bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic variation and structure of house sparrow populations: is there an island effect?
Authors: Jensen Henrik , Moe Rune , Hagen Ingerid Julie , Holand Anna Marie , Kekkonen Jaana , Tufto Jarle , Sæther Bernt‐Erik
Published: February 2013

Population genetic structure and intrapopulation levels of genetic variation have important implications for population dynamics and evolutionary processes. Habitat fragmentation is one of the major threats to biodiversity. It leads to smaller population sizes and reduced gene flow between populations and will thus also affect genetic structure. We use a natural system of island and mainland populations of house sparrows along the coast ofNorway to characterize the different population genetic properties of fragmented populations. We genotyped 636 individuals distributed across 14 populations at 15 microsatellite loci. The level of genetic differentiation was estimated usingF‐statistics and specially designedMantel tests were conducted to study the influence of population type (i.e. mainland or island) and geographic distance on the genetic population structure. Furthermore, the effects of population type, population size and latitude on the level of genetic variation within populations were examined. Our results suggest that genetic processes on islands and mainland differed in two important ways. First, the intrapopulation level of genetic variation tended to be lower and the occurrence of population bottlenecks more frequent on islands than the mainland. Second, although the general level of genetic differentiation was low to moderate, it was higher between island populations than between mainland populations. However, differentiation increased in mainland populations somewhat faster with geographical distance. These results suggest that population bottleneck events and genetic drift have been more important in shaping the genetic composition of island populations compared with populations on the mainland. Such knowledge is relevant for a better understanding of evolutionary processes and conservation of threatened populations.
Patterns and trends in the diet of long‐finned pilot whales (Globicephala melas) in the northeast Atlantic
Authors: Santos M. Begoña , Monteiro Silvia S. , Vingada José V. , Ferreira Marisa , López Alfredo , Martínez Cedeira José A. , Reid Robert J. , Brownlow Andrew , Pierce Graham J.
Published: February 2013

There is little previous information on feeding habits of long‐finned pilot whales (Globicephala melas) in the northeast Atlantic. The present study analyzed stomach contents of pilot whales stranded in Portugal (n = 6), Galicia (northwest Spain) (n = 32), and Scotland (United Kingdom) (n = 10), from 1990 to 2011. These animals ranged from 213 to 555 cm in length (24 females, 19 males and 5 of unknown sex). The main prey identified were cephalopods of the families Octopodidae and Ommastrephidae, the former being numerically more important in Iberia (Portugal and Galicia) and the latter more important in Scotland, with Iberian whales also showing a more diverse diet. Multivariate analysis revealed evidence of geographical and seasonal variation in diet. Generalized Additive Modeling results indicated that more octopus (Eledone cirrhosa) were eaten in Iberia than in Scotland, more in the first half of the year, and more in larger whales. Numbers of ommastrephid squids in the stomach decreased over the study period and varied with season and whale length. This study confirms cephalopods as the main prey of pilot whales, as previously reported, although our results also suggest that, in the northeast Atlantic, ommastrephid squid are largely replaced as the main prey by octopods at lower latitudes.
Factors Associated with Improvement in Utilization of Cardiac Resynchronization Therapy in Eligible Heart Failure Patients: Findings from IMPROVE HF
Authors: SHUKLA ASHISH , CURTIS ANNE B. , MEHRA MANDEEP R. , ALBERT NANCY M. , GHEORGHIADE MIHAI , HEYWOOD J. THOMAS , LIU YANG , O'CONNOR CHRISTOPHER M. , REYNOLDS DWIGHT , WALSH MARY NORINE , YANCY CLYDE W. , FONAROW GREGG C.
Published: February 2013

Background

There is a well‐recognized gap between the number of patients in whom cardiac resynchronization therapy (CRT) is indicated based on current guidelines and its actual utilization. In the Registry to Improve the Use of Evidence‐Based Heart Failure Therapies in the Outpatient Setting (IMPROVE HF) study, there was a significant increase in the use of CRT at 24 months in patients with heart failure (HF) in comparison to baseline. This study evaluated patient, physician, and practice factors associated with this increase in CRT utilization.

Methods

Patients with reduced left ventricular ejection fraction and chronic HF who met the eligibility criteria for CRT at baseline and 24 months were analyzed. Multivariate analyses using patient, physician, and practice characteristics were performed to evaluate factors associated with increased CRT utilization at 24 months.

Results

There were 440 patients eligible for CRT both at baseline and 24 months, with 217 (49.3%) treated at baseline and 374 (85%) treated at 24 months, leading to an absolute increase in use of CRT of 35.7%, P < 0.001. Although serum sodium and the absence of rales had modest associations, none of the patient, physician, or practice characteristics had any significant association with the extent of increase in CRT utilization. There was a significant reduction in the variation of CRT utilization across practice sites after the implementation of the performance improvement initiative.

Conclusions

The performance improvement initiative in IMPROVE HF was the most important factor associated with an increase in guideline‐recommended CRT utilization. This improvement in CRT utilization and reduced practice variability was found across a variety of cardiology and multispecialty practice sites.
Myotonic Dystrophies type 1 and 2: anesthetic care
Authors: Veyckemans Francis , Scholtes Jean‐Louis
Published: February 2013

Myotonic dystrophy is classified as one of the myotonic syndromes although myotonia is only a minor characteristic of it. It is, in fact, also a multisystem disease with cardiac, digestive, ocular, and endocrine abnormalities. Two subgroups are currently identified with many similarities: DM1 refers to classic dystrophia myotonica (Steinert disease), while DM2, formerly called proximal myotonic myopathy has a later onset. The congenital form is present only in DM1. The genetic causes of DM1 and 2 are different but end up in a similar way of altering RNAm processing and splicing of other genes. The anesthetic risk is increased in case of DM1 type. This review summarizes current knowledge concerning the pathophysiology and anesthetic management of this disease in children and adults.
A new phenotyping technique for screening for drought tolerance in lentil (Lens culinaris Medik.)
Authors: Singh Dharmendra , Dikshit Harsh K. , Singh Rajendra
Published: February 2013

Screening for drought tolerance is severely handicapped by the lack of a simple and reliable phenotyping technique. The objective of this study was to develop a new screening technique based on seedling survivability, drought tolerance score, root and shoot length, and fresh and dry weight of roots and shoots of lentil plants exposed to drought under hydroponic conditions. Its effectiveness was compared with two soil culture techniques. The hydroponic technique involved removing 15‐day‐old seedlings of 80 genotypes from the nutrient solution and exposing them to air for 5 h daily for 6 days. Three genotypes received from ICARDA, ‘ILL‐10700’, ‘ILL‐10823’ and ‘FLIP‐96‐51’, showed maximum seedling survivability and minimum reduction in the growth parameters with a drought score of 0.0–0.2 indicating higher tolerance to drought stress, while Indian genotypes ‘JL‐3’, ‘E‐153’ and ‘VL‐507’ showed no seedling survivability and maximum reduction in growth parameters with a drought score of 4.0 indicating low drought tolerance. The results suggest that this new phenotyping technique is effective, rapid and easy for screening a large number of genotypes.
Effect of early measles vaccination (AIK‐C strain) for preterm infants
Authors: Ichikawa Tomonori , Tsuji Atsutoshi , Fujino Motoko , Kusano Ryousuke , Sugiyama Ryusuke , Oomori Sayu , Mori Kazuhiro , Maeyama Katsuhiro , Nakayama Tetsuo
Published: February 2013

Background

The level of maternal antibodies decreases more quickly in preterm than term infants, leaving them unprotected against measles. To protect premature infants from measles, an early vaccination trial was investigated.

Methods

Changes in the serum measles neutralization test (NT) antibody titer were examined in 152 infants (average gestational period, 29 weeks; average birthweight, 1203 g).

Results

The average antibody titer (2n) was 23.5 at birth and 22.2 at 1–3 months of age, and in all cases, NT antibody titer decreased to <1:4 (150 IU/mL). The AIK‐C measles vaccine was given to 17 preterm infants at the age of 6 months, and induced sufficient serological responses without any serious adverse events. NT antibody level did not decay during 12 months after vaccination.

Conclusion

Early immunization at 6 months of age is effective to protect preterm infants in the outbreak setting.
The spatiotemporal spread of esca disease in a Cabernet Sauvignon vineyard: a statistical analysis of field data
Authors: Zanzotto A. , Gardiman M. , Serra S. , Bellotto D. , Bruno F. , Greco F. , Trivisano C.
Published: February 2013

The occurrence and spread of plants showing esca symptoms were assessed in a vineyard located on the plains of a northern Italian wine‐growing region. Esca disease symptoms were assessed over 16 consecutive years, beginning one year after planting. The number of plants with symptoms was recorded over time, considering both vines with foliar symptoms in the year of assessment (manifest esca) and vines with foliar symptoms in previous years (hidden esca). The sum of manifest and hidden esca was indicated as cumulative esca. The first symptoms of esca appeared in the sixth year of cultivation, with the incidence of manifest esca increasing to approximately 3% nine years after planting. The number of cumulative plants with symptoms increased exponentially in the final period of observation. The aim of this work was to investigate the spatiotemporal spread of esca infection throughout the vineyard and to assess the distribution pattern of plants with symptoms using Bayesian spatiotemporal models. The research results seem to support a higher probability of infection along rows rather than among adjacent rows. This observation may have implications for the technical management of the vineyard.
Tolerance of submerged germinating rice to 50–200 mM NaCl in aerated solution
Authors: Kurniasih Budiastuti , Greenway Hank , Colmer Timothy David
Published: February 2013

This paper concerns tolerance to 50–200 mM NaCl of submerged rice (Oryza sativa cv. Amaroo) during germination and the first 138–186 h of development in aerated solution. Rice was able to germinate and the seedlings even tolerated exposure to 200 mM NaCl, albeit with severe growth restrictions. After return to 0.3 mM NaCl, growth increased, indicating that even at 200 mM NaCl there was no irreparable injury. Osmotic adjustment was achieved by using Na+ and Cl– as the major osmotica. At 200 mM NaCl commenced at sowing, the shoot Na+ and Cl– concentrations between 50–110 h were about 210 and 260 mM, respectively, i.e. above the external concentration. Thus, there was a high tissue tolerance to NaCl. The internal concentrations declined subsequently, concurrent with a decline in growth. At 50–200 mM NaCl, the contributions from ions to πsap were 81–92% in roots and 62–74% in shoots. The assessed turgor pressures at 200 mM NaCl were 0.33 MPa in shoots and 0.15 MPa in roots, compared to 0.62 and 0.43 MPa at 0.3 mM NaCl. In the General Discussion section, we compare the different responses of submerged seedlings to the responses of transpiring rice plants, reported in the literature, and suggest that the submerged system is useful to evaluate effects of NaCl on turgor pressure and particularly to establish whether there are specific effects of Na+ and Cl– in tissues.
In vitro Release of Ovarian Progesterone is Decreased During the Oestrous Cycle and Pregnancy of Swine with Obesity/Leptin Resistance
Authors: Astiz S , Gonzalez‐Bulnes A , Perez‐Solana ML , Sanchez‐Sanchez R , Torres‐Rovira L
Published: February 2013

Contents

Previous studies indicate that reproductive prolificacy of obese swine breeds is markedly influenced by embryo losses in early pregnancy. In such period, adequate secretion of progesterone (P4) by the ovary is essential for pregnancy success. This study analyses the luteal functionality during the oestrous cycle and early pregnancy of Iberian sows and Large White x Landrace females, in terms of P4 secretion after in vitro culture of luteal tissue stimulated or not with luteinizing hormone (LH). The secretion of progesterone (expressed in ng/mg of luteal tissue or ng/mgLT) of the corpora lutea of obese Iberian swine was always hampered when compared to lean genotypes, either during early oestrous cycle (110.7 ± 37.8 vs 259.7 ± 10.2 ng/mgLT; p < 0.0001), late oestrous cycle (49.0 ± 3.5 vs 75.92 ± 7.14 ng/mgLT; p < 0.0001) or early pregnancy (38.4 ± 2.1 vs 70.7 ± 5.3 ng/mgLT; p < 0.0001). The differences in basal P4 secretion remained after stimulation with LH. Finally, P4 secretion during early pregnancy of Iberian sows decreased with age and, hence, with obesity features (46.6 ± 4.2 vs 65.5 ± 4.8 ng/mgLT; p < 0.001). In conclusion, the results of the present study provide convincing evidence of a reduced luteal function during oestrous cycle and early pregnancy of sows with obesity/leptin resistance like Iberian sows, which may contribute to the low reproductive efficiency reported in this breed.
The Nation of Islam and the Muslim World: Theologically Divorced and Politically United
Authors: Fishman Jason Eric , Soage Ana Belén
Published: February 2013

The Nation of Islam (NOI) is an African American religious movement that originated in Detroit, Michigan, during the 1930s based on a rather heterodox form of the Muslim religion. Founded by the enigmatic Wallace D. Fard and taken over by the Honorable Elijah Muhammad upon Fard’s disappearance in 1934, the NOI came to exert important economic, political, and cultural influence in the African American community with its program of economic independence and charismatic high profile members such as Malcolm X and Muhammad Ali. Advocating the complete separation of Black people from the White race of “blue‐eyed devils”, the NOI was a lightning rod for controversy. With Elijah Muhammad’s death in 1975, leadership of the organization passed into the hands of Warith Deen Mohammed, who dropped the name “Nation of Islam” and radically reorganized the group along quasi‐Sunni Islamic lines. However, in 1977, long time NOI member Minister Louis Farrakhan reestablished the Nation of Islam according to Elijah Muhammad’s doctrine, and subsequently propelled it back into America’s national consciousness with his controversial involvement in Jesse Jackson’s 1984 presidential campaign and the 1995 Million Man March in Washington D.C. Although the NOI has done much to popularize Islam in the U.S., the Nation’s religious beliefs bear little resemblance to traditional Islamic theology. While the Nation shares a common vocabulary with Muslims around the world, the NOI’s teachings concerning God, cosmology, Prophet Muhammad and the afterlife can be deemed heterodox, or even heretical, by Islamic standards. But despite its vast ideological differences from the international Muslim community, the NOI has come to be seen like a partner, even an ally, by many in the Arab and Muslim worlds. This paper explores the NOI’s trajectory and ideology, together with the reasons behind that apparent paradox, and shows it to be built on common interest rather than a common faith.
The Arabidopsis cer26 mutant, like the cer2 mutant, is specifically affected in the very long chain fatty acid elongation process
Authors: Pascal Stéphanie , Bernard Amélie , Sorel Maud , Pervent Marjorie , Vile Denis , Haslam Richard P. , Napier Johnathan A. , Lessire René , Domergue Frédéric , Joubès Jérôme
Published: February 2013

Plant aerial organs are covered by cuticular waxes, which form a hydrophobic crystal layer that mainly serves as a waterproof barrier. Cuticular wax is a complex mixture of very long chain lipids deriving from fatty acids, predominantly of chain lengths from 26 to 34 carbons, which result from acyl‐CoA elongase activity. The biochemical mechanism of elongation is well characterized; however, little is known about the specific proteins involved in the elongation of compounds with more than 26 carbons available as precursors of wax synthesis. In this context, we characterized the three Arabidopsis genes of the CER2‐like family: CER2, CER26 and CER26‐like . Expression pattern analysis showed that the three genes are differentially expressed in an organ‐ and tissue‐specific manner. Using individual T–DNA insertion mutants, together with a cer2 cer26 double mutant, we characterized the specific impact of the inactivation of the different genes on cuticular waxes. In particular, whereas the cer2 mutation impaired the production of wax components longer than 28 carbons, the cer26 mutant was found to be affected in the production of wax components longer than 30 carbons. The analysis of the acyl‐CoA pool in the respective transgenic lines confirmed that inactivation of both genes specifically affects the fatty acid elongation process beyond 26 carbons. Furthermore, ectopic expression of CER26 in transgenic plants demonstrates that CER26 facilitates the elongation of the very long chain fatty acids of 30 carbons or more, with high tissular and substrate specificity.
Ion flux and ion distribution function measurements in synchronously pulsed inductively coupled plasmas
Authors: Brihoum Melisa , Cunge Gilles , Darnon Maxime , Gahan David , Joubert Olivier , Braithwaite Nicholas St. J.
Published: February 2013

Changes in the ion flux and the time-averaged ion distribution functions are reported for pulsed, inductively coupled RF plasmas (ICPs) operated over a range of duty cycles. For helium and argon plasmas, the ion flux increases rapidly after the start of the RF pulse and after about 50 μs reaches the same steady state value as that in continuous ICPs. Therefore, when the plasma is pulsed at 1 kHz, the ion flux during the pulse has a value that is almost independent of the duty cycle. By contrast, in molecular electronegative chlorine/chlorosilane plasmas, the ion flux during the pulse reaches a steady state value that depends strongly on the duty cycle. This is because both the plasma chemistry and the electronegativity depend on the duty cycle. As a result, the ion flux is 15 times smaller in a pulsed 10% duty cycle plasma than in the continuous wave (CW) plasma. The consequence is that for a given synchronous RF biasing of a wafer-chuck, the ion energy is much higher in the pulsed plasma than it is in the CW plasma of chlorine/chlorosilane. Under these conditions, the wafer is bombarded by a low flux of very energetic ions, very much as it would in a low density, capacitively coupled plasma. Therefore, one can extend the operating range of ICPs through synchronous pulsing of the inductive excitation and capacitive chuck-bias, offering new means by which to control plasma etching.
Effect of basilar membrane radial velocity profile on fluid coupling in the cochlea
Authors: Ni Guangjian , Elliott Stephen J.
Published: February 2013

The effects of different radial distributions of basilar membrane velocity on the fluid coupling in the cochlea are studied. Different mode shapes across the width of the basilar membrane, modeled as a beam, are simulated by assuming various boundary conditions. The results suggest that the fluid coupling is insensitive to the resulting differences in mode shape. This validates the assumption commonly made in cochlear models that the fluid coupling can be reasonably well predicted by assuming a single modal shape across the basilar membrane width, even if the exact form of the radial profile is not known.
Multivariate acoustic detection of small explosions using Fisher's combined probability test
Authors: Arrowsmith Stephen J. , Taylor Steven R.
Published: February 2013

A methodology for the combined acoustic detection and discrimination of explosions, which uses three discriminants, is developed for the purpose of identifying weak explosion signals embedded in complex background noise. By utilizing physical models for simple explosions that are formulated as statistical hypothesis tests, the detection/discrimination approach does not require a model for the background noise, which can be highly complex and variable in practice. Fisher's Combined Probability Test is used to combine the p-values from all multivariate discriminants. This framework is applied to acoustic data from a 400 g explosion conducted at Los Alamos National Laboratory.
Mitochondrial Reactive Oxygen Species Promote Epidermal Differentiation and Hair Follicle Development
Authors: Hamanaka Robert B. , Glasauer Andrea , Hoover Paul , Yang Shuangni , Blatt Hanz , Mullen Andrew R. , Getsios Spiro , Gottardi Cara J. , DeBerardinis Ralph J. , Lavker Robert M. , Chandel Navdeep S.
Published: February 2013

Skin development requires reactive oxygen species generated by mitochondria in keratinocytes.
Sterical Hindrance Promotes Selectivity of the Autophagy Cargo Receptor NDP52 for the Danger Receptor Galectin-8 in Antibacterial Autophagy
Authors: Li Sai , Wandel Michal P. , Li Fudong , Liu Zhonghua , He Chao , Wu Jihui , Shi Yunyu , Randow Felix
Published: February 2013

A crystal structure of an autophagy receptor with a ligand reveals how
Salmonella
is specifically targeted for degradation.
Separating Fat Functions
Authors: VanHook Annalisa M.
Published: February 2013

The Hippo and PCP signaling activities of the atypical cadherin Fat rely on different regions of the Fat intracellular domain.
Aminoglycoside Cross-Resistance in Mycobacterium tuberculosis Due to Mutations in the 5′ Untranslated Region of
whiB7
Authors: Reeves Analise Z. , Campbell Patricia J. , Sultana Razvan , Malik Seidu , Murray Megan , Plikaytis Bonnie B. , Shinnick Thomas M. , Posey James E.
Published: February 2013

Since the discovery of streptomycin's bactericidal activity against
Mycobacterium tuberculosis
, aminoglycosides have been utilized to treat tuberculosis (TB). Today, the aminoglycosides kanamycin and amikacin are used to treat multidrug-resistant (MDR) TB, and resistance to any of the second-line injectable antibiotics, including kanamycin, amikacin, or capreomycin, is a defining characteristic of extensively drug-resistant (XDR) TB. Resistance to kanamycin and streptomycin is thought to be due to the acquisition of unlinked chromosomal mutations. However, we identified eight independent mutations in the 5′ untranslated region of the transcriptional activator
whiB7
that confer low-level resistance to both aminoglycosides. The mutations lead to 23- to 145-fold increases in
whiB7
transcripts and subsequent increased expression of both
eis
(
Rv2416c
) and
tap
(
Rv1258c
). Increased expression of
eis
confers kanamycin resistance in these mutants, while increased expression of
tap
, which encodes an efflux pump, is a previously uncharacterized mechanism of low-level streptomycin resistance. Additionally, high-level resistance to streptomycin arose at a much higher frequency in
whiB7
mutants than in a wild-type (WT) strain. Although
whiB7
is typically associated with intrinsic antibiotic resistance in
M. tuberculosis
, these data suggest that mutations in an uncharacterized regulatory region of
whiB7
contribute to cross-resistance against clinically used second-line antibiotics. As drug resistance continues to develop and spread, understanding the mechanisms and molecular basis of antibiotic resistance is critical for the development of rapid molecular tests to diagnose drug-resistant TB strains and ultimately for designing regimens to treat drug-resistant cases of TB.
Experimental Evidence That Granulocyte Transfusions Are Efficacious in Treatment of Neutropenic Hosts with Pulmonary Aspergillosis
Authors: Martinez Marife , Chen Vicky , Tong Ann-Jay , Hamilton Kelsey , Clemons Karl V. , Stevens David A.
Published: February 2013

Although polymorphonuclear leukocytes (PMNs) are powerfully anti-
Aspergillus
, transfusion therapy remains controversial, with conflicting results, and experimental support has been lacking. We devised a pulmonary infection model in neutropenic BALB/c mice, used an antibacterial regimen to prevent confounding sepsis, and optimized PMN induction, purifications, and dose. Mice were given 150 mg/kg cyclophosphamide every 4 days and a gentamicin-vancomycin-clindamycin-imipenem regimen daily beginning 4 days before intranasal challenge with 5 × 10
5
Aspergillus
conidia. This regimen produced leukopenia (∼10% of normal white blood cell [WBC] count; ≤10% PMNs) for 10 days, without bacterial superinfection. PMN donors given 100 μg/kg recombinant murine granulocyte colony-stimulating factor (G-CSF) for 10 days yielded 11 × 10
7
to 13.6 × 10
7
WBC/ml (81 to 87% PMNs). Infected mice were given PMN transfusions intravenously. In 2 experiments with up to 70% mortality of neutropenic controls, transfusion of 10
7
PMNs 1 and 4 days after challenge had negligible effects on peripheral WBC counts but improved survival (
P
= 0.007, 0.02), decreased lung CFU (
P
= 0.03, 0.005), and cleared infection in 28 to 50% of survivors. Transfusion of 5 × 10
6
PMNs showed partial protection. Transfusions given every other day did not improve protection. Our present results provide an experimental basis for enthusiasm for PMN transfusions in the therapy of aspergillosis in humans.
The Contraceptive Depot Medroxyprogesterone Acetate Impairs Mycobacterial Control and Inhibits Cytokine Secretion in Mice Infected with Mycobacterium tuberculosis
Authors: Kleynhans Léanie , Du Plessis Nelita , Allie Nasiema , Jacobs Muazzam , Kidd Martin , van Helden Paul D. , Walzl Gerhard , Ronacher Katharina
Published: February 2013

The contraceptive depot medroxyprogesterone acetate (DMPA), with progestin as the single active compound, possesses selective glucocorticoid activity and can alter the expression of glucocorticoid receptor-regulated genes. We therefore propose that pharmacological doses of DMPA used for endocrine therapy could have significant immune modulatory effects and impact on susceptibility to, as well as clinical manifestation and outcome of, infectious diseases. We investigated the effect of contraceptive doses of DMPA in two different murine
Mycobacterium tuberculosis
models. Multiplex bead array analysis revealed that DMPA altered serum cytokine levels of tumor necrosis factor alpha (TNF-α), granulocyte colony-stimulating factor (G-CSF), and interleukin 10 (IL-10) in C57BL/6 mice and gamma interferon (IFN-γ) in BALB/c mice. DMPA also suppressed antigen-specific production of TNF-α, G-CSF, IL-10, and IL-6 and induced the production of IP-10 in C57BL/6 mice. In BALB/c mice, DMPA altered the antigen-specific secretion of IFN-γ, IL-17, granulocyte-macrophage colony-stimulating factor (GM-CSF), IL-6, and monocyte chemotactic protein 1 (MCP-1). Furthermore, we show that C57BL/6 mice treated with doses of DMPA, which result in serum concentrations similar to those observed in contraceptive users, have a significantly higher bacterial load in their lungs. Our data show for the first time that DMPA impacts tuberculosis (TB) disease severity in a mouse model and that the effects of this contraceptive are not confined to infections of the genital tract. This could have major implications for the contraceptive policies not only in developing countries like South Africa but also worldwide.
An Improved Recombination-Based
In Vivo
Expression Technology-Like Reporter System Reveals Differential
cyaA
Gene Activation in Bordetella Species
Authors: Byrd Matthew S. , Mason Eliza , Henderson Michael W. , Scheller Erich V. , Cotter Peggy A.
Published: February 2013

Bordetella pertussis
and
Bordetella bronchiseptica
rely on the global two-component regulatory system BvgAS to control expression of distinct phenotypic phases. In the Bvg
−
phase, expression of
vrg
genes, including those required for motility in
B. bronchiseptica
, is activated and genes encoding virulence factors are not expressed. Conversely, in the Bvg
+
phase, genes encoding virulence factors are highly expressed while genes necessary for motility are repressed. Although several genetic analyses have demonstrated the importance of the Bvg
+
phase during respiratory infection, Bvg-regulated gene activation in
B. bronchiseptica
has not been investigated
in vivo
. To address this, we developed a plasmid, pGFLIP, that encodes a sensitive Flp recombinase-based fluorescent reporter system able to document gene activation both
in vitro
and
in vivo
. Using pGFLIP, we demonstrated that
cyaA
, considered to be a “late” Bvg
+
phase gene, is activated substantially earlier in
B. bronchiseptica
than
B. pertussis
following a switch from Bvg
−
to Bvg
+
phase conditions. We show that the altered activation of
cyaA
is not due to differences in the
cyaA
promoter or in the
bvgAS
alleles of
B. bronchiseptica
compared to
B. pertussis
, but appears to be species specific. Finally, we used pGFLIP to show that
flaA
remains repressed during infection, confirming that
B. bronchiseptica
does not modulate to the Bvg
−
phase
in vivo
.
Pseudomyxoma extraperitonei: a rare presentation of a rare tumour
Authors: Diaz-Zorrilla Carmina , Ramos-De la Medina Antonio , Grube-Pagola Peter , Ramirez-Gutierrez de Velasco Alfredo
Published: February 2013

Pseudomyxoma extraperitonei is rare lesion resulting from the rupture of an appendiceal mucocele into the extraperitoneal tissues. We report a case of an 80-year-old woman with a medical history for a left hemicolectomy and a laparoscopic cholecystectomy 11 and 6 years, respectively, referred to our hospital for abdominal pain of increasing severity localised to the right hemiabdomen. The abdominal examination revealed a mobile mass a multidetector CT was performed; the patient was taken to surgery which was performed with no complications. Histopathological analysis of the tumour reported a pseudomyxoma associated to a moderately differentiated adenocarcinoma. The patient remains asymptomatic at a 1-year follow-up.
An unusual breast lump: osseous metaplasia
Authors: Joshi Meera , Remoundos Dionysios D , Ahmed Farid , Rees Gabrielle , Cunnick Giles
Published: February 2013

We present a rare case of osseous metaplasia in the breast with no other associated breast pathology. A 46-year-old HIV-positive lady presented to the breast clinic with new onset intermittent left-sided mastalgia. Clinical examination revealed an indeterminate mass in the left breast with palpable left axillary lymphadenopathy. Mammography and ultrasonography were suggestive of a possible malignancy, with the latter also detecting the presence of abnormal nodes in the axilla. An ultrasound-guided core biopsy of the breast lesion showed only hyalinised normal breast tissue on two occasions. Owing to the diagnostic uncertainty, the patient underwent a wire-guided excision biopsy of the breast lesion, with the final histology demonstrating bone matrix deposition with viable osteocytes within lacunae and associated osteoclasts with spindle cells, consistent with osseous metaplasia. A core biopsy of the axillary lymph nodes was normal. The patient was therefore reassured and discharged from the clinic.
An unusual cause of postmenopausal bleeding
Authors: Gowri Vaidyanathan
Published: February 2013

A 68-year-old postmenopausal woman presented to the gynaecology clinic with a 1-week history of vaginal bleeding. She was investigated to rule out local and systemic causes including genital malignancy. The investigations were negative for genital malignancy and her symptoms settled spontaneously. The bleeding was attributed to a corticosteroid treatment for shoulder joint pain. A short literature review of this rare side effect is discussed.
Nuclear organization of RNA polymerase II transcription
Authors: Davidson Scott , Macpherson Neil , Mitchell Jennifer A.
Published: February 2013

Transcription occurs at distinct nuclear compartments termed transcription factories that are specialized for transcription by 1 of the 3 polymerase complexes (I, II, or III). Protein-coding genes appear to move in and out of RNA polymerase II (RNAPII) compartments as they are expressed and silenced. In addition, transcription factories are sites where several transcription units, either from the same chromosome or different chromosomes, are transcribed. Chromosomes occupy distinct territories in the interphase nucleus with active genes preferentially positioned on the periphery or even looped out of the territory. These chromosome territories have been observed to intermingle in the nucleus, and multiple interactions among different chromosomes have been identified in genome-wide studies. Deep sequencing of the transcriptome and RNAPII associated on DNA obtained by chromatin immunoprecipitation have revealed a plethora of noncoding transcription and intergenic accumulations of RNAPII that must also be considered in models of genome function. The organization of transcription into distinct regions of the nucleus has changed the way we view transcription with the evolving model for silencing or activation of gene expression involving physical relocation of the transcription unit to a silencing or activation compartment, thus, highlighting the need to consider the process of transcription in the 3-dimensional nuclear space.
Critical review of the evolution of the design storm event concept
Authors: Watt Ed , Marsalek Jiri
Published: February 2013

A critical review of the literature and practice indicates that design storm events, which have been used in specific fields of Canadian and US engineering practice for more than 100 years, can be ascribed to six basic attributes: (a) design return period, (b) storm duration, (c) intensity–duration–frequency (idf) relations (representing a summary of historical rainfall data, with some extrapolation for longer return periods), (d) temporal distribution (design hyetograph), (e) areal reduction factor, and (f) antecedent moisture conditions. Concerns about climate change (or variability) and the need to adapt to the associated climatic conditions prompted many agencies, and particularly municipalities, to revisit the design storm event issue, particularly in connection with drainage design. It would appear that this analysis has mostly focused on a single property of design storms — idf relations and projected increases in rainfall intensities. The review concludes that the design practice would be well served by adopting a comprehensive approach considering all design storm event characteristics and their sensitivity to climate change and inherent uncertainties in the existing idf relations as well as hydraulic design of sewer networks.
Patterns and influences on Dolly Varden migratory timing in the Chignik Lakes, Alaska, and comparison of populations throughout the northeastern Pacific and Arctic oceans
Authors: Bond Morgan H. , Quinn Thomas P.
Published: February 2013

Dolly Varden (Salvelinus malma) are a facultatively anadromous salmonid common around much of the North Pacific Rim, but little is known about the environmental factors affecting the timing and diversity of their migration. We combined telemetry of anadromous fish with long-term monitoring of Dolly Varden upstream migration timing and environmental data in the Chignik Lakes watershed in Alaska and then compared the timing data with that of other streams where only count data were available. Telemetry revealed two upstream migration modes: midsummer and late fall at the Chignik Lakes. Weir counts indicated that timing fluctuated markedly over the monitoring period (1996–2011) and was negatively correlated with June sea surface temperature. The relationship between sea surface temperature and migration timing in other watersheds with long-term records was as follows: negative (Buskin River), positive (Auke Creek), or nonexistent (Goodnews and Kanektok rivers). Among 18 streams and rivers throughout the eastern Pacific range of Dolly Varden, median upstream migration date increased with latitude. Overall, Dolly Varden migration timing is more variable, protracted, and more strongly influenced by local sea surface temperatures than is typical of semelparous salmonids. These results are likely indicative of other iteroparous salmonids in Pacific waters that share similar environments and life-history characteristics.
Optimizing stand management involving the effect of genetic gain: preliminary results for Scots pine in Finland
Authors: Ahtikoski Anssi , Salminen Hannu , Ojansuu Risto , Hynynen Jari , Kärkkäinen Katri , Haapanen Matti
Published: February 2013

A solid starting point for assessing tree-improvement programs would be to determine the effect of genetic gain in economic terms at stand level. This paper presents a stand-level optimization analysis of the use of improved seed material in reforestation from the perspective of forest owners. We used a genetic algorithm to study the effects of optimized stand management on the bare land value (BLV) for both genetically improved and unimproved reforestation material, with increase in BLV (ΔBLV > 0) representing the deployment benefit over the standard tree-improvement program. The stand-level optimization analysis was applied to a case representative of economic and climatic circumstances in Finland. The results show that the absolute increase in the BLV is distinctly higher in southern Finland than in central Finland, let alone northern Finland, regardless of the interest rate (3% or 4%) or genetic gain (3% or 15%). Sensitivity analyses revealed that market-related risks need to be taken into account carefully. Our tentative results provide new insight on the financial incentives for using genetically improved seed material in Scots pine (Pinus sylvestris L.) stand establishment under varying climatic conditions, but the subject merits further investigation — with greater detail and a more systematic data structure.
Magnon transmission by an atomic interface in Ni–Fe and Fe–Ni systems
Authors: Bourahla Boualem , Nafa Ouahiba , Khater Antoine
Published: February 2013

This work describes spin wave localized states and coherent magnon transport in ferromagnetic systems. The model system, A–B, consists of a semi-infinite bcc ferromagnetically ordered lead B joined to another fcc semi-infinite ferromagnetically ordered lead A, oriented in the same direction. It is applied to the systems Ni–Fe and the inverse Fe–Ni. The magnon transmission, scattering coherently at the interface boundary, and the localized density of spin states are calculated and analyzed. Transmission and reflection scattering cross sections are determined from elements of a Landauer-type scattering matrix. The theoretical calculations are carried out using the matching procedure. The results highlight the localized spin states on the interface domain and their interactions with incident magnons. The calculated properties are presented for arbitrary incidence angles of the magnons on the boundary, for all accessible frequencies in the propagating bands, and for the interatomic magnetic exchange of the A and B subsystems, and their spin intensity, with no externally applied magnetic field. The spin waves associated with the surface and the interface, in layered magnetic structures, interact with each other leading to interesting magnetic behaviors and give symmetry properties of spin layers at a microscopic scale.
AN ADVANCED OPTIMIZATION TECHNIQUE FOR LAYER-SPECIFIC CHARACTERIZATION OF SLAB METAMATERIALS
Authors: RYBIN OLEG
Published: February 2013

A new optimization technique for evaluating the complex effective relative permittivity and permeability of elementary sub-slab whose thickness equals to the constant of a unit cell of a slab metamaterial is developed. The objective of the technique is based on a numerical solving of appropriate minimization problem for a cascaded network representation of the slab metamaterial utilizing the Effective Medium Theory (EMT) and the definition of S- and T-parameters of the metamaterials considered as a four-pole network. The technique is tested using the open source FDTD software package and the optimization technique obtained [O. Rybin and M. Raza, Int. J. Appl. Electrom. Mech.32, 207 (2010)].
ASTROSAT: SOME KEY SCIENCE PROSPECTS
Authors: PAUL BISWAJIT
Published: February 2013

ASTROSAT is an astronomy satellite designed for simultaneous multi-wavelength studies in the Optical/UV and a broad X-ray energy range. With four X-ray instruments and a pair of UV-Optical telescopes, ASTROSAT will provide unprecedented opportunity for simultaneous multi-wavelength observations, which is of immense value in study of highly variable sources, especially X-ray binaries and active galactic nuclei. The Large Area X-ray Proportional Counters (LAXPC) of ASTROSAT, which has the largest effective area in the hard X-ray band compared to all previous X-ray missions, will enable high time resolution X-ray measurements in the 2–80 keV band with moderate energy resolution. Here we give a brief summary of the payload characteristics of ASTROSAT and discuss some of the main science topics that will be addressed with the LAXPC, and with simultaneous observations with the UVIT telescopes, with particular emphasis on X-ray binaries and compact objects. The possibility of aiding gravitational wave experiments is also briefly mentioned.
Systematizing pragmatic software reuse
Authors: Holmes Reid , Walker Robert J.
Published: February 2013

Many software reuse tasks involve reusing source code that was not designed in a manner conducive to those tasks, requiring that ad hoc modifications be applied. Such
pragmatic
reuse tasks are a reality in
disciplined
industrial practice; they arise for a variety of organizational and technical reasons. To investigate a pragmatic reuse task, a developer must navigate through, and reason about, source code dependencies in order to identify program elements that are relevant to the task and to decide how those elements should be reused. The developer must then convert his mental model of the task into a set of actions that he can perform. These steps are poorly supported by modern development tools and practices.

We provide a model for the process involved in performing a pragmatic reuse task, including the need to capture (mentally or otherwise) the developer's decisions about how each program element should be treated: this is a
pragmatic-reuse plan
. We provide partial support for this model via a tool suite, called Gilligan; other parts of the model are supported via standard IDE tools. Using a pragmatic-reuse plan, Gilligan can semiautomatically transform the selected source code from its originating system and integrate it into the developer's system.

We have evaluated Gilligan through a series of case studies and experiments (each involving industrial developers) using a variety of source systems and tasks; we report in particular on a previously unpublished, formal experiment. The results show that pragmatic-reuse plans are a robust metaphor for capturing pragmatic reuse intent and that, relative to standard IDE tools, Gilligan can (1) significantly decrease the time that developers require to perform pragmatic reuse tasks, (2) increase the likelihood that developers will successfully complete pragmatic reuse tasks, (3) decrease the time required by developers to identify infeasible reuse tasks, and (4) improve developers' sense of their ability to manage the risk in such tasks.
Lexical normalization for social media text
Authors: Han Bo , Cook Paul , Baldwin Timothy
Published: February 2013

Twitter provides access to large volumes of data in real time, but is notoriously noisy, hampering its utility for NLP. In this article, we target out-of-vocabulary words in short text messages and propose a method for identifying and normalizing lexical variants. Our method uses a classifier to detect lexical variants, and generates correction candidates based on morphophonemic similarity. Both word similarity and context are then exploited to select the most probable correction candidate for the word. The proposed method doesn't require any annotations, and achieves state-of-the-art performance over an SMS corpus and a novel dataset based on Twitter.
Social factors in group recommender systems
Authors: Quijano-Sanchez Lara , Recio-Garcia Juan A. , Diaz-Agudo Belen , Jimenez-Diaz Guillermo
Published: February 2013

In this article we review the existing techniques in group recommender systems and we propose some improvement based on the study of the different individual behaviors when carrying out a decision-making process. Our method includes an analysis of group personality composition and trust between each group member to improve the accuracy of group recommenders. This way we simulate the argumentation process followed by groups of people when agreeing on a common activity in a more realistic way. Moreover, we reflect how they expect the system to behave in a long term recommendation process. This is achieved by including a memory of past recommendations that increases the satisfaction of users whose preferences have not been taken into account in previous recommendations.
Social temporal collaborative ranking for context aware movie recommendation
Authors: Liu Nathan N. , He Luheng , Zhao Min
Published: February 2013

Most existing collaborative filtering models only consider the use of user feedback (e.g., ratings) and meta data (e.g., content, demographics). However, in most real world recommender systems, context information, such as time and social networks, are also very important factors that could be considered in order to produce more accurate recommendations. In this work, we address several challenges for the context aware movie recommendation tasks in CAMRa 2010: (1) how to combine multiple heterogeneous forms of user feedback? (2) how to cope with dynamic user and item characteristics? (3) how to capture and utilize social connections among users? For the first challenge, we propose a novel ranking based matrix factorization model to aggregate explicit and implicit user feedback. For the second challenge, we extend this model to a sequential matrix factorization model to enable time-aware parametrization. Finally, we introduce a network regularization function to constrain user parameters based on social connections. To the best of our knowledge, this is the first study that investigates the collective modeling of social and temporal dynamics. Experiments on the CAMRa 2010 dataset demonstrated clear improvements over many baselines.
An online system for multiple interacting targets tracking
Authors: Song Xuan , Zhao Huijing , Cui Jinshi , Shao Xiaowei , Shibasaki Ryosuke , Zha Hongbin
Published: February 2013

Multitarget tracking becomes significantly more challenging when the targets are in close proximity or frequently interact with each other. This article presents a promising online system to deal with these problems. The novelty of this system is that laser and vision are integrated with tracking and online learning to complement each other in one framework: when the targets do not interact with each other, the laser-based independent trackers are employed and the visual information is extracted simultaneously to train some classifiers online for “possible interacting targets”. When the targets are in close proximity, the classifiers learned online are used alongside visual information to assist in tracking. Therefore, this mode of cooperation not only deals with various tough problems encountered in tracking, but also ensures that the entire process can be completely online and automatic. Experimental results demonstrate that laser and vision fully display their respective advantages in our system, and it is easy for us to obtain a good trade-off between tracking accuracy and the time-cost factor.