bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic stratigraphy of composite peripheral unconformity in a foredeep basin
Authors: Leszczyński Stanisław , Nemec Wojciech 
Published: August 2014

AbstractThis study employs facies analysis and basic principles of sequence stratigraphy to correlate isolated outcrop sections and reveal the depositional history of the Chmielnik Formation – a prominent mid‐Serravalian clastic wedge formed on the basinward forebulge flank of the Polish Carpathian Foredeep. The coarse‐grained clastic wedge, up to 30 m thick and spanningca1·1 Ma within biozoneNN6, consists of fluvio‐deltaic, foreshore and shoreface deposits with a range of large littoral sand bars, all enveloped in muddy offshore‐transition deposits. Its dynamic stratigraphy indicates rapid shoreline shifts and environmental changes due to the interplay of forebulge tectonism, sediment supply and third‐order eustatic cycles. A similar interplay of tectonism and eustasy is recognizable in the whole middle Miocene sedimentary succession deposited on the forebulge flank, demonstrating an extreme case of an accommodation‐controlled shelf and indicating tectonic cycles of the forebulge uplift and subsidence spanningca800 to 900 ka. The episodes of forebulge uplift correlate with the main pulses of orogen thrusting. The resulting composite peripheral unconformity differs markedly from the idealized model of a ‘steady‐state’ stepwise onlap driven by forebulge continuous retreat. It is concluded that the foredeep peripheral unconformities, instead of being simplified in accordance with this idealized model, should rather be studied in detail because they bear a valuable high‐resolution record of regional events and give unique insights into the local role of tectonics, eustasy and sediment supply.
A novel FY*A allele with the 265T and 298A SNPs formerly associated exclusively with the FY*B allele and weak Fyb antigen expression: implication for genotyping interpretative algorithms
Authors: Lopez G. H. , Condon J. A. , Wilson B. , Martin J. R. , Liew Y.‐W. , Flower R. L. , Hyland C. A. 
Published: August 2014

Background and ObjectivesAn Australian Caucasian blood donor consistently presented a serology profile for the Duffy blood group as Fy(a+b+) with Fya antigen expression weaker than other examples of Fy(a+b+) red cells. Molecular typing studies were performed to investigate the reason for the observed serology profile.Material and MethodsBlood group genotyping was performed using a commercial SNP microarray platform. Sanger sequencing was performed using primer sets to amplify across exons 1 and 2 of the FY gene and using allele‐specific primers.ResultsThe propositus was genotyped as FY*A/B, FY*X heterozygote that predicted the Fy(a+b+w) phenotype. Sequencing identified the 265T and 298A variants on the FY*A allele. This link between FY*A allele and 265T was confirmed by allele‐specific PCR.ConclusionThe reduced Fya antigen reactivity is attributed to a FY*A allele‐carrying 265T and 298A variants previously defined in combination only with the FY*B allele and associated with weak Fyb antigen expression. This novel allele should be considered in genotyping interpretative algorithms for generating a predicted phenotype.
A sieve algorithm based on overlattices
Authors: Becker Anja , Gama Nicolas , Joux Antoine 
Published: August 2014

AbstractIn this paper, we present a heuristic algorithm for solving exact, as well as approximate, shortest vector and closest vector problems on lattices. The algorithm can be seen as a modified sieving algorithm for which the vectors of the intermediate sets lie in overlattices or translated cosets of overlattices. The key idea is hence no longer to work with a single lattice but to move the problems around in a tower of related lattices. We initiate the algorithm by sampling very short vectors in an overlattice of the original lattice that admits a quasi-orthonormal basis and hence an efficient enumeration of vectors of bounded norm. Taking sums of vectors in the sample, we construct short vectors in the next lattice. Finally, we obtain solution vector(s) in the initial lattice as a sum of vectors of an overlattice. The complexity analysis relies on the Gaussian heuristic. This heuristic is backed by experiments in low and high dimensions that closely reflect these estimates when solving hard lattice problems in the average case.This new approach allows us to solve not only shortest vector problems, but also closest vector problems, in lattices of dimension$\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}n$in time$2^{0.3774\, n}$using memory$2^{0.2925\, n}$. Moreover, the algorithm is straightforward to parallelize on most computer architectures.
Traps to the BGJT-algorithm for discrete logarithms
Authors: Cheng Qi , Wan Daqing , Zhuang Jincheng 
Published: August 2014

AbstractIn the recent breakthrough paper by Barbulescu, Gaudry, Joux and Thomé, a quasi-polynomial time algorithm is proposed for the discrete logarithm problem over finite fields of small characteristic. The time complexity analysis of the algorithm is based on several heuristics presented in their paper. We show that some of the heuristics are problematic in their original forms, in particular when the field is not a Kummer extension. We propose a fix to the algorithm in non-Kummer cases, without altering the heuristic quasi-polynomial time complexity. Further study is required in order to fully understand the effectiveness of the new approach.
Subexponential class group and unit group computation in large degree number fields
Authors: Biasse Jean-François , Fieker Claus 
Published: August 2014

AbstractWe describe how to compute the ideal class group and the unit group of an order in a number field in subexponential time. Our method relies on the generalized Riemann hypothesis and other usual heuristics concerning the smoothness of ideals. It applies to arbitrary classes of number fields, including those for which the degree goes to infinity.
The multiple number field sieve for medium- and high-characteristic finite fields
Authors: Barbulescu Razvan , Pierrot Cécile 
Published: August 2014

AbstractIn this paper we study the discrete logarithm problem in medium- and high-characteristic finite fields. We propose a variant of the number field sieve (NFS) based on numerous number fields. Our improved algorithm computes discrete logarithms in $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\mathbb{F}_{p^n}$ for the whole range of applicability of the NFS and lowers the asymptotic complexity from $L_{p^n}({1/3},({128/9})^{1/3})$ to $L_{p^n}({1/3},(2^{13}/3^6)^{1/3})$ in the medium-characteristic case, and from $L_{p^n}({1/3},({64/9})^{1/3})$ to $L_{p^n}({1/3},((92 + 26 \sqrt{13})/27)^{1/3})$ in the high-characteristic case.
Hyper-and-elliptic-curve cryptography
Authors: Bernstein Daniel J. , Lange Tanja 
Published: August 2014

AbstractThis paper introduces ‘hyper-and-elliptic-curve cryptography’, in which a single high-security group supports fast genus-2-hyperelliptic-curve formulas for variable-base-point single-scalar multiplication (for example, Diffie–Hellman shared-secret computation) and at the same time supports fast elliptic-curve formulas for fixed-base-point scalar multiplication (for example, key generation) and multi-scalar multiplication (for example, signature verification).
Randomized, Double-Blind, Placebo-Controlled Clinical Trial of a Two-Day Regimen of Dihydroartemisinin-Piperaquine for Malaria Prevention Halted for Concern over Prolonged Corrected QT Interval
Authors: Manning Jessica , Vanachayangkul Pattaraporn , Lon Chanthap , Spring Michele , So Mary , Sea Darapiseth , Se Youry , Somethy Sok , Phann Sut-Thang , Chann Soklyda , Sriwichai Sabaithip , Buathong Nillawan , Kuntawunginn Worachet , Mitprasat Mashamon , Siripokasupkul Raveewan , Teja-Isavadharm Paktiya , Soh Eugene , Timmermans Ans , Lanteri Charlotte , Kaewkungwal Jaranit , Auayporn Montida , Tang Douglas , Chour Char Meng , Prom Satharath , Haigney Mark , Cantilena Louis , Saunders David 
Published: August 2014

ABSTRACT

Dihydroartemisinin-piperaquine, the current first-line drug for uncomplicated malaria caused by
Plasmodium falciparum
and
Plasmodium vivax
in Cambodia, was previously shown to be of benefit as malaria chemoprophylaxis when administered as a monthly 3-day regimen. We sought to evaluate the protective efficacy of a compressed monthly 2-day treatment course in the Royal Cambodian Armed Forces. The safety and efficacy of a monthly 2-day dosing regimen of dihydroartemisinin-piperaquine were evaluated in a two-arm, randomized, double-blind, placebo-controlled cohort study with 2:1 treatment allocation. Healthy military volunteers in areas along the Thai-Cambodian border where there is a high risk of malaria were administered two consecutive daily doses of 180 mg dihydroartemisinin and 1,440 mg piperaquine within 30 min to 3 h of a meal once per month for a planned 4-month period with periodic electrocardiographic and pharmacokinetic assessment. The study was halted after only 6 weeks (69 of 231 projected volunteers enrolled) when four volunteers met a prespecified cardiac safety endpoint of QTcF (Fridericia's formula for correct QT interval) prolongation of >500 ms. The pharmacodynamic effect on the surface electrocardiogram (ECG) peaked approximately 4 h after piperaquine dosing and lasted 4 to 8 h. Unblinded review by the data safety monitoring board revealed mean QTcF prolongation of 46 ms over placebo at the maximum concentration of drug in serum (
C
max
) on day 2. Given that dihydroartemisinin-piperaquine is one of the few remaining effective antimalarial agents in Cambodia, compressed 2-day treatment courses of dihydroartemisinin-piperaquine are best avoided until the clinical significance of these findings are more thoroughly evaluated. Because ECG monitoring is often unavailable in areas where malaria is endemic, repolarization risk could be mitigated by using conventional 3-day regimens, fasting, and avoidance of repeated dosing or coadministration with other QT-prolonging medications. (This study has been registered at
ClinicalTrials.gov
under registration no. NCT01624337.)
Kinetic Study of the Effect of Histidines 240 and 164 on TEM-149 Enzyme Probed by β-Lactam Inhibitors
Authors: Perilli Mariagrazia , Mancini Alisia , Celenza Giuseppe , Bottoni Carlo , Bellio Pierangelo , Sabatini Alessia , Di Pietro Letizia , Brisdelli Fabrizia , Segatore Bernardetta , Amicosante Gianfranco 
Published: August 2014

ABSTRACT

In the present study, we performed a detailed kinetic analysis of the enzymes TEM-149, TEM-149
H240
, and TEM-149
H164-H240
versus a large panel of inhibitors/inactivators, including penicillins, penems, carbapenems, monobactams, cephamycin, and carbacephem. These compounds behaved as poor substrates versus TEM-149, TEM-149
H240
, and TEM-149
H164-H240
β-lactamases, and the

K
i

(inhibition constant),
K
(dissociation constant of the Henri-Michaelis complex),
k
+2
and
k
+3
(first-order acylation and deacylation constants, respectively), and
k
+2
/
K
values were calculated.
A Conserved Apicomplexan Microneme Protein Contributes to Toxoplasma gondii Invasion and Virulence
Authors: Huynh My-Hang , Boulanger Martin J. , Carruthers Vern B. 
Published: August 2014

ABSTRACT

The obligate intracellular parasite
Toxoplasma gondii
critically relies on host cell invasion during infection. Proteins secreted from the apical micronemes are central components for host cell recognition, invasion, egress, and virulence. Although previous work established that the sporozoite protein with an altered thrombospondin repeat (SPATR) is a micronemal protein conserved in other apicomplexan parasites, including
Plasmodium
,
Neospora
, and
Eimeria
, no genetic evidence of its contribution to invasion has been reported. SPATR contains a predicted epidermal growth factor domain and two thrombospondin type 1 repeats, implying a role in host cell recognition. In this study, we assess the contribution of
T. gondii
SPATR (TgSPATR) to
T. gondii
invasion by genetically ablating it and restoring its expression by genetic complementation. Δ
spatr
parasites were ∼50% reduced in invasion compared to parental strains, a defect that was reversed in the complemented strain. In mouse virulence assays, Δ
spatr
parasites were significantly attenuated, with ∼20% of mice surviving infection. Given the conservation of this protein among the Apicomplexa, we assessed whether the
Plasmodium falciparum
SPATR ortholog (PfSPATR) could complement the absence of the TgSPATR. Although PfSPATR showed correct micronemal localization, it did not reverse the invasion deficiency of Δ
spatr
parasites, because of an apparent failure in secretion. Overall, the results suggest that TgSPATR contributes to invasion and virulence, findings that have implications for the many genera and life stages of apicomplexans that express SPATR.
Baculovirus-Vectored Multistage Plasmodium vivax Vaccine Induces Both Protective and Transmission-Blocking Immunities against Transgenic Rodent Malaria Parasites
Authors: Mizutani Masanori , Iyori Mitsuhiro , Blagborough Andrew M. , Fukumoto Shinya , Funatsu Tomohiro , Sinden Robert E. , Yoshida Shigeto 
Published: August 2014

ABSTRACT

A multistage malaria vaccine targeting the pre-erythrocytic and sexual stages of
Plasmodium
could effectively protect individuals against infection from mosquito bites and provide transmission-blocking (TB) activity against the sexual stages of the parasite, respectively. This strategy could help prevent malaria infections in individuals and, on a larger scale, prevent malaria transmission in communities of endemicity. Here, we describe the development of a multistage
Plasmodium vivax
vaccine which simultaneously expresses
P. vivax
circumsporozoite protein (PvCSP) and P25 (Pvs25) protein of this species as a fusion protein, thereby acting as a pre-erythrocytic vaccine and a TB vaccine, respectively. A new-concept vaccine platform based on the baculovirus dual-expression system (BDES) was evaluated. The BDES-Pvs25-PvCSP vaccine displayed correct folding of the Pvs25-PvCSP fusion protein on the viral envelope and was highly expressed upon transduction of mammalian cells
in vitro
. This vaccine induced high levels of antibodies to Pvs25 and PvCSP and elicited protective (43%) and TB (82%) efficacies against transgenic
P. berghei
parasites expressing the corresponding
P. vivax
antigens in mice. Our data indicate that our BDES, which functions as both a subunit and DNA vaccine, can offer a promising multistage vaccine capable of delivering a potent antimalarial pre-erythrocytic and TB response via a single immunization regimen.
Development of automated quantification methodologies of immunohistochemical markers to determine patterns of immune response in breast cancer: a retrospective cohort study
Authors: López Carlos , Callau Cristina , Bosch Ramon , Korzynska Anna , Jaén Joaquín , García-Rojo Marcial , Bueno Gloria , Salvadó Mª Teresa , Álvaro Tomás , Oños Montse , Fernández-Carrobles María del Milagro , Llobera Montserrat , Baucells Jordi , Orero Guifré , Lejeune Marylène 
Published: August 2014

IntroductionLymph nodes are one of the main sites where an effective immune response develops. Normally, axillary nodes are the first place where breast cancer produces metastases. Several studies have demonstrated the importance of immune cells, especially dendritic cells, in the evolution of breast cancer. The goal of the project is to identify differences in the patterns of immune infiltrates, with particular emphasis on dendritic cells, in tumour and axillary node biopsies between patients with and without metastases in the axillary nodes at the time of diagnosis. It is expected that these differences will be able to explain differences in survival, relapse and clinicopathological variables between the two groups.Methods and analysisThe study will involve 100 patients diagnosed with invasive breast cancer between 2000 and 2007, 50% of whom have metastases in the axillary lymph node at diagnosis. In selected patients, two cylinders from biopsies of representative areas of tumour and axillary nodes (with and without metastasis) will be selected and organised in tissue microarrays. Samples will be stained using immunohistochemical techniques for different markers of immune response and dendritic cells. Two images of each cylinder will be captured under standardised conditions for each marker. Each marker will be quantified automatically by digital image procedures using Image-Pro Plus and Image-J software. Associations of survival, relapse and other clinicopathological variables with the automatically quantified levels of immune infiltrates in patients with and without axillary node metastasis will be sought.Ethics and disseminationThe present project has been approved by the Clinical Research Ethics Committee of the Hospital Universitari Joan XXIII (Ref: 22p/2011). Those patients whose biopsies and clinical data are to be used will give their signed informed consent. Results will be published in peer-reviewed journals.
Pegmatite mylonites: origin and significance
Authors: Gapais Denis , Laouan Brem Boundi Awa 
Published: August 2014

Abstract
Pegmatites generally behave as resistant objects compared to their host rocks during solid-state deformation. They usually show folding or boudinage within their host rocks, features observed from low-grade to high-grade deformations, up to upper-amphibolite metamorphic conditions. Here we describe mylonitic pegmatite veins emplaced within S-C fabric-bearing two-mica granites. Pegmatites consist mainly of feldspar and quartz ribbons, with remnants of coarse-grained Kfs phenocrysts. Quartz ribbons are made of large grains elongated in the shearing direction, with evidence of dynamic recrystallization involving grain boundary migration. Ribbons show very strong lattice-preferred orientations of c-axes at low angles to the stretching lineation. From these, we propose that quartz ribbons are formed by oriented growth during syn-shearing crystallization of the pegmatite. Subsequent syn-shearing solid-state deformation involved grain size reduction accompanied by prism <a> slip. The occurrence of pegmatite mylonites within granitoid intrusions should be considered as a univocal argument for synkinematic emplacement.
Uncontrolled Inflammation Induced by AEG-1 Promotes Gastric Cancer and Poor Prognosis
Authors: Li Guanghua , Wang Zhao , Ye Jinning , Zhang Xinhua , Wu Hui , Peng Jianjun , Song Wu , Chen Chuangqi , Cai Shirong , He Yulong , Xu Jianbo 
Published: August 2014

AbstractGastric cancer is one of the most common causes of cancer-related death worldwide. Helicobacter pylori infection plays an important role in the development and progression of gastric cancer. The expression of astrocyte-elevated gene-1 (AEG-1) is increased in gastric cancer tissues, thereby contributing to the inflammatory response. We investigated whether and how AEG-1 regulated proinflammatory signaling in gastric cancer cells. We used human gastric cancer cell lines and athymic nude mice to investigate the role of AEG-1 in the regulation of the TLR4/nuclear factor-κB (NF-κB) signaling pathway and cancer invasion and compared the expression of AEG-1 and related proteins in 93 patients with gastric cancer by immunohistochemistry. In human gastric cancer cells, both AEG-1 and TLR4 could be induced by lipopolysaccharide (LPS) stimulation. AEG-1 was upregulated via LPS-TLR4 signaling and in turn promoted nuclear translocation of the NF-κB p65 subunit. At the same time, AEG-1 overexpression decreased the levels of suppressor of cytokine signaling (SOCS) protein SOCS-1, a negative regulator of the TLR4 pathway. Furthermore, nude mice engrafted with AEG-1/TLR4-expressing cells demonstrated larger tumor volumes than control animals. In patients with gastric cancer, the expression of AEG-1 correlated with that of TLR4, SOCS-1, and NF-κB and was higher in tumors compared with noncancerous adjacent tissues. Overall survival in patients with gastric cancer with simultaneous expression of AEG-1 and TLR4 was poor. Our results demonstrate that AEG-1 can promote gastric cancer progression by a positive feedback TLR4/NF-κB signaling-related mechanism, thus providing new mechanistic explanation for the role of inflammation in cancer progression. Cancer Res; 74(19); 5541–52. ©2014 AACR.
Molecular Markers of Carcinogenesis for Risk Stratification of Individuals with Colorectal Polyps: A Case–Control Study
Authors: Gupta Samir , Sun Han , Yi Sang , Storm Joy , Xiao Guanghua , Balasubramanian Bijal A. , Zhang Song , Ashfaq Raheela , Rockey Don C. 
Published: August 2014

AbstractRisk stratification using number, size, and histology of colorectal adenomas is currently suboptimal for identifying patients at increased risk for future colorectal cancer. We hypothesized that molecular markers of carcinogenesis in adenomas, measured via immunohistochemistry, may help identify high-risk patients. To test this hypothesis, we conducted a retrospective, 1:1 matched case–control study (n = 216; 46% female) in which cases were patients with colorectal cancer and synchronous adenoma and controls were patients with adenoma but no colorectal cancer at baseline or within 5 years of follow-up. In phase I of analyses, we compared expression of molecular markers of carcinogenesis in case and control adenomas, blind to case status. In phase II of analyses, patients were randomly divided into independent training and validation groups to develop a model for predicting case status. We found that seven markers [p53, p21, Cox-2, β-catenin (BCAT), DNA-dependent protein kinase (DNApkcs), survivin, and O6-methylguanine-DNA methyltransferase (MGMT)] were significantly associated with case status on unadjusted analyses, as well as analyses adjusted for age and advanced adenoma status (P &lt; 0.01 for at least one marker component). When applied to the validation set, a predictive model using these seven markers showed substantial accuracy for identifying cases [area under the receiver operation characteristic curve (AUC), 0.83; 95% confidence interval (CI), 0.74–0.92]. A parsimonious model using three markers performed similarly to the seven-marker model (AUC, 0.84). In summary, we found that molecular markers of carcinogenesis distinguished adenomas from patients with and without colorectal cancer. Furthermore, we speculate that prospective studies using molecular markers to identify individuals with polyps at risk for future neoplasia are warranted. Cancer Prev Res; 7(10); 1023–34. ©2014 AACR.