bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Formalism, Puritanicalism, Traditionalism: Approaches to Islamic Legal Reasoning in the 19th‐Century Russian Empire”
Authors: Spannaus Nathan 
Published: July 2014

AbstractAs early as the 1730s, the Russian imperial state sought to incorporate its Muslim subjects into the tsarist bureauacracy, first by co‐opting Muslim legal scholars, and later, beginning in 1788, by placing the whole of the ulama under government control. This led to a marginalization of Islamic legal institutions and a transformation of Islamic legal practice under Russian rule.In the early 19th century, ulama sought ways to adapt Islamic law to these institutional changes, and vibrant debates about the purpose and function of legal theory represented an important part of the religious discourse among these Muslim communities. This paper addresses the approaches of three scholars, Abu Nasr Qursawi (1776–1812), ῾Abd al‐Rahim Utiz‐Imani (1754–1834) and Fath Allah Uriwi (1767–1843), who strongly disagreed regarding issues such as the use of usul and furu῾, the permissibility of ijtihad, and the relationship between the ulama and the community.I argue that while each scholar puts forward a different approach to the law — which I term, respectively, formalism, puritanicalism and traditionalism — each of these positions represents a response to their communities' shifting circumstances under Russian rule and a way for the discursive tradition of Islamic law to continue despite the marginalization of legal institutions.
The chloroplast view of the evolution of polyploid wheat
Authors: Gornicki Piotr , Zhu Huilan , Wang Junwei , Challa Ghana S. , Zhang Zhengzhi , Gill Bikram S. , Li Wanlong 
Published: July 2014

Summary

Polyploid wheats comprise four species: Triticum turgidum (AABB genomes) and T. aestivum (AABBDD) in the Emmer lineage, and T. timopheevii (AAGG) and T. zhukovskyi (AAGGAmAm) in the Timopheevi lineage. Genetic relationships between chloroplast genomes were studied to trace the evolutionary history of the species.

Twenty‐five chloroplast genomes were sequenced, and 1127 plant accessions were genotyped, representing 13 Triticum and Aegilops species.

The A. speltoides (SS genome) diverged before the divergence of T. urartu (AA), A. tauschii (DD) and the Aegilops species of the Sitopsis section. Aegilops speltoides forms a monophyletic clade with the polyploid Emmer and Timopheevi wheats, which originated within the last 0.7 and 0.4 Myr, respectively. The geographic distribution of chloroplast haplotypes of the wild tetraploid wheats and A. speltoides illustrates the possible geographic origin of the Emmer lineage in the southern Levant and the Timopheevi lineage in northern Iraq.

Aegilops speltoides is the closest relative of the diploid donor of the chloroplast (cytoplasm), as well as the B and G genomes to Timopheevi and Emmer lineages. Chloroplast haplotypes were often shared by species or subspecies within major lineages and between the lineages, indicating the contribution of introgression to the evolution and domestication of polyploid wheats.
Transcriptome sequencing of different narrow‐leafed lupin tissue types provides a comprehensive uni‐gene assembly and extensive gene‐based molecular markers
Authors: Kamphuis Lars G. , Hane James K. , Nelson Matthew N. , Gao Lingling , Atkins Craig A. , Singh Karam B. 
Published: July 2014

SummaryNarrow‐leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome‐derived gene‐based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome‐derived markers and 66 BAC‐end sequence‐derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map.
Maternal Life Course Socio‐Economic Position and Offspring Body Composition at Birth in a Multi‐Ethnic Population
Authors: Sletner Line , Jenum Anne Karen , Mørkrid Kjersti , Vangen Siri , Holme Ingar M. , Birkeland Kåre I. , Nakstad Britt 
Published: July 2014

AbstractBackgroundSize and body composition at birth may affect long‐term health. Mean birthweight and body composition differ between ethnic groups living in Europe. We wanted to explore if this relates to differences in socio‐economic conditions in country of origin and over the maternal life course.MethodsThis is a population‐based cohort study of healthy pregnant women living in Oslo, Norway. Data on maternal early life and present socio‐economic position (SEP) were collected in early gestation, and SEP scores were extracted through two separate principal components analyses. The associations between maternal present SEP and four different offspring anthropometric measures at birth were assessed separately, stratified by maternal early life SEP (dichotomised score) and Human Development Index (HDI, a country‐level socio‐economic indicator) in the country of origin [high HDI (Reference), n = 287 and low HDI, n = 250].ResultsA strong positive association between maternal present SEP and offspring birthweight was observed if maternal early life SEP was high, but not if maternal early life SEP was low (P < 0.001 for the interaction term). This interactional effect was observed in both HDI groups. Maternal life course SEP affected offspring birthweight mainly through an effect on length and sum of skin folds. Offspring of mothers with origin from low HDI countries had smaller abdominal circumference, possibly indicating less fat‐free mass, regardless of maternal life course SEP.ConclusionOur results suggest that there are transgenerational effects of maternal past socio‐economic conditions on offspring size and body composition at birth that modify the associations with present socio‐economic factors.
Multiple-Change-Point Detection for High Dimensional Time Series via Sparsified Binary Segmentation
Authors: Cho Haeran , Fryzlewicz Piotr 
Published: July 2014

Summary
Time series segmentation, which is also known as multiple-change-point detection, is a well-established problem. However, few solutions have been designed specifically for high dimensional situations. Our interest is in segmenting the second-order structure of a high dimensional time series. In a generic step of a binary segmentation algorithm for multivariate time series, one natural solution is to combine cumulative sum statistics obtained from local periodograms and cross-periodograms of the components of the input time series. However, the standard ‘maximum’ and ‘average’ methods for doing so often fail in high dimensions when, for example, the change points are sparse across the panel or the cumulative sum statistics are spuriously large. We propose the sparsified binary segmentation algorithm which aggregates the cumulative sum statistics by adding only those that pass a certain threshold. This ‘sparsifying’ step reduces the influence of irrelevant noisy contributions, which is particularly beneficial in high dimensions. To show the consistency of sparsified binary segmentation, we introduce the multivariate locally stationary wavelet model for time series, which is a separate contribution of this work.
The Arabidopsis nitrate transporter NRT2.5 plays a role in nitrate acquisition and remobilization in nitrogen‐starved plants
Authors: Lezhneva Lina , Kiba Takatoshi , Feria‐Bourrellier Ana‐Belen , Lafouge Florence , Boutet‐Mercey Stéphanie , Zoufan Parzhak , Sakakibara Hitoshi , Daniel‐Vedele Françoise , Krapp Anne 
Published: July 2014

SummaryNitrogen is a key mineral nutrient playing a crucial role in plant growth and development. Understanding the mechanisms of nitrate uptake from the soil and distribution through the plant in response to nitrogen starvation is an important step on the way to improve nitrogen uptake and utilization efficiency for better growth and productivity of plants, and to prevent negative effects of nitrogen fertilizers on the environment and human health. In this study, we show that Arabidopsis NITRATE TRANSPORTER 2.5 (NRT2.5) is a plasma membrane‐localized high‐affinity nitrate transporter playing an essential role in adult plants under severe nitrogen starvation. NRT2.5 expression is induced under nitrogen starvation and NRT2.5 becomes the most abundant transcript amongst the seven NRT2 family members in shoots and roots of adult plants after long‐term starvation. GUS reporter analyses showed that NRT2.5 is expressed in the epidermis and the cortex of roots at the root hair zone and in minor veins of mature leaves. Reduction of NRT2.5 expression resulted in a decrease in high‐affinity nitrate uptake without impacting low‐affinity uptake. In the background of the high‐affinity nitrate transporter mutant nrt2.4, an nrt2.5 mutation reduced nitrate levels in the phloem of N‐starved plants further than in the single nrt2.4 mutants. Growth analyses of multiple mutants between NRT2.1, NRT2.2, NRT2.4, and NRT2.5 revealed that NRT2.5 is required to support growth of nitrogen‐starved adult plants by ensuring the efficient uptake of nitrate collectively with NRT2.1, NRT2.2 and NRT2.4 and by taking part in nitrate loading into the phloem during nitrate remobilization.
A new background distribution‐based active contour model for three‐dimensional lesion segmentation in breast DCE‐MRI
Authors: Liu Hui , Liu Yiping , Zhao Zuowei , Zhang Lina , Qiu Tianshuang 
Published: July 2014

Purpose:To develop and evaluate a computerized semiautomatic segmentation method for accurate extraction of three‐dimensional lesions from dynamic contrast‐enhanced magnetic resonance images (DCE‐MRIs) of the breast.Methods:The authors propose a new background distribution‐based active contour model using level set (BDACMLS) to segment lesions in breast DCE‐MRIs. The method starts with manual selection of a region of interest (ROI) that contains the entire lesion in a single slice where the lesion is enhanced. Then the lesion volume from the volume data of interest, which is captured automatically, is separated. The core idea of BDACMLS is a new signed pressure function which is based solely on the intensity distribution combined with pathophysiological basis. To compare the algorithm results, two experienced radiologists delineated all lesions jointly to obtain the ground truth. In addition, results generated by other different methods based on level set (LS) are also compared with the authors’ method. Finally, the performance of the proposed method is evaluated by several region‐based metrics such as the overlap ratio.Results:Forty‐two studies with 46 lesions that contain 29 benign and 17 malignant lesions are evaluated. The dataset includes various typical pathologies of the breast such as invasive ductal carcinoma, ductal carcinomain situ, scar carcinoma, phyllodes tumor, breast cysts, fibroadenoma, etc. The overlap ratio for BDACMLS with respect to manual segmentation is 79.55% ± 12.60% (mean ± s.d.).Conclusions:A new active contour model method has been developed and shown to successfully segment breast DCE‐MRI three‐dimensional lesions. The results from this model correspond more closely to manual segmentation, solve the weak‐edge‐passed problem, and improve the robustness in segmenting different lesions.
An initial study on the estimation of time‐varying volumetric treatment images and 3D tumor localization from single MV cine EPID images
Authors: Mishra Pankaj , Li Ruijiang , Mak Raymond H. , Rottmann Joerg , Bryant Jonathan H. , Williams Christopher L. , Berbeco Ross I. , Lewis John H. 
Published: July 2014

Purpose:In this work the authors develop and investigate the feasibility of a method to estimate time‐varying volumetric images from individual MV cine electronic portal image device (EPID) images.Methods:The authors adopt a two‐step approach to time‐varying volumetric image estimation from a single cine EPID image. In the first step, a patient‐specific motion model is constructed from 4DCT. In the second step, parameters in the motion model are tuned according to the information in the EPID image. The patient‐specific motion model is based on a compact representation of lung motion represented in displacement vector fields (DVFs). DVFs are calculated through deformable image registration (DIR) of a reference 4DCT phase image (typically peak‐exhale) to a set of 4DCT images corresponding to different phases of a breathing cycle. The salient characteristics in the DVFs are captured in a compact representation through principal component analysis (PCA). PCA decouples the spatial and temporal components of the DVFs. Spatial information is represented in eigenvectors and the temporal information is represented by eigen‐coefficients. To generate a new volumetric image, the eigen‐coefficients are updated via cost function optimization based on digitally reconstructed radiographs and projection images. The updated eigen‐coefficients are then multiplied with the eigenvectors to obtain updated DVFs that, in turn, give the volumetric image corresponding to the cine EPID image.Results:The algorithm was tested on (1) Eight digital eXtended CArdiac‐Torso phantom datasets based on different irregular patient breathing patterns and (2) patient cine EPID images acquired during SBRT treatments. The root‐mean‐squared tumor localization error is (0.73 ± 0.63 mm) for the XCAT data and (0.90 ± 0.65 mm) for the patient data.Conclusions:The authors introduced a novel method of estimating volumetric time‐varying images from single cine EPID images and a PCA‐based lung motion model. This is the first method to estimate volumetric time‐varying images from single MV cine EPID images, and has the potential to provide volumetric information with no additional imaging dose to the patient.
Synchronization of North Pacific and Greenland climates preceded abrupt deglacial warming
Authors: Praetorius Summer K. , Mix Alan C. 
Published: July 2014

Climates conspire together to make big changes
The regional climates of the North Pacific and North Atlantic fluttered between synchrony and asynchrony during the last deglaciation, with correspondingly more and less intense effects on the rest of the world, researchers have found. The climate system can be highly nonlinear, meaning that small changes in one part can lead to much larger changes elsewhere. This type of behavior is especially evident during transitions from glacial to interglacial conditions, when climate is affected by a wide variety of time-varying influences and is relatively unstable. Praetorius and Mix present a record of North Pacific climate over the past 18,000 years. When the climates of the more local high-latitude Pacific and Atlantic sectors varied in parallel, large, abrupt climate fluctuations occurred on a more global scale.

Science
, this issue p.
444
A Novel Live Vector Group A StreptococcalemmType 9 Vaccine Delivered Intranasally Protects Mice against Challenge Infection withemmType 9 Group A Streptococci
Authors: Wozniak Aniela , García Patricia , Geoffroy Enrique A. , Aguirre Daniel B. , González Samantha A. , Sarno Victoria A. , Dale James B. , Salazar-Echegarai Francisco J. , Vera Andrea , Bueno Susan M. , Kalergis Alexis M. 
Published: July 2014

ABSTRACTThe availability of a protective vaccine againstStreptococcus pyogenes(group AStreptococcus[GAS]) is a priority for public health worldwide. Here, we have generated six live vaccine strains, each engineered to express an N-terminal M protein peptide from one of six of the most prevalentemmtypes of GAS (M1, M2, M4, M9, M12, and M28). The vaccine strains are based on a food-gradeLactococcus lactisstrain and do not bear any antibiotic resistance. Mice immunized with the vaccine strain expressing the M9 peptide (termed here theL. lactisM9 strain) showed high titers of serum antibodies when delivered intranasally. Mice immunized with theL. lactisM9 strain were protected against infection after intranasal challenge with type 9 streptococci. Several parameters of disease, such as weight loss, body temperature, colony counts in mouth washes, and lung histology, were significantly improved in immunized mice compared to naive control mice. Our results indicate that intranasal delivery of theL. lactisM9 strain live bacterial vaccine induced GAS-specific IgG titers, prevented pharyngeal colonization of GAS, and protected mice from disease upon challenge. The design of this vaccine prototype may provide a lower cost alternative to vaccines comprised of purified recombinant proteins.
Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant Growth-Promoting Bacterium Isolated from Rice Rhizosphere
Authors: Wang Yinghuan , Wang Xiaoyi , Greenfield Paul , Jin Decai , Bai Zhihui 
Published: July 2014

ABSTRACT

Bacillus amyloliquefaciens
strain EBL11 is a bacterium that can promote plant growth by inhibiting the growth of fungi on plant surfaces and providing nutrients as a nonchemical biofertilizer. The estimated genome of this strain is 4.05 Mb in size and harbors 3,683 coding genes (CDSs).
Detection of Mycobacterium leprae by PCR Testing of Sputa from a Patient with Pulmonary Cryptococcus Coinfection in Northern Australia
Authors: Edwards Laura J. , Price Ric N. , Krause Vicki L. , Huffam Sarah E. , Globan Maria , Fyfe Janet , Hajkowicz Krispin M. 
Published: July 2014

ABSTRACT

A case of fever, sepsis, and chest lesions evident on a computed tomography scan of an indigenous man in northern Australia following burns to the feet is described. Sputum PCR testing revealed
Mycobacterium leprae
, and a fine-needle aspirate of the chest lesions demonstrated
Cryptococcus
coinfection.
Using Crude Whole-Genome Assemblies of Neisseria gonorrhoeae as a Platform for Strain Analysis: Clonal Spread of Gonorrhea Infection in Saskatchewan, Canada
Authors: Vidovic Sinisa , Caron Carolyn , Taheri Ali , Thakur Sidharath D. , Read Timothy D. , Kusalik Anthony , Dillon Jo-Anne R. 
Published: July 2014

ABSTRACT

Using crude whole-genome assemblies, we analyzed 25 isolates of
Neisseria gonorrhoeae
by using a high-resolution single nucleotide polymorphism (SNP) approach for nine housekeeping genes, characterizing
penA
alleles, and antimicrobial susceptibility phenotypes coupled with population structure analysis. Two clonal complexes, characterized by their spatial and geographical persistence, were identified. In addition, the clonal spread of penicillin-resistant/intermediate phenotypes and a novel introduction of the azithromycin resistance phenotype in Saskatchewan, Canada, were ascertained using this method.
Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?
Authors: Spinali Sébastien , van Belkum Alex , Goering Richard V. , Girard Victoria , Welker Martin , Van Nuenen Marc , Pincus David H. , Arsac Maud , Durand Géraldine 
Published: July 2014

ABSTRACT
The integration of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has revolutionized species identification of bacteria, yeasts, and molds. However, beyond straightforward identification, the method has also been suggested to have the potential for subspecies-level or even type-level epidemiological analyses. This minireview explores MALDI-TOF MS-based typing, which has already been performed on many clinically relevant species. We discuss the limits of the method's resolution and we suggest interpretative criteria allowing valid comparison of strain-specific data. We conclude that guidelines for MALDI-TOF MS-based typing can be developed along the same lines as those used for the interpretation of data from pulsed-field gel electrophoresis (PFGE).
False-Positive Results for Rapid Diagnostic Tests for Malaria in Patients with Rheumatoid Factor
Authors: Lee Jong-Han , Jang Jin Woo , Cho Chi Hun , Kim Ju Yeon , Han Eun Taek , Yun Seung Gyu , Lim Chae Seung 
Published: July 2014

ABSTRACT

Four different rapid diagnostic tests (RDTs) for malaria were evaluated by testing 82 healthy control patients, 89
Plasmodium vivax
-infected patients, and 92 rheumatoid factor (RF)-positive nonmalaria patients. The false-positive rate ranged from 2.2% to 13% in RF-positive patients. High RF levels are associated with malaria RDT false positivity.
Comparison of Two Commercial Real-Time PCR Assays for Detection of Dengue Virus in Patient Serum Samples
Authors: Saengsawang J. , Nathalang O. , Kamonsil M. , Watanaveeradej V. 
Published: July 2014

ABSTRACT

This study evaluated and compared the performance of two real-time PCR assays using nested reverse transcription (RT)-PCR as the reference method. Among 117 nested RT-PCR-positive cases, the
ab
TES DEN 5 qPCR kit detected 97.4% of dengue virus (DENV) infections, while the innuDETECT Dengue TwoStep assay did so for 44.4%. Sensitivity varied by infecting serotype and the stage of infection. The
ab
TES kit has the potential to replace nested RT-PCR for the rapid diagnosis of DENV infection.