała Góra (the White Mountain) near Tomaszów Lubelski, South-East Poland. To achieve these aims I used the following sets of data: phytosociological relev,s made in plant communities in an interval of 16-18 years; repeated elaboration of the numbers and life-stage structure of the population, both by non-surface and surface method; observation of plants, life cycle in 50 labelled genets; population reproduction and seed rain amounts. The area of an open xerothermic grassland decreased due to the process of overgrowing by bushes which was accompanied by the increasing coverage of forest and meadow herbs as well as monocotyledons, mainly Brachypodium pinnatum and Calamagrostis epigejos. The abundance of the S. macrophyllus population noticable diminished. The flowering mode has been changing during years from an oscillation to a chaotic type which caused the significant decreasing of the individual fecundity, population reproduction and seed rain. In last years it was reflected in the interruption of juveniles’ recruitment.
Last two hundred individuals: rediscovery of Scilla mesopotamica Speta (Hyacinthaceae), a threatened endemic species in Turkey
Authors: Eker Ismail , Akan Hasan
Published: April 2013

In this paper, the rediscovery of endemic and long missing species, Scilla mesopotamica Speta which had been only known from the type gathering, is given. The species has not been collected again after Sintenis in 1888, whose specimens served Speta for description of the new taxon. In 2004, the authors found it in a steppic rocky area, near Halfeti in Şanliurfa province, South East Anatolia, Turkey. After analyzing Sintenis' original collection notes, they concluded that this area is identical with the type locality. S. mesopotamica has an extremely limited distribution and is represented by less than 200 specimens in the single known population that covers less than 50 m2. Taxonomy of the species, detailed description with illustrations, geographical distribution, habitat, ecology and status of IUCN extinction risk and some comments on conservation of the plant are also presented.
Spontaneous occurrence and dispersion of Aronia ×prunifolia (Marshall) Rehder (Rosaceae) in Poland on the example of the "Bagna" bog complex near Chlebowo (western Poland)
Authors: Celka Zbigniew , Szkudlarz Piotr
Published: April 2013

This study presents information on a new to Poland synanthropic species - Aronia ×prunifolia (purple chokeberry).Purple chokeberry is cultivated worldwide as a fruit and decorative plant. In various regions of the world the process of its naturalisation outside the places of cultivation has been observed. In Europe, it is visible, among others, in Holland and Germany. In Poland, the first case was recorded in the "Bagna" bog complex near Chlebowo (Wielkopolska region). In this study, the distribution of Aronia ×prunifolia in Poland has been presented (square ATPOL BC67, BC68) as well as its spread and conditions of occurrence.
The hybrid origin of Calamagrostis ×gracilescens (Poaceae) in Poland inferred from morphology and AFLP data
Authors: Paszko Beata , Nobis Marcin
Published: April 2013

The morphology of Calamagrostis canescens and C. stricta recorded in the Małopolska Upland (the vicinity of Zbijów Mały, ca. 10 km northeast of the town of Skarżysko-Kamienna, Central Poland) was examined due to intermediate individuals found in sympatric populations of these species. Both putative parents as well as individuals that appeared hybrid-like were found in an extensive, wet hay-meadow. Various vegetative and reproductive characteristics were studied to identify hybrids. Interestingly, Polish accessions of C. ×gracilescens exhibited some degree of morphological intermediacy but resembled C. stricta in spikelet morphology. Branching of the mid-culm, the number of nodes per culm, callus hair length and relative callus hair length are the best characters to distinguish the Polish C. ×gracilescens. AFLP analysis proved to be suitable for detecting recent hybridization events between C. canescens and C. stricta. Analysis of the Bayesian clustering analysis showed that C. ×gracilescens were subjected to gene flow from the C. canescens gene pool as well as from the C. stricta gene pool.
The distribution of Elatine macropoda Guss. (Elatinaceae)
Authors: Popiela Agnieszka , Łysko Andrzej
Published: April 2013

Data on distribution of Elatine macropoda Guss. are given, listing distribution map and a list of localities. Disjunctive distribution pattern of the species within the Mediterranean region as well as distribution of other species of the section Elatinella Seub. and the genera suggests a long history of the range formation.
Tree-like pines on the Mshana peat bog in the Gorgany Mountains: a trace of Pinus uliginosa migration in the East Carpathians?
Authors: Boratyńska Krystyna , Sulikowska Anna , Iakushenko Dmytro M. , Jasińska Anna K.
Published: April 2013

The taxonomic position of the population of tree-like, mostly polycormic individuals of pines from the Mshana peat bog in the Gorgany Mountains (East Carpathians, Ukraine) has been studied on the basis of the morphological characteristics of cones and needles, and anatomical characteristics of the needles. These features have been compared with the surrounding Pinus mugo population as well as P. uliginosa, P. mugo, P. sylvestris and P. uncinata from natural populations of the taxa. Tree-like individuals were found to have the most similar needles to P. uliginosa, but most similar cone characteristics to P. mugo. It was concluded, that the tree-like population has a relic character and can present the trace of the early migration of P. uliginosa from the West and its hybridisation with P. mugo.
Leaf indumentum types in Potentilla (Rosaceae) and related genera in Iran
Authors: Faghir Marzieh B. , Attar Farideh , Farazmand Ali , Ertter Barbara , Eriksen Bente
Published: April 2013

Indumentum types of the leaves in 31 species of Potentilla L. (Rosaceae) and four related genera, especially Tylosperma Botsch., Schistophyllidium (Juz. ex Fed.) Ikonn., Drymocallis Fourr. ex Rydb., and Sibbaldia L. from Iran were investigated. Indumentum ultrastructure was studied by scanning electron microscopy (SEM). SEM observation revealed three type classes based on leaf indumentum: 1) straight (appressed-erect); 2) straight-erect and crispate, and 3) crispate-floccose. The straight hair character (I type class) is widely distributed among all genera sampled and six sections of Potentilla. In contrast the crispate-floccose indumentum (III type class) is confined to all examined species of sections Speciosae and Pensylvanicae. While some sections especially Rectae (straight and straight-crispate hairs) and Terminales (straight-crispate and floccose-crispate) posses two indumentum type classes. The present survey shows that indumentum types are of systematic importance and may form good key characters for identification purposes.
Baeothryon alpinum (L.) T.V. Egorova (Cypercaeae) in the Polish Lowlands: distribution, population decrease and implications for conservation
Authors: Pawlikowski Paweł
Published: April 2013

A total of 47 localities of Baeothryon alpinum, hosting population of more than 100 000 shoots, were recorded in the lowland part of Poland during field surveys in the years 2003-2009. Among them were 25 populations discovered for the first time. Out of 57 sites of the species known from literature and unpublished (including herbarium) sources, 35 were not confirmed during the survey, 27 of them being definitely extinct. B. alpinum shows a clear pattern of distribution in Poland, with three main areas of occurrence: 1) the north-easternmost Poland (Lithuanian Lake District with the adjacent parts of the Masurian Lake District and the upper Biebrza river valley in North Podlasie Lowlands), which is part of the species boreal main range; 2) scattered localities in north-western Poland; 3) mountain mires at higher altitudes in the Sudetes and Tatra mountains and the adjacent part of southern Poland. The main aggregation of localities is found in Augustów Forest (including the Sejny Lakeland and Wigry National Park), and in the Góry Sudawskie region with adjacent areas. The biggest Polish population in the "Kobyla Biel" fen near Augustów consisted of several dozens of thousands of shoots. The Lithuanian Lake District is an area of general importance for the conservation of B. alpinum in Poland. The species is threatened, first of all, due to secondary succession (mires overgrowing with shrubs, trees and reed) and requires conservation measures as well as establishing nature reserves in places where it occurs. The degree that B. alpinum decreases in number is strikingly different in particular regions of Poland - it has lost most of its localities in north-western Poland and in Masurian Lake District, while in the Lithuanian Lake District and the upper Biebrza valley there are minor losses only. Depending on the region (from the west to the east and from the south-west to the north-east), the species should be given extinct or critically endangered (regions of north-western and southern Poland), endangered (Masurian Lake District), vulnerable (North Podlasie Lowlands) and near threatened (Lithuanian lake District) status. Although the disappearance of the populations beyond the species main range is a common phenomenon, the presented pattern is man-related and connected with differences in land management.
Tetraploa aristata Berkeley & Broome (Fungi, Pleosporales), a new taxon to Poland
Authors: Karpińska-Kołaczek Monika , Kołaczek Piotr , Heise Waldemar , Worobiec Grzegorz
Published: April 2013

Tetraploa aristata Berkeley & Broome represents the anamorphic stage of a pleomorphic fungus with holomorph Tetraplosphaeria tetraploa (Scheuer) Kaz. Tanaka & K. Hiray (Lophiostoma tetraploa (Scheuer) Aptroot & K.D. Hyde). Until now this taxon has not been reported in Poland, where it is probably on the fringe of its distribution. Conidia of Tetraploa aristata were found during palynological analyses of modern surface samples and later on the decaying leaves of Phleum phleoides from xeric grasslands in Kraków and its vicinity. Since Tetraploa aristata was discovered during palynological analysis, this method might be considered to be a useful tool for investigations of contemporary microfungal mycobiota.
Analysis and distributional patterns of the invasive flora in a protected mountain area - a case study of Medvednica Nature Park (Croatia)
Authors: Vuković Nina , Bernardić Anita , Nikolić Toni , Hršak Vladimir , Plazibat Miško , Jelaska Sven D.
Published: April 2013

In this paper we have analysed invasive flora of Medvednica Nature Park, Croatia with respect to their origins, life forms, systematic positions, types of seed dispersal, Ellenberg indicator values and spatial distributions using MTB 1/64 grid units for analyses. A total of 27 invasive plant species, belonging to 14 families, were recorded with Asteraceae being the most frequently occurring family. Therophytes were the most common life form, as is generally true of Croatian invasive plants; however, hemicryptophytes and geophytes were more frequent in Medvednica. Here, invasive plants originated mainly from both Americas with slightly lower portion in comparison to all Croatian invasive plants, while contrary was the case when comparing those originated from Asia. The most widespread species was Erigeron annuus (L.) Pers., and the species with the lowest occurrence were Chamomilla suaveolens (Pursh.) Rydb and Datura innoxia Mill. A multiple regression model explains 44% of the spatial variability in the invasive plants data per MTB 1/64 unit, using the number of all recorded plant species, the average elevation and the lengths of paths and roads as estimators. The latter two variables also had the most influence on the ordination axes in analyses of the spatial distribution of seed dispersal types present in each MTB 1/64 unit. Anemochory was the most frequent type of seed dispersal.
Involvement of aba in flower induction of Pharbitis nil
Authors: Wilmowicz Emilia , Frankowski Kamil , Glazińska Paulina , Kęsy Jacek , Kopcewicz Jan
Published: April 2013

Flowering of plants is controlled by hormones among which both stimulators and inhibitors are present. The role of abscisic acid (ABA) in flower induction of the short day plant Pharbitis nil was shown in our experiments through exogenous applications and endogenous level determination of the hormone in cotyledons of seedlings grown under special light conditions.

The application of ABA to cotyledons or shoot apices during the first half of a 24-h long inductive night inhibits flowering. The same compound applied towards the end of or after a 14-h long subinductive night increases the number of flower buds produced by these plants.

Exposing P. nil seedlings at the beginning of a 24-h long inductive night to far red light (FR) decreases the level of endogenous abscisic acid in cotyledons and leads to flower inhibition. However, a pulse of red light (R) reversing the inhibitory effect of far red light on the flowering of P. nil increases the ABA content.

The results obtained confirm previous observations that ABA may play a dual and an important role in the regulation of floral bud formation in P. nil. The flowering occurs when the level of endogenous abscisic acid is low at the beginning and is high toward the end of the inductive night.
Arbuscular mycorrhizal fungi (Glomeromycota) associated with roots of Ammophila arenaria growing in maritime dunes of Bornholm (Denmark)
Authors: Błaszkowski Janusz , Czerniawska Beata
Published: April 2013

155 rhizosphere soil and root mixtures were collected from under Ammophila arenaria colonizing maritime dunes of the island Bornholm (Denmark) to determine arbuscular mycorrhizal fungi (AMF) of the phylum Glomeromycota co-existing with this plant. In the laboratory, each mixture was divided into two parts. One part was used to establish a pot culture with Plantago lanceolata as the host plant to initiate sporulation of fungi that had not produced spores in field conditions. In the second part, the numerical and species composition of the spore populations of AMF sporulating in the field was determined. Spores of AMF were found in 70 field-collected samples and 134 trap cultures. They represented 26 species and six undescribed morphotypes in six genera of the Glomeromycota. Of them, 20 species and three morphotypes in five genera occurred in the field, and 16 species and three morphotypes in five genera were found in trap cultures. The fungi most frequently revealed were members of the genus Glomus; a total of 17 species and six morphotypes of this genus were recognized. Considering the occurrence of spores in both field samples and trap cultures, the fungi most frequently co-occurring with roots of A. arenaria growing in the dunes of Bornholm were G. irregulare (present in 73.6% of samples), followed by Scutellospora dipurpurescens (19.4%) and Archaeospora trappei (10.3%). However, Glomus irregulare mainly sporulated in trap cultures; spores of this fungus were found in only 0.6% of field samples. Other relatively frequently found species were G. aggregatum (9.0%), G. eburneum (7.1%), Paraglomus laccatum (5.2%), and S. armeniaca (6.5%). The species most abundantly sporulating in the field were G. aggregatum (produced 28.36% of all spores isolated), G. badium (11.00%), and S. dipurpurescens (21.55%).
Variation in size-dependent fitness components in a terrestrial orchid, Dactylorhiza majalis (Rchb.) Hunt et Summerh., in relation to environmental factors
Authors: Mróz Lucyna , Kosiba Piotr
Published: April 2013

We investigated the flowering probability and flower production in relation to plant size in a terrestrial orchid, Dactylorhiza majalis at 10 meadow sites in central and southwestern Poland. These sites differed in altitude (low, high) and management (presence or absence of mowing). At all sites, concentrations of nutrients in the soil were also measured. The probability of flowering increased significantly with the size of the plant in all populations, indicating that individuals do not flower until they reach a threshold size. Populations at high altitudes and the unmown sites had significantly lower threshold sizes for reproduction and showed sharp increase in flowering probability with plant size, compared to other populations. The threshold sizes for reproduction tended to decrease at sites rich in N and Mg and poor in P and S. Flower production was also size-dependent in all populations. Considerable between-site differences were found in the slope and the intercept of the regression between plant size and flower production. Flower production at some sites, at high altitudes, increased more steeply with plant size than at other sites. However, no pattern in size-dependent flower production was found relative to the measured environmental variables. Most of the size-dependent components of flowering probability were related to each other but not with the size-dependent flower production.
Charophytes of the Lubelszczyzna region (Eastern Poland)
Authors: Urbaniak Jacek , Sugier Piotr , Gąbka Maciej
Published: April 2013

The distribution and ecology of charophytes in Lubelszczyzna (Eastern Poland) is described based on herbaria collections, literature data, and the author's own investigations. Maps showing the distribution of all 22 charophyte species identified so far are presented, as well as the details of habitats ecology. Some data on species frequency, conservation, and threats are added.
Occurrence of the fungi from the genus Ampelomyces – hyperparasites of powdery mildews (Erysiphales) infesting trees and bushes in the municipal environment
Authors: Sucharzewska Ewa , Dynowska Maria , Kempa Aneta B.
Published: April 2013

The studies refer to the phenomenon of hyperparasitism in the municipal environment. The paper presents the occurrence of fungi of the genus Ampelomyces on Erysiphales – important group of phytopathogenic fungi. For the first time in Poland analyzed degree of infestation of Erysiphales mycelium by Ampelomyces and effect of the hyperparsites on the degree of infestation plants by Erysiphales. The high participation of the Ampelomyces was noted in each year of the study. Substantial differences were noted in the occurrence of Ampelomyces depending on the developmental stage of the host fungi and considerable differences in the prevalence of the hyperparasites on particular Erysiphales species. In all cases examined, the mean index of infestation of host plants by Erysiphales was higher than the mean degree of infestation of powdery mildew mycelium by Ampelomyces. The results indicate that under natural conditions they do not play any significant role in the reduction of the degree of infestation of host plants by Erysiphales and do not disturb drastically their life cycle.
Seed sexing revealed female bias in two Rumex species
Authors: Kwolek Dagmara , Joachimiak Andrzej J.
Published: April 2013

Sex-ratio bias in seeds of dioecious Rumex species with sex chromosomes is an interesting and still unsettled issue. To resolve gender among seeds of R. acetosa and R. thyrsiflorus (two species with an XX/XY1Y2 sex chromosome system), this work applied a PCR-based method involving DNA markers located on Y chromosomes. Both species showed female-biased primary sex ratios, with female bias greater in R. acetosa than in R. thyrsiflorus. The observed predominance of female seeds is consistent with the view that the female biased sex ratios in Rumex are conditioned not only postzygotically but also prezygotically.
Patterns of bryophyte diversity in arable fields of Lithuania
Authors: Andriušaitytė Danguolė , Jukonienė Ilona
Published: April 2013

The paper presents research data on bryophyte diversity in arable land throughout the territory of Lithuania. The bryoflora was analyzed regarding systematic structure and morphological forms, life-history strategies, mode of reproduction and frequency of species. Bryophyte diversity in arable fields of Lithuania was compared with that of Slovakia and the British Isles, which are positioned in different geographical regions of Europe.

A total of 97 species of bryophytes of 25 families and 48 genera were ascertained. Dominance of acrocarpous mosses and thalloid liverworts, high representation of Pottiaceae, Bryaceae, Mielichhoferiaceae and Ricciaceae families as well as Bryum, Dicranella, Pohlia and Riccia genera, wide distribution of annual shuttles and ephemeral colonists, high reproduction effort of the species (frequent sporophytes and asexual propagules) were specific features of the bryophytes of the studied habitats as a result of adaptations to regular disturbances. The distribution of species into six frequency groups seemed to be uneven. The most abundant group of species with the lowest frequency (1–3 records) covered 53.6% of all species. The group contained about 90% of all many-year potential life span species recorded in the habitat. Species with short life span were distributed quite evenly throughout frequency groups. No regionally-specific species were ascertained in the studied habitat. Most of arable-land-specific species recorded in Lithuania is distributed throughout different regions of Europe.
An Optimal Fuzzy High-Gain Observer for an Uncertain Nonlinear System
Authors: Yu Sung-Hoon , Kim Yong-Tae , Park Chang-Woo , Hyun Chang-Ho
Published: April 2013

This paper proposes an alternative optimal fuzzy high-gain observer design scheme. The structure of the proposed observer is represented by the Takagi-Sugeno fuzzy model and has the integrator of the estimation error. It improves the performance of a high-gain observer and makes the observer robust against noisy measurements, uncertainties and parameter perturbation. The proposed observer adopts the [Formula: see text] control technique and an adaptive projection algorithm. This technique results in a reduction of both the fuzzy approximation error and time-varying disturbances. In addition, the proposed observer accomplishes a fast transient response and parameter convergence. Some simulation results are given to present the validity of the theoretical derivations and the performance of the proposed observer.
A Study of the Determinants of Corporate Environmental Disclosure in MENA Emerging Markets
Authors: Akrout Mejda Mahmoudi , Othman Hakim Ben
Published: April 2013

Abstract: The purpose of this study is to investigate environmental disclosure determinants in Arab Middle Eastern and North African (MENA) companies. In this regard, we investigate factors which are specific to this context. We include the â€˜business culture' variable inherited from former colonisers and main economic partners and the â€˜state ownership' and â€˜family ownership' variables. In addition, we consider â€œCountry's Internet Penetrationâ€ as a new explanatory variable which is expected to influence environmental disclosure on the web site. Using a sample of 153 web sites of listed companies, findings show a negative and significant relationship between environmental disclosure and â€˜family ownership'. Moreover, consistent with prior work, the level of environmental disclosure is substantially affected by company size and performance.
High School Library Data Processing
Authors: Flora Betty , Willhardt John
Published: April 2013

Planning and operation of an automated high school library system is described which utilizes an IBM 1401 data processing system installed for teaching purposes. Book orfering, shelf listing and circulation have been computerized.
Experiences of Migrating to Open Source Integrated Library Systems
Authors: Singh Vandana
Published: April 2013

Interest in migrating to open source integrated library systems is continually growing in libraries. Along with the interest, lack of empirical research and evidence to compare the process of migration brings a lot of anxiety to the interested librarians. In this research, twenty librarians who have worked in libraries that migrated to open source ILS or are in the process of migrating were interviewed. The interviews focused on their experiences and the lessons learned in the process of migration. The results from the interviews are used to create guidelines/best practices for each stage of the adoption process of open source ILS. These guidelines will be helpful or librarians who want to research and/or adopt open source ILS.
Mapping for the Masses: GIS Lite & Online Mapping Tools in Academic Libraries
Authors: Weessies Kathleen W. , Dotson Daniel S.
Published: April 2013

Customized colorful maps depicting complex social data are much more prevalent today than in the past. Not only in formal published outlets, interactive map sites make it easy to create and publish custom maps in more casual outlets such as social media. This article defines GIS Lite, describes three licensed products currently licensed by institutions, and discusses issues that arise from their varied functionality and license restrictions.
Efficacy of raltegravir in late‐presenting HIV‐infected pregnant women: a case series presentation
Authors: Nobrega I , Travassos A , Haguihara T , Brites C
Published: April 2013

The risk of HIV perinatally transmition is highest in the 3rd trimester and is correlated with the imune status and especially with the maternal viral load close to delivery. The speed of the viral load decay is an importante strategy for the prevention of mother‐to‐child transmition (MTCT) in late‐presenting pregnant women. Poor access to prenatal care and HIV late diagnosis during pregnancy remains a major problem in Bahia, Brazil. The integrase inhibitor raltegravir has significantly higher first and second phase viral decay rates, has a high placental transfer with a potential preloading effect for neonate, and demonstrated effective accumulation in cervicovaginal secretions. These characteristics make RGV a potential candidate to treat late‐presenting pregant women. We report 13 cases in which raltegravir (400 mg twice daily) was used late in pregnancy, as part of the antirretroviral regimen for MTCT prophylaxis. Table 1 contains the main characteristics of the 13 cases.

Characteristics of the 13 cases. Numbers represent means (range)

Variable

Maternal age (yr)
28.6 (17–37)

Years since HIV diagnosis
4.6 (<1–16)

Week of pregnancy at RGV initiation
35.8 (34–38)

Maternal CD4+ T‐cell count at RGV initiation (cl/ml)
357 (65–1.203)

Maternal viral load at RGV initiation (cp/ml)
73.765 (636–391.535)

Other ARV in regimen
ZDV+3TC+LPV/r+RGV (7), ZDV+3TC+RGV (3), ZDV+3TC+DRV/r+RGV (2), ZDV+3TC+ATV+RGV (1)

Exposure to RGV (days)
17.7 (7–35)

Adverse events with RGV
None

Viral load at delivery (cp/ml)
181 (<50–457)

Gestational age at delivery (wk)
38.3 (37‐40)

Mode of delivery
Elective C‐section (10), Non‐elective C‐section (2), Spontaneous vaginal delivery (1)

Infant birth weight (kg)
2.942 (2.215–3.525)

Obstetrical complications
None

Birth defects
None

Intravenus ZDV during labour and delivery
Yes (13)

Oral ZDV post‐exposure prophylaxis for infant
Yes (13)

Four mothers for whom viral load data were available had undetectable levels (<50 HIV‐RNA cp/ml) at the time of delivery. The remaining 9 women had viral load <460 cp/ml one week before delivery. All but one infant's HIV‐RNA were undetectable at 1 and 3 months. The only positive case was an intrauterine transmission, since the baby viral loads at birth and at 1 month were>500.000 cp/ml and mother had 64 cp/ml at delivery (elective C‐section). In conclusion, this and other previous reports suggest that RGV is an useful and safe ARV drug to reduce the MTCT in late‐presenting HIV‐infected pregnant women.
The discovery of S/GSK1265744: a carbamoyl pyridone HIV‐1 integrase inhibitor
Authors: Taoda Y , Johns B , Weatherhead J , Temelkoff D , Kawasuji T , Yoshida H , Taishi T , Kiyama R , Fuji M , Murai H , Yoshinaga T , Sato A , Fujiwara T
Published: April 2013

Background

HIV‐1 integrase is a virally encoded enzyme essential for lentiviral replication. Assiduous medicinal chemistry efforts culminated in the discovery of raltegravir, the first marketed HIV‐1 integrase inhibitor (INI). However, there is significant opportunity for improvement including overall dose burden, dosing interval and potency against resistant viruses. Our molecular design approach used a two‐metal binding pharmacophore strategy and succeeded in identification of carbamoyl pyridone HIV‐1 INIs. This enriched core scaffold has abundant structural features expanding the opportunity to control drug properties, leading to the discovery of S/GSK1265744.

Methods

The carbamoyl pyridone scaffold was derivatized and evaluated for antiviral activity against wild‐type virus (±HSA) along with key INI‐resistant mutants. Animal pharmacokinetic profiles including a key measure of the trough drug concentration over protein‐adjusted antiviral potency (C24/PAIC50) along with in vitro DMPK properties, were used along with the virological data for compound selection.

Results

The carbamoyl pyridone series inhibitors exhibited potent antiviral profiles with promising DMPK properties. S/GSK1265744 demonstrated good coverage of C24 over PAIC50 predicting low mg unboosted once daily dosing, now validated in phase 2 clinical studies. These preclinical data along with a long human T1/2 of ~30 hours in oral tablet study supports S/GSK1265744 as a long acting parenteral agent for once‐monthly or less frequent dosing.

Conclusions

A medicinal chemistry approach utilizing key viral mutants in combination with C24/PAIC50 has allowed for discovery of S/GSK1265744. This agent is currently in phase 2 development evaluating a novel, long‐acting parenteral route of administration and may enable new approaches to HIV therapy and prevention.
DNA Isolation from Mammalian Samples
Authors: Liu Ximeng , Harada Shuko
Published: April 2013

DNA isolation is a fundamental initial step for molecular genetic studies. Two quite different methodologies are described in this unit: silica spin column and phenol/chloroform extraction. Currently, the most commonly used technique is the silica‐based spin column, although phenol/chloroform extraction is still widely used. This unit also presents basic procedures for extraction of DNA from both fresh tissues and formalin‐fixed, paraffin‐embedded (FFPE) tissue samples. Curr. Protoc. Mol. Biol. 102:2.14.1–2.14.13. © 2013 by John Wiley & Sons, Inc.
Exome Sequencing by Targeted Enrichment
Authors: Clark Michael James , Chen Rui , Snyder Michael
Published: April 2013

This unit describes methods for targeted enrichment of the exon‐coding portions of the genome using Agilent SureSelect Human All Exon 50 Mb and Roche Nimblegen SeqCap EZ Exome platforms. Each platform targets and enriches a large overlapping portion of the greater human exome. The protocols here describe the biochemical procedures used to enrich exomic DNA with each platform, including recommended modifications to the manufacturers' protocols. In addition, a brief description of the sequencing protocol and estimation of the needed amount of sequencing for each platform is included. Finally, a detailed analytical pipeline for processing the subsequent data is described. These protocols focus specifically on human exome sequencing platforms, but can be applied with some modification to other organisms and targeted enrichment approaches. Curr. Protoc. Mol. Biol. 102:7.12.1–7.12.21. © 2013 by John Wiley & Sons, Inc.
Basic Image Analysis and Manipulation in ImageJ
Authors: Hartig Sean M.
Published: April 2013

Image analysis methods have been developed to provide quantitative assessment of microscopy data. In this unit, basic aspects of image analysis are outlined, including software installation, data import, image processing functions, and analytical tools that can be used to extract information from microscopy data using ImageJ. Step‐by‐step protocols for analyzing objects in a fluorescence image and extracting information from two‐color tissue images collected by bright‐field microscopy are included. Curr. Protoc. Mol. Biol. 102:14.15.1–14.15.12. © 2013 by John Wiley & Sons, Inc.
A Detailed Protocol for Formaldehyde‐Assisted Isolation of Regulatory Elements (FAIRE)
Authors: Simon Jeremy M. , Giresi Paul G. , Davis Ian J. , Lieb Jason D.
Published: April 2013

Nucleosome displacement is a key event in the regulation of gene expression in the eukaryotic genome. This unit details an approach called Formaldehyde‐Assisted Isolation of Regulatory Elements (FAIRE) for isolating nucleosome‐depleted regions. FAIRE does not rely on the use of antibodies or enzymes, and has proven successful in most eukaryotic cells and tissues. The set of regulatory elements enriched by FAIRE is similar to those identified through DNase hypersensitivity. The enriched fragments can be detected by quantitative PCR, tiling DNA microarrays, or next‐generation sequencing. Although the signal‐to‐noise ratio is typically lower than that observed for DNase assays, FAIRE has high sample‐to‐sample reproducibility, requires very low amounts of input material, is inexpensive, is amenable to high‐throughput adaptations, and is a relatively simple procedure with a high rate of success, even for those without extensive experience in molecular biology protocols. Curr. Protoc. Mol. Biol. 102:21.26.1–21.26.15. © 2013 by John Wiley & Sons, Inc.
Assessment of Cell Viability
Authors: Johnson Simon , Nguyen Vy , Coder David
Published: April 2013

Cell viability may be judged by morphological changes or by changes in membrane permeability and/or physiological state inferred from the exclusion of certain dyes or the uptake and retention of others. This unit presents methods based on dye exclusion, esterase activity, and mitochondrial membrane potential, as well as protocols for determining the pre‐fixation viability of fixed cells either before or after fixation with amine‐reactive dyes suitable for a range of excitation wavelengths. Membrane‐impermeable dead cell and live cell dyes as well as dye‐exclusion procedures for microscopy are also included. Curr. Protoc. Cytom. 64:9.2.1‐9.2.26. © 2013 by John Wiley & Sons, Inc.
Levels of Serum Anti–Müllerian Hormone, a Marker for Ovarian Reserve, in Women With Rheumatoid Arthritis
Authors: Brouwer Jenny , Laven Joop S. E. , Hazes Johanna M. W. , Schipper Izaäk , Dolhain Radboud J. E. M.
Published: April 2013

Objective

Fertility is reduced in women with rheumatoid arthritis (RA), even before diagnosis. This may be due to a diminished ovarian reserve. The current study examined serum levels of anti–Müllerian hormone (AMH), the most reliable endocrine marker for ovarian reserve, in early RA patients and the influence of disease activity and methotrexate (MTX) use on AMH concentrations.

Methods

Serum AMH levels were measured in 72 women with recent‐onset RA ages 18–42 years and compared to 509 healthy women. The association between AMH and rheumatoid factor (RF), anti–cyclic citrullinated peptide (anti‐CCP), erosions, C‐reactive protein (CRP) level, disease activity (Disease Activity Score in 28 joints [DAS28]), and use of MTX was assessed.

Results

At diagnosis, age‐adjusted serum AMH levels did not differ significantly between patients and controls (P = 0.254). AMH levels were not related to the presence of RF (P = 0.487), anti‐CCP (P = 0.686), or erosions (P = 0.350), and showed no significant correlation with CRP levels (r = −0.207, P = 0.083) or disease activity scores (DAS28; r = 0.007, P = 0.955). After 6 months of treatment, AMH levels in patients (n = 53) were lower than at the time of diagnosis (P < 0.001), but did not differ from controls (P = 0.741). There was no significant difference in AMH values after 6 months of treatment between patients who did (n = 31) or did not (n = 22) receive MTX (P = 0.287).

Conclusion

AMH levels in women with early RA are comparable to those of healthy controls, indicating that the reduced fertility in this patient group is not caused by diminished ovarian reserve. AMH levels are not affected either by disease activity or by short‐term MTX use.
Biomechanical Deviations During Level Walking Associated With Knee Osteoarthritis: A Systematic Review and Meta‐Analysis
Authors: Mills Kathryn , Hunt Michael A. , Ferber Reed
Published: April 2013

Objective

To identify which gait deviations are consistently associated with knee osteoarthritis (KOA) and how these are influenced by disease severity, the involved compartment, and sex.

Methods

Five electronic databases and reference lists of publications were searched. Cross‐sectional, observational studies comparing temporospatial variables, joint kinematics, and joint moments between individuals with KOA and healthy controls or between KOA subgroups were considered for review. Only publications scoring ≥50% on a modified methodology quality index were included. Because of the number of gait deviations examined, only biomechanical variables reported by ≥4 publications were further analyzed. Where possible, a meta‐analysis was performed using effect sizes (ES) calculated from discrete variables.

Results

In total, 41 publications examining 20 variables were included. The majority of consistent gait deviations associated with KOA were exhibited by those with severe disease in the temporospatial domain. Individuals with severe KOA exhibited greater stride duration than controls (ES 1.35 [95% confidence interval (95% CI) 1.03, 1.67]) and a decrease in cadence (ES −0.75 [95% CI −1.12, −0.39]) compared with controls. The evidence for kinematic and joint moment change was primarily limited or conflicting. There was a lack of evidence for alterations in the external knee adduction moment.

Conclusion

Individuals with KOA exhibit a range of gait deviations compared with controls. Despite its common usage in KOA gait studies, we did not find consistent evidence that knee adduction moment differs between those with and without KOA or between disease severity levels. Further research examining the reasons for a lack of difference in many gait variables in those with knee OA is needed.
Association of Frequent Knee Bending Activity With Focal Knee Lesions Detected With 3T Magnetic Resonance Imaging: Data From the Osteoarthritis Initiative
Authors: Virayavanich Warapat , Alizai Hamza , Baum Thomas , Nardo Lorenzo , Nevitt Michael C. , Lynch John A. , McCulloch Charles E. , Link Thomas M.
Published: April 2013

Objective

To evaluate the association of baseline frequent knee bending activities with the prevalence and progression of cartilage and meniscal abnormalities over 3 years and to assess the effect of frequent knee bending on the different knee compartments with 3T magnetic resonance imaging (MRI).

Methods

We studied 115 subjects without radiographic knee osteoarthritis (OA) but with risk factors for OA from the Osteoarthritis Initiative database. The inclusion criteria at baseline were age 45–55 years, body mass index of 19–27 kg/m2, Western Ontario and McMaster Universities Osteoarthritis Index pain score of 0, and Kellgren/Lawrence grade <2. Knee bending activities (kneeling, squatting, stair climbing, and weight lifting) were assessed by questionnaire at the baseline clinic visit. Cartilage and meniscal abnormalities were graded using the Whole‐Organ MRI Score. Logistic regression was used to determine the association of frequent knee bending with cartilage and meniscal abnormalities.

Results

Frequent knee bending activities were associated with an increased risk of prevalent cartilage lesions (odds ratio [OR] 3.63, 95% confidence interval [95% CI] 1.39–9.52), in particular in the patellofemoral compartment (OR 3.09, 95% CI 1.22–7.79). The increase in risk was higher in subjects involved in ≥2 knee bending activities. At 3‐year followup, individuals reporting frequent knee bending were more likely to show progression of cartilage damage (OR 4.12, 95% CI 1.27–13.36) and meniscal abnormalities (OR 4.34, 95% CI 1.16–16.32).

Conclusion

Frequent knee bending activities were associated with a higher prevalence of knee cartilage lesions (particularly in the patellofemoral compartment) and with an increased risk of progression of cartilage and meniscal lesions in asymptomatic middle‐aged subjects.
Creatine Supplementation in Fibromyalgia: A Randomized, Double‐Blind, Placebo‐Controlled Trial
Authors: Alves Christiano R. R. , Santiago Bianca M. , Lima Fernanda R. , Otaduy Maria C. G. , Calich Ana Luisa , Tritto Aline C. C. , de Sá Pinto Ana Lúcia , Roschel Hamilton , Leite Cláudia C. , Benatti Fabiana B. , Bonfá Eloisa , Gualano Bruno
Published: April 2013

Objective

To investigate the efficacy and safety of creatine supplementation in fibromyalgia patients.

Methods

A 16‐week, randomized, double‐blind, placebo‐controlled, parallel‐group trial was conducted. Fibromyalgia patients were randomly assigned to receive either creatine monohydrate or placebo in a double‐blind manner. The patients were evaluated at baseline and after 16 weeks. Muscle function, aerobic conditioning, cognitive function, quality of sleep, quality of life, kidney function, and adverse events were assessed. Muscle phosphorylcreatine content was measured through 31P magnetic resonance spectroscopy.

Results

After the intervention, the creatine group presented higher muscle phosphorylcreatine content when compared with the placebo group (+80.3% versus −2.7%; P = 0.04). Furthermore, the creatine group presented greater muscle strength than the placebo group in the leg press and chest press exercises (+9.8% and +1.2% for creatine versus −0.5% and −7.2% for placebo, respectively; P = 0.02 and P = 0.002, respectively). Isometric strength was greater in the creatine group than in the placebo group (+6.4% versus −3.2%; P = 0.007). However, no general changes were observed in aerobic conditioning, pain, cognitive function, quality of sleep, and quality of life. Food intake remained unaltered and no side effects were reported.

Conclusion

Creatine supplementation increased intramuscular phosphorylcreatine content and improved lower‐ and upper‐body muscle function, with minor changes in other fibromyalgia features. These findings introduce creatine supplementation as a useful dietary intervention to improve muscle function in fibromyalgia patients.
Brief Report: Rheumatoid Arthritis Is Associated With Left Ventricular Concentric Remodeling: Results of a Population‐Based Cross‐Sectional Study
Authors: Myasoedova Elena , Davis John M. , Crowson Cynthia S. , Roger Véronique L. , Karon Barry L. , Borgeson Daniel D. , Therneau Terry M. , Matteson Eric L. , Rodeheffer Richard J. , Gabriel Sherine E.
Published: April 2013

Objective

To study left ventricular (LV) geometry in patients with rheumatoid arthritis (RA) and no history of heart failure compared with that in subjects with neither RA nor a history of heart failure, and to determine the impact of RA on LV remodeling.

Methods

A cross‐sectional, community‐based study was conducted among adult (age ≥50 years) patients with RA and age‐ and sex‐matched subjects with neither RA nor a history of heart failure. All participants underwent standard 2‐dimensional Doppler echocardiography. LV geometry was classified into the following 4 categories based on relative wall thickness and sex‐specific cutoffs for the LV mass index: concentric remodeling, concentric hypertrophy, eccentric hypertrophy, or normal geometry.

Results

Among 200 patients with RA and 600 age‐ and sex‐matched subjects without RA, the mean age was 65 years, and 74% of the individuals in both cohorts were female. Compared with subjects without RA, patients with RA were significantly more likely to have abnormal LV geometry (odds ratio [OR] 1.44, 95% confidence interval [95% CI] 1.03–2.00), even after adjusting for cardiovascular risk factors and comorbidities. Among subjects with abnormal LV geometry, the odds of concentric LV remodeling were significantly increased in patients with RA (OR 4.73, 95% CI 2.85–7.83). In linear regression analyses, the LV mass index appeared to be lower in patients with RA who were currently receiving corticosteroids (β ± SE −0.082 ± 0.027, P = 0.002), even after adjusting for cardiovascular risk factors and comorbidities.

Conclusion

RA was strongly associated with abnormal LV remodeling (particularly concentric LV remodeling) among RA patients without heart failure. This association remained significant after adjustment for cardiovascular risk factors and comorbidities. RA disease–related factors may promote changes in LV geometry. The biologic mechanisms underlying LV remodeling warrant further investigation.
Vitamin D in Systemic Lupus Erythematosus: Modest Association With Disease Activity and the Urine Protein‐to‐Creatinine Ratio
Authors: Petri Michelle , Bello Kayode J. , Fang Hong , Magder Laurence S.
Published: April 2013

Objective

To investigate whether an increase in vitamin D levels in patients with systemic lupus erythematosus (SLE) was associated with improvement in disease activity.

Methods

A total of 1,006 SLE patients were monitored over 128 weeks. SLE patients with low levels of 25‐hydroxyvitamin D (25[OH]D; <40 ng/ml) were given supplements of 50,000 units of vitamin D2 weekly plus 200 units of calcium/vitamin D3 twice daily. Longitudinal regression models were used to estimate the association between levels of 25(OH)D and various measures of disease activity.

Results

The SLE patients had the following characteristics: 91% were female, their mean age was 49.6 years, and their ethnicity was 54% Caucasian, 37% African American, and 8% other. For those with levels of 25(OH)D <40 ng/ml, a 20‐unit increase in the 25(OH)D level was associated with a mean decrease of 0.22 (95% confidence interval [95% CI] −0.41, −0.02) (P = 0.032) in the Safety of Estrogens in Lupus Erythematosus National Assessment (SELENA) version of the Systemic Lupus Erythematosus Disease Activity Index (SLEDAI). This corresponded to a 21% decrease in the odds of having a SELENA–SLEDAI ≥5 (95% CI 1, 37). The mean urine protein‐to‐creatinine ratio decreased by 2% (95% CI −0.03, −0.01) (P = 0.0001), corresponding to a 15% decrease in the odds of having a ratio >0.5 (95% CI 2, 27).

Conclusion

We found that a 20‐ng/ml increase in the 25(OH)D level was associated with a 21% decrease in the odds of having a high disease activity score and a 15% decrease in the odds of having clinically important proteinuria. Although these associations were statistically significant, the clinical importance is relatively modest. There was no evidence of additional benefit of 25(OH)D beyond a level of 40 ng/ml.