bluuebunny/crossref_metadata_2025_split huggingface dataset:
Online exercise for the design and simulation of PCR and PCR-RFLP experiments
Authors: San Millán Rosario María , Martínez-Ballesteros Ilargi , Rementeria Aitor , Garaizar Javier , Bikandi Joseba 
Published: December 2013

Abstract

Background
Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool.

Findings
An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes, compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive.

Conclusions
The exercise is freely available at http://insilico.ehu.es/edu.
Genetic diversity and structure in Leishmania infantum populations from southeastern Europe revealed by microsatellite analysis
Authors: Gouzelou Evi , Haralambous Christos , Antoniou Maria , Christodoulou Vasiliki , Martinković Franjo , Živičnjak Tatjana , Smirlis Despina , Pratlong Francine , Dedet Jean-Pierre , Özbel Yusuf , Toz Seray Özensoy , Presber Wolfgang , Schönian Gabriele , Soteriadou Ketty 
Published: December 2013

Abstract

Background
The dynamic re-emergence of visceral leishmaniasis (VL) in south Europe and the northward shift to Leishmania-free European countries are well-documented. However, the epidemiology of VL due to Leishmania infantum in southeastern (SE) Europe and the Balkans is inadequately examined. Herein, we aim to re-evaluate and compare the population structure of L. infantum in SE and southwestern (SW) Europe.

Methods

Leishmania strains collected from humans and canines in Turkey, Cyprus, Bulgaria, Greece, Albania and Croatia, were characterized by the K26-PCR assay and multilocus enzyme electrophoresis (MLEE). Genetic diversity was assessed by multilocus microsatellite typing (MLMT) and MLM Types were analyzed by model- and distance- based algorithms to infer the population structure of 128 L. infantum strains.

Results

L. infantum MON-1 was found predominant in SE Europe, whilst 16.8% of strains were MON-98. Distinct genetic populations revealed clear differentiation between SE and SW European strains. Interestingly, Cypriot canine isolates were genetically isolated and formed a monophyletic group, suggesting the constitution of a clonal MON-1 population circulating among dogs. In contrast, two highly heterogeneous populations enclosed all MON-1 and MON-98 strains from the other SE European countries. Structure sub-clustering, phylogenetic and Splitstree analysis also revealed two distinct Croatian subpopulations. A mosaic of evolutionary effects resulted in consecutive sub-structuring, which indicated substantial differentiation and gene flow among strains of both zymodemes.

Conclusions
This is the first population genetic study of L. infantum in SE Europe and the Balkans. Our findings demonstrate the differentiation between SE and SW European strains; revealing the partition of Croatian strains between these populations and the genetic isolation of Cypriot strains. This mirrors the geographic position of Croatia located in central Europe and the natural isolation of the island of Cyprus. We have analysed the largest number of MON-98 strains so far. Our results indicate extensive gene flow, recombination and no differentiation between MON-1 and MON-98 zymodemes. No correlation either to host specificity or place and year of strain isolation was identified. Our findings may be associated with intensive host migration and common eco-epidemiological characteristics in these countries and give valuable insight into the dynamics of VL.
Increased soluble IL-2 receptor levels in serum from a patient with painless thyroiditis
Authors: Hamamoto Kae , Inaba Masaaki , Yamada Shinsuke , Yoda Maki , Yoda Koichiro , Goto Hitoshi , Kurajoh Masafumi , Koyama Hidenori 
Published: December 2013

Abstract

Context
Serum concentration of soluble interleukin-2 receptor (sIL-2R) has been established as a reliable marker of T-lymphocyte activation. However, there have been no reports describing the relationship between serum sIL-2R and painless thyroiditis.

Objective
We report a case of a 76-yr-old female with a significant and temporary increase of sIL-2R concomitant with painless thyroiditis.

Case illustration
The patient was diagnosed with malignant lymphoma at the age of 73. After 6 cycles of CHOP-R complete remission was induced and no recurrence was observed up to 3.5 years. At 76 years of age, she exhibited hyperthyroidism and was diagnosed with painless thyroiditis based upon US examination and 99mTc-Thyroid scintigraphy. Her AST and ALT were mildly elevated, and her serum level of sIL-2R increased up to 2230 U/mL from the approximately 540 U/mL, which had been stable for 3 years before.
These abnormal data normalized without requiring any treatment. The time-course of the reduction in sIL-2R did not correlate with FT4 or FT3, but was very similar to that of AST and ALT.

Conclusion
There was no evidence of relapse of the malignant lymphoma. We conclude that the increase of sIL-2R was associated with painless thyroiditis. Considering the similar time-course between the reduction of serum sIL-2R and those of AST and ALT, which are often accompanied by autoimmune processes in painless thyroiditis during the development of hyperthyroidism, it was suggested that the increase of serum sIL-2R in this case resulted from activation of an autoimmune process.
Naupliar development of Pseudocyclops sp. (Copepoda: Calanoida: Pseudocyclopidae): description of an unusual set of character states
Authors: Ferrari Frank D , Dahms Hans-Uwe , Kangtia Pawana , Chullasorn Supawadee , Schick Mark 
Published: December 2013

Abstract

Background
Naupliar development is known for only one other species of the calanoid taxon Pseudocyclopidae as yet.

Results
Six naupliar stages are described from an as yet unnamed population of Pseudocyclops cultured at the John G. Shedd Aquarium in Chicago, IL. The naupliar body is divided into a deep anterior section and a shallow posterior section, although the posterior section is poorly defined at NI. The posterior section bears a long, thin mediodorsal seta; short thick setae are added during molts to NIII ~ NV. The posterior section does not bear limb buds except for the caudal ramus and is presumed to represent the anal segment of the copepod. Throughout naupliar development, the antennule is five-segmented, a uniquely high number for a calanoid copepod. The distal segment is broadened, and three proximal segments are foreshortened during the molt to NIII, and remain so thereafter. Setae are added dorsally and ventrally to the distal segment during each molt. The naupliar arthrite is a simple, seta-like structure on the coxa of the antenna of all naupliar stages. On the exopod of the antenna, setae are added to the segment adjacent to the proximal one during molts to NIV ~ NVI in a manner consistent with the model of ramal patterning. The gnathobase is added to the coxa of the mandible during the molt to NIV, but its ventral attenuations are lost during the molt to NVI. The endopod of the mandible significantly changes between stages NIII and NIV; setae originate dorsally rather than ventrally on the proximal endopodal segment. These unique changes are reversed during the molt to NVI.

Conclusions
Many of these changes have not been reported for any other calanoid. The morphological restoration at NVI is particularly noteworthy.
A framework to integrate speech based interface for blind web users on the websites of public interest
Authors: Verma Prabhat , Singh Raghuraj , Singh Avinash Kumar 
Published: December 2013

AbstractDespite many assistive tools available for browsing the web, blind persons are not able to perform the tasks using internet that are done by persons without such disability. Even the futuristic social networking sites and other websites using the features of web 2.0 indicate a lesser accessible/responsible web. In this paper, we propose a framework, which can be used by the websites of public interest to make their important utilities better accessible and usable to blind web users. The approach is based on providing an alternate access system on the fly using one single website. The framework makes use of existing technologies like JavaScript, available speech APIs etc. and therefore provides a lightweight and robust solution to the accessibility problem. As a case study, we demonstrate the usefulness of the proposed framework by showing its working on a key functionality of the Indian Railways Reservation Website.
Proteomic response of marine invertebrate larvae to ocean acidification and hypoxia during metamorphosis and calcification
Authors: Mukherjee Joy , Wong Kelvin K. W. , Chandramouli Kondethimmanahalli H. , Qian Pei-Yuan , Leung Priscilla T. Y. , Wu Rudolf S. S. , Thiyagarajan Vengatesen 
Published: December 2013

SUMMARY
Calcifying marine invertebrates with complex life cycles are particularly at risk to climate changes as they undergo an abrupt ontogenetic shift during larval metamorphosis. Although our understanding of the larval response to climate changes is rapidly advancing, the proteome plasticity involved in a compensatory response to climate change is still unknown. In this study, we investigated the proteomic response of metamorphosing larvae of the tubeworm Hydroides elegans, challenged with two climate change stressors, ocean acidification (OA; pH 7.6) and hypoxia (HYP; 2.8 mg O2 l−1), and with both combined. Using a two-dimensional gel electrophoresis (2-DE)-based approach coupled with mass spectrometry, we found that climate change stressors did not affect metamorphosis except under OA, but altered the larval proteome and phosphorylation status. Metabolism and various stress and calcification-related proteins were downregulated in response to OA. In OA and HYP combined, HYP restored the expression of the calcification-related proteins to the control levels. We speculate that mild HYP stress could compensate for the negative effects of OA. This study also discusses the potential functions of selected proteins that might play important roles in larval acclimation and adaption to climate change.
Characterization and Phenylacetylene-Assisted Cyclometalation of an Isolable Hydrido–Selenolato PtII Complex Having Phosphite Ligands, cis-[PtH(SeTrip){P(OPh)3}2]
Authors: Kamon Hitomi , Aoki Yutaro , Nakata Norio , Ishii Akihiko 
Published: December 2013

Abstract
A hydrido–selenolato PtII complex having P(OPh)3 ligands, cis-[PtH(SeTrip){P(OPh)3}2] (Trip: 9-triptycyl), was synthesized by the reaction of TripSeH with [Pt{P(OPh)3}2]. The structure was characterized by NMR spectroscopy and X-ray crystallography in comparison with the corresponding PPh3 complex, cis-[PtH(SeTrip)(PPh3)2], indicating the stronger coordination of P(OPh)3 to the Pt center than that of PPh3. On heating at 130 °C in xylene for 17 h, cis-[PtH(SeTrip){P(OPh)3}2] was converted to the corresponding 1,2-selenaplatinacycle (SP-4–2)-[Pt(κC1,κSe9-TripSe(2−)){P(OPh)3}2] through an intramolecular cyclization (cyclometalation). The reaction with dimethyl acetylenedicarboxylate (DMAD) gave a mixture of hydroselenation products (E)- and (Z)-(MeO2C)CH=C(SeTrip)CO2Me non-stereoselectively together with 1H-2-benzoselenin, dimethyl 7H-7,11b[1′,2′]-benzenoanthra[9,1-bc]selenin-2,3-dicarboxylate. In the reaction with phenylacetylene in toluene at 110 °C, phenylacetylene served as a hydrogen acceptor to form the 1,2-selenaplatinacycle and styrene. Based on the results of controlled experiments using cis-[PtD(SeTrip){P(OPh)3}2] and phenylacetylene-d, the mechanism of the cyclometalation was proposed as the 1,2- (major) and 2,1- (minor) insertions of phenylacetylene into the Pt–H bond followed by cyclometalation between the Pt center and the triptycyl group. The reaction with phenylacetylene in the presence of excess P(OPh)3 furnished a 1,2,3-oxaphosphaplatinacycle, (SP-4–2)-[Pt{κC,κP-(Z)-CH=C(Ph)OP(OPh)2}(SeTrip){P(OPh)3}], as a minor product, together with the 1,2-selenaplatinacycle in a decreased yield.
Tantalum(V) Fluoride-catalyzed N-Alkylation of Arylamines with Benzyl Alcohols
Authors: Gangaram Sathaiah , Adimulam Chandra Shekhar , Akula Ravi Kumar , Kengiri Raju , Pamulaparthy Shanthan Rao , Madabhushi Sridhar , Banda Narsaiah 
Published: December 2013

Abstract
This paper describes a simple and efficient protocol for the N-alkylation of arylamines with benzyl alcohols using tantalum(V) fluoride as the catalyst.
Epitypification of Ganoderma sichuanense J.D. Zhao & X.Q. Zhang (Ganodermataceae)
Authors: Yao Yi-Jian , Wang Xin-Cun , Wang Bo 
Published: December 2013

AbstractThe widely cultivated Chinese Ganoderma, as Ling‐zhi in Chinese and previously named as “G. lucidum”, is an important fungus with significant medicinal and economic values. The species identity of the fungus was recently clarified as G. sichuanense based on both morphological and molecular data, but an unusual ITS sequence inconsistent with morphological characters was also reported from the holotype of G. sichuanense. The ITS sequence is proved to be of G. weberianum, a species distinctly different from G. sichuanense in morphology. However, repeated amplifications of DNA fragments from the holotype of G. sichuanense were unsuccessful because of the specimen's condition. In order to interpret the species concept of the taxon, both morphologically and molecularly, an epitype of G. sichuanense is designated in this paper from recent collections with living strains from the type locality of the species. Ganoderma lingzhi, a recently proposed new species name for Ling‐zhi widely cultivated in China, is determined as a later synonym of G. sichuanense.
Lectotypification of the name Crocus sativus var. vernus L. (Iridaceae) and its consequences within Crocus ser. Verni
Authors: Peruzzi Lorenzo , Carta Angelino , Garbari Fabio 
Published: December 2013

AbstractThe typification of the Linnaean name Crocus sativus var. vernus is discussed. A lectotype is designated from the Burser Herbarium at UPS. Due to changes in taxonomy and this lectotypification, it has not been possible to maintain the present strict usage of the name. Crocus vernus (L.) Hill should correctly be applied to the plants previously known as C. vernus subsp. albiflorus (Kit.) Ces. (≡ C. albiflorus Kit.). The next available name for the species to which the name C. vernus subsp. vernus has been misapplied is C. neapolitanus (Ker Gawl.) Loisel.
Cinema on the steppes of Central Asia: Mongolian film culture from communism to commercialization
Authors: Grøn Nis 
Published: December 2013

Abstract
In Mongolia cinema has been a medium of artistic expression and documentation for more then seventy years and a popular leisure activity for the Mongolians for even longer. This article frames the investigation of Mongolian Cinema within the field of small nation cinema studies and subsequently traces the historical development of a national based film culture in Mongolia from its implementation in the 1930s under communist rule to its present state. The article explores the question of what happened to the national based film culture in the wreck of the Soviet meltdown around 1990 and how the socio-political transformation of the country since the early 1990s has challenged the existence of a locally rooted film culture in Mongolia.
Imperfectible narrative within colonial melancholia: Gendered sovereignty and the technology of colonial subjects in the wartime Korean propaganda film, The Volunteer (1941)
Authors: Lee Yongwoo 
Published: December 2013

Abstract
This article examines colonial melancholia among conflicting positions of colonial subjects represented in the 1941 film, Jiwŏnbyŏng/The Volunteer. This wartime propaganda film tells the story of a colonial Korean man who joins the Imperial Japanese Army following implementation of the Special Volunteer Army System in 1938. By showing the ways in which discourses of assimilation into, and imperialization by, the Japanese empire become an ‘imperfectible’ narrative in colonial Koreans’ production of local discourses, this paper conveys the discourse of Koreans’ Imperial subjecthood as an expression of melancholia through a close examination of narratives from the literary works of female writer Ch’oe Chong-Hui and the pro-Japanese The Volunteer. I aim to establish a theoretical and historical framework for analysing colonial mentality during the Total War era and the formation of continual colonial epistemology.
Hardy spaces
associated with a pair of commuting operators
Authors: Cao Jun , Fu Zunwei , Jiang Renjin , Yang Dachun 
Published: December 2013

Abstract
Let

L
1

,

L
2

${L_1,L_2}$

be a pair of one-to-one commuting sectorial
operators such that each Li
for

i
∈
{
1
,
2
}

${i\in \lbrace 1,2\rbrace }$

satisfies
the mi
order L
2 off-diagonal estimates and

m
1

≥

m
2

>
0

${m_1\ge m_2&gt;0}$

.
Let

H

L
i

p

(

ℝ
n

)

${H_{L_i}^p(\mathbb {R}^n)}$

,

i
∈
{
1
,
2
}

${i\in \lbrace 1,2\rbrace }$

, and

H

L
1

+

L
˜

2

p

(

ℝ
n

)

${H_{L_1+\widetilde{L}_2}^p(\mathbb {R}^n)}$

be
the Hardy spaces associated, respectively, to the operators Li
and

L
1

+

L
˜

2

${L_1+\widetilde{L}_2}$

,
where

L
˜

2

:
=

L
2

m
1

/

m
2

${\widetilde{L}_2:=L_2^{m_1/m_2}}$

is a fractional power of L
2.
In this paper, the authors give out some real-variable properties of these
Hardy spaces. More precisely, the authors first establish the bounded joint
H
∞ functional calculus in these Hardy spaces and prove that the abstract
Riesz transform

D

m
i

(

L
1

+

L
2

)

-
1
/
2

${D^{m_i}(L_1+L_2)^{-1/2}}$

is bounded from

H

L
i

p

(

ℝ
n

)

${H_{L_i}^p(\mathbb {R}^n)}$

to the classical Hardy space

H
p

(

ℝ
n

)

${H^p(\mathbb {R}^n)}$

for all

p
∈
(

n

n
+

m
i

,
1
]

${p\in (\frac{n}{n+m_i},1]}$

,
where

i
∈
{
1
,
2
}

${i\in \lbrace 1,2\rbrace }$

. Moreover, for all

p
∈
(
0
,
1
]

${p\in (0, 1]}$

,
the authors show that

H

L
1

+

L
˜

2

p

(

ℝ
n

)

=

H

L
1

p

(

ℝ
n

)

+

H

L
2

p

(

ℝ
n

)

$
{H_{L_1+\widetilde{L}_2}^p(\mathbb {R}^n)=
H_{L_1}^p(\mathbb {R}^n)+H_{L_2}^p(\mathbb {R}^n)}\vspace*{-1.42262pt}
$

and give a sufficient
condition to guarantee

H

L
1

p

(

ℝ
n

)

⊂

H

L
2

p

(

ℝ
n

)

${H_{L_1}^p(\mathbb {R}^n)\subset H_{L_2}^p(\mathbb {R}^n)}$

.
Bayesian posterior contraction rates for linear severely ill-posed inverse problems
Authors: Agapiou Sergios , Stuart Andrew M. , Zhang Yuan-Xiang 
Published: December 2013

Abstract.
We consider a class of linear ill-posed inverse problems
arising from inversion of a compact operator with singular
values which decay exponentially to zero. We adopt a
Bayesian approach, assuming a Gaussian prior on the unknown
function. The observational noise is assumed to be
Gaussian; as a consequence the prior is conjugate to the likelihood so that
the posterior distribution is also Gaussian. We study
Bayesian posterior consistency in the small observational noise
limit. We assume that the forward operator and the
prior and noise covariance operators commute with one another.
We show how, for given smoothness
assumptions on the truth, the scale parameter of the
prior, which is a constant multiplier of the prior covariance operator, can be adjusted to optimize the rate of posterior
contraction to the truth, and we explicitly compute
the logarithmic rate.
Reconstruction of dynamic objects with affine deformations in computerized tomography
Authors: Hahn Bernadette 
Published: December 2013

Abstract.
The data acquisition in computerized tomography takes a certain amount of time since the x-ray source has to be rotated around the specimen. An object that changes during the scanning causes inconsistent data sets. To avoid the motion artefacts in reconstructions, the algorithm has to take the dynamic behavior of the specimen into account. In this context, some a priori information about the movement is required. A reconstruction method is proposed that compensates for the motion with a special focus on affine deformations. It also permits the combination of reconstruction and image analysis tools to extract features of the object without motion artefacts. The algorithm is validated with a numerical example from medical imaging.
Analysis of the factorization method for a general class of boundary conditions
Authors: Chamaillard Mathieu , Chaulet Nicolas , Haddar Houssem 
Published: December 2013

Abstract
We analyze the factorization method (introduced by Kirsch in 1998 to solve inverse
scattering problems at fixed frequency from the far field operator) for a general class of boundary conditions
that generalizes impedance boundary conditions. For instance, when the surface impedance
operator is of pseudo-differential type, our main result stipulates that the
factorization method works if the order of this operator is different from
one and the operator is Fredholm of index zero with non-negative imaginary
part. We
also provide some validating numerical examples for boundary operators of
second order with discussion on the choice of the test function.
Repetitive administration of acetylcholine receptor agonist rescues brain inflammation and brain damage after hypoxia-ischemia in newborn rat
Authors: Furukawa Seishi , Yang Li , Sameshima Hiroshi , Ikenoue Tsuyomu 
Published: December 2013

Abstract

Objective: We examined the effect of repetitive administration of acetylcholine receptor agonist (carbachol) on brain damage and microglial accumulation in three brain regions after hypoxia-ischemia (HI) in newborn rat.

Study Design: Seven-day-old Wistar rats were divided into two groups, one receiving a 0.1 mg/kg dose of carbachol on days 7, 8 and 9 to examine the attenuating effect on brain damage with decreasing accumulation of microglia, and the other group receiving saline as a control. Rats were subjected to left carotid artery ligation followed by hypoxia. We evaluated brain damage and the number of microglias in three regions on days 10 and 14.

Results: Brain tissue was better preserved in the carbachol group on days 10 and 14. Microglial accumulation in the cortex was strong and persisted from day 10s to 14 in the control. Conversely, the accumulation of microglias was attenuated in the hippocampus and white matter on day 14. Carbachol significantly reduced the number of microglias in the hippocampus and white matter on day 10 and in the cortex on days 10 and 14.

Conclusion: The main area of late inflammation was the cortex. Repetitive administration of carbachol reduces early and late inflammation after HI in the developing brain.