bluuebunny/crossref_metadata_2025_split huggingface dataset:
Backscattering intensity measurements in optical coherence tomography as a method to identify parathyroid glands
Authors: Sommerey Sandra , Ladurner Roland , Al Arabi Norah , Mortensen Uwe , Hallfeldt Klaus , Gallwas Julia 
Published: May 2015

Background and ObjectivePrevious studies have shown that the use of optical coherence tomography (OCT) permits the differentiation between parathyroid tissue, thyroid tissue, lymph nodes and adipose tissue. We investigated the backscattering intensity profiles of OCT images in order to determine whether significant differences between these tissue types exist.MethodsMean backscattering intensity profiles were obtained from OCT images of parathyroid glands, thyroid tissue, lymph nodes and adipose tissue. The profiles were analyzed employing Fisher's Linear Discriminant Analysis (LDA). The results were cross validated employing improved parameter estimation techniques.ResultsMean backscattering intensity profiles from 300 OCT images of 34 patients undergoing thyroid or parathyroid surgery were analyzed. The overall rate of correct classifications was 96.15%. The cross validation employing improved parameter estimation techniques yielded results identical to those derived from Fisher's LDA.ConclusionBesides the individual assessment of OCT images by interpreting morphological criteria, backscattering intensity measurements can reliably distinguish between different tissue entities. Lasers Surg. Med. 47:526–532, 2015. © 2015 Wiley Periodicals, Inc.
Minimally symptomatic mcardle disease, expanding the genotype–phenotype spectrum
Authors: Petrou Petros , Pantzaris Marios , Dionysiou Maria , Drousiotou Anthi , Kyriakides Theodoros 
Published: May 2015

ABSTRACTIntroduction: We report the clinical, biochemical, and molecular findings in a Cypriot family with minimally symptomatic McArdle disease. Methods: Myophosphorylase in muscle was assessed by histochemistry, quantitative spectrophotometry, and western blot analysis. Mutation identification was performed by PCR amplification of all PYGM exons, followed by bidirectional sequencing. Screening for the new mutation was performed by restriction enzyme analysis. Results: We found that a novel c.1151C>T transition in exon 10 of the myophosphorylase gene (PYGM) is associated with minimally symptomatic McArdle disease. Homozygous carriers displayed an ischemic exercise response characterized by a blunted increase in post‐exercise blood lactate levels in conjunction with an exaggerated increase in ammonia. Myophosphorylase activity in muscle was 3.75% of normal, whereas the size and abundance of the enzyme were unaffected. Conclusions: These findings expand the genotype–phenotype spectrum of McArdle disease and suggest that enzymatic activity as low as 4% may be sufficient to ameliorate the phenotype. Muscle Nerve 52: 891–895, 2015
Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of β‐turns in peptide immunogenicity
Authors: Shukla Rashmi Tambe , Sasidhar Yellamraju U. 
Published: May 2015

ABSTRACTEarlier immunological experiments with a synthetic 36‐residue peptide (75‐110) from Influenza hemagglutinin have been shown to elicit anti‐peptide antibodies (Ab) which could cross‐react with the parent protein. In this article, we have studied the conformational features of a short antigenic (Ag) peptide (98YPYDVPDYASLRS110) from Influenza hemagglutinin in its free and antibody (Ab) bound forms with molecular dynamics simulations using GROMACS package and OPLS‐AA/L all‐atom force field at two different temperatures (293 K and 310 K). Multiple simulations for the free Ag peptide show sampling of ordered conformations and suggest different conformational preferences of the peptide at the two temperatures. The free Ag samples a conformation crucial for Ab binding (β‐turn formed by “DYAS” sequence) with greater preference at 310 K while, it samples a native‐like conformation with relatively greater propensity at 293 K. The sequence “DYAS” samples β‐turn conformation with greater propensity at 310 K as part of the hemagglutinin protein also. The bound Ag too samples the β‐turn involving “DYAS” sequence and in addition it also samples a β‐turn formed by the sequence “YPYD” at its N‐terminus, which seems to be induced upon binding to the Ab. Further, the bound Ag displays conformational flexibility at both 293 K and 310 K, particularly at terminal residues. The implications of these results for peptide immunogenicity and Ag–Ab recognition are discussed. Proteins 2015; 83:1352–1367. © 2015 Wiley Periodicals, Inc.
Identification of universal selectivity‐determining positions in cytochrome P450 monooxygenases by systematic sequence‐based literature mining
Authors: Gricman Łukasz , Vogel Constantin , Pleiss Jürgen 
Published: May 2015

ABSTRACTCytochrome P450 monooxygenases (CYPs) are a large, highly diverse protein family with a common fold. The sequences, structures, and functions of CYPs have been extensively studied resulting in more than 53,000 scientific articles. A sequence‐based literature mining algorithm was designed to systematically analyze this wealth of information on SNPs, designed mutations, structural interactions, or functional roles of individual residues. Structurally corresponding positions in different CYPs were compared and universal selectivity‐determining positions were identified. Based on the Cytochrome P450 Engineering Database (www.CYPED.BioCatNet.de) and a standard numbering scheme for all CYPs, 4000 residues in 168 CYPs mentioned in 2400 articles could be assigned to 440 structurally corresponding standard positions of the CYP fold, covering 96% of all standard positions. Seventeen individual standard positions were mentioned in the context of more than 32 different CYPs. The majority of these most frequently mentioned positions are located on the six substrate recognition sites and are involved in control of selectivity, such as the well‐studied position 87 in CYP102A1 (P450BM‐3) which was mentioned in the articles on 63 different CYPs. The recurrent citation of the 17 frequently mentioned positions for different CYPs suggests their universal functional relevance. Proteins 2015; 83:1593–1603. © 2015 Wiley Periodicals, Inc.
Agreement between preoperative transvaginal ultrasound and intraoperative macroscopic examination for assessing myometrial infiltration in low‐risk endometrioid carcinoma
Authors: Pineda L. , Alcázar J. L. , Caparrós M. , Mínguez J. A. , Idoate M. A. , Quiceno H. , Solórzano J. L. , Jurado M. 
Published: May 2015

AbstractObjectiveTo compare diagnostic performance of preoperative transvaginal ultrasound (TVS) and intraoperative macroscopic examination for determining myometrial infiltration in women with low‐risk endometrial cancer, and to estimate the agreement between the two methods.MethodsThis was a single‐center observational study comprising women with preoperative diagnosis of well‐ or moderately differentiated endometrioid carcinoma of the endometrium. All women underwent preoperative TVS by a single examiner. According to the examiner's subjective impression, myometrial infiltration was stated as ≥ 50% or < 50%. Surgical staging was performed in all cases. Intraoperative macroscopic examination of the removed uterus was performed by pathologists who were unaware of the ultrasound findings, and myometrial infiltration was stated as ≥ 50% or < 50%. Definitive histological diagnosis of myometrial infiltration was made by frozen section analysis and was used as the gold standard. Sensitivity and specificity with 95% CIs were calculated for TVS and intraoperative macroscopic inspection and compared using McNemar's test. Agreement between TVS and intraoperative macroscopic inspection was estimated using Cohen's kappa index (κ) and percentage of agreement.ResultsOf 209 eligible women, 152 were ultimately included. Mean (± SD) age was 60.9 ± 10.2 years, with a range of 32–91 years. Definitive histological diagnosis revealed that myometrial infiltration was < 50% in 114 women and ≥ 50% in 38 women. Sensitivity and specificity of TVS for detecting deep myometrial infiltration were 81.6% and 89.5%, respectively, whereas the respective values for intraoperative macroscopic examination were 78.9% and 90.4% (McNemar's test, P > 0.05 when comparing TVS and intraoperative macroscopic examination). Agreement between methods was moderate with κ = 0.54 (95% CI, 0.39–0.69) and percentage of agreement of 82%.ConclusionsAlthough the agreement between preoperative TVS and intraoperative macroscopic examination for detecting deep myometrial infiltration was only moderate, both methods had similar accuracy when compared with frozen section histology. Preoperative TVS might reasonably be proposed as a method for assessing myometrial infiltration as an alternative to intraoperative macroscopic examination, especially when performed by an experienced examiner and image quality is not poor. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.
Transvaginal/transrectal ultrasound for preoperative identification of high‐risk cases in well‐ or moderately differentiated endometrioid carcinoma
Authors: Alcázar J. L. , Pineda L. , Caparrós M. , Utrilla‐Layna J. , Juez L. , Mínguez J. A. , Jurado M. 
Published: May 2015

ABSTRACTObjectiveTo evaluate the role of transvaginal/transrectal ultrasound for preoperative identification of high‐risk cases among women with well‐differentiated (G1) or moderately differentiated (G2) endometrioid carcinoma of the endometrium.MethodsThis was a single‐center prospective observational cohort study comprising a consecutive series of women with a preoperative diagnosis of G1/G2 endometrioid carcinoma of the endometrium. All women underwent transvaginal or transrectal ultrasound examination by a single examiner. According to the examiner's subjective impression, patients were considered high risk if myometrial infiltration was ≥ 50% and/or involvement of the cervix and/or adnexa was suspected. FIGO surgical staging was performed in all cases. According to definitive histological data regarding myometrial infiltration, cervical involvement and adnexal involvement, women were classified as low risk (no myometrial infiltration, no cervical involvement and no adnexal involvement) or high risk (myometrial infiltration ≥ 50% and/or cervical involvement and/or adnexal involvement). Sensitivity, specificity and positive (LR+) and negative (LR−) likelihood ratios, with 95% CIs, of transvaginal/transrectal ultrasound for detecting stage ≥ IB were calculated. Agreement between risk determined by transvaginal/transrectal ultrasound and postoperative definitive histology was calculated.ResultsOf 209 eligible women, 169 were included in the study. Mean (± SD) age of the study cohort was 60.7 ± 10.3 years, with a range of 32–91 years. Sensitivity, specificity, LR+ and LR− of transvaginal/transrectal ultrasound identifying high‐risk cases according to myometrial infiltration, cervical involvement and adnexal involvement were 78.0% (95% CI, 63.7–88.0%), 89.1% (95% CI, 81.7–93.8%), 7.14 (95% CI, 4.19–12.18) and 0.25 (95% CI, 0.15–0.42), respectively.ConclusionsPreoperative transvaginal/transrectal ultrasound may play a significant role in identifying high‐risk cases among those with G1/G2 endometrioid carcinoma of the endometrium according to preoperative biopsy, and could be a useful test in this clinical setting. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.
Predictive accuracy of second‐trimester uterine artery Doppler indices for stillbirth: a systematic review and meta‐analysis
Authors: Allen R. E. , Morlando M. , Thilaganathan B. , Zamora J. , Khan K. S. , Thangaratinam S. , Bhide A. 
Published: May 2015

AbstractObjectiveTo assess the predictive accuracy for stillbirth of second‐trimester uterine artery Doppler.MethodsWe searched MEDLINE, EMBASE and The Cochrane Library databases from inception until March 2015 without language restrictions. The included studies were those that assessed the association of abnormal uterine artery Doppler parameters and stillbirth. Two independent reviewers selected the studies, extracted data and assessed quality. Results for studies that were performed in the second trimester were pooled and summary estimates of sensitivity, specificity, likelihood ratios and their 95% confidence intervals were obtained. An overall summary of test accuracy was provided by the diagnostic odds ratio. Subgroup analysis was performed according to whether the study population was high risk or unselected.ResultsLiterature searches returned 338 relevant citations with 32 considered in full. Thirteen studies met our search criteria (85 845 women, 508 stillbirths) and were included in the review. Bivariate pooled estimate for sensitivity was 65% (95% CI, 38–85%) and for specificity 82% (95% CI, 72–88%). The positive likelihood ratio was 3.5 (95% CI, 2.3–5.5) and negative likelihood ratio 0.43 (95% CI, 0.22–0.85). The diagnostic odds ratio was 8.3 (95% CI, 3.0–22.4). Heterogeneity was high in the studies of high‐risk women.ConclusionsAbnormal uterine artery Doppler indices are associated with a three‐ to four‐fold increase in the risk of stillbirth. The heterogeneity was particularly high in the high‐risk group rendering it impossible to draw firm conclusions. In view of this, there is a role for individual patient data meta‐analysis to define which Doppler parameter and threshold value should be measured. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.
Regional Structural Analysis and Reinterpretation in the Bonai-Keonjhar Belt, Singhbhum Craton: Implication for Revision of the Lithostratigraphic Succession
Authors: Mohakul J. P. , Bhutia S. P. 
Published: May 2015

Abstract:
The Mesoarchaean Iron Ore Group (IOG) of rocks in Bonai-Keonjhar belt is disposed in a horseshoe shaped synclinorium structure in the western part of the Singhbhum Craton. Morphology of this synclinorium is expressed by a near continuous western ridge and dissected eastern highlands with the broad Jamda-Koira valley at the centre. Detailed structural analysis in the northern part of the belt suggests that the synclinorium is in fact a series of NE-SW to NNESSW trending shallow plunging, second generation (D2) syncline and anticline which have overturned, inclined, relatively tight geometry in the western part and upright, open to gentle in the eastern part. This structure is clearly manifested by synclinal ridges and anticlinal valleys. Evidence of an early deformational event (D1) manifested by the presence of isoclinal folds on outcrop scale has been recorded. D1 and D2 are near co-axial. The last deformational event (D3) has led to dome and basin interference pattern due to cross folding along NW-SE striking axial planes. The volcano-sedimentary package in the belt commenced with platformal package represented by basic volcanic-quartzite association. The Bonai range volcanic, Nuakot volcanic and the Jagannathpur volcanic occurring in the western, southern and eastern parts of the belt has been interpreted to be correlatable representing the basal volcanic suite. The linear body of basic volcanic occurring at the central part of the belt is found to be occupying the core part of a shallow plunging anticlinal axial trace and thus has also been equated with the basal volcanic suite. There is but only one major BIF horizon in the Bonai-Keonjhar belt which has been structurally repeated across the belt, BIF occurring as NNE-SSW trending synclinal ridges flanked on either side by the older phyllitic sequences.
The Cauvery Suture Zone: Map of Structural Architecture and Recent Advances
Authors: Chetty T. R. K. 
Published: May 2015

Abstract
A new structural-architectural map of the Cauvery Suture Zone revealing broad lithology, shear zones, fold forms, foliation trajectories and other structural fabrics, along with kinematic displacements has been brought out by making use of available data sets to fulfill the essential requirement of all geoscientists. Recent advances in understanding the tectonothermal history of the CSZ are also highlighted.
Climatically Induced Levee Break and Flood Risk Management of the Gorakhpur Region, Rapti River Basin, Ganga Plain, India
Authors: Singh Dhruv Sen , Prajapati Shailendra Kumar , Singh Prashant , Singh Kailash , Kumar Dhirendra 
Published: May 2015

Abstract
A densely populated city, Gorakhpur, located on the bank of Rapti river in the Ganga plain, is frequently affected by flooding. The Rapti river exhibits narrow channel within wide valley, channel bars, natural levee and river terraces. Artificial levees are constructed in the valley during low discharge period to mitigate the flood and also to provide the additional land to the society. These levees break during prolonged heavy rain and induce the catastrophic flood because it is not constructed by analyzing the capacity of the bracketed channel to accommodate the high discharge of the river. The precipitation, discharge, sediment load, and river water levels are correlated by making graphs between these parameters to analyze and identify the threshold limits and main reasons for flood. It explains that discharge and sediment load increases with precipitation during monsoon season, whereas the water storage capacity of the river decreases due to siltation and artificial levee. Hence, during heavy rain in this region, water rises in the channel, which either overtops the bank or breaks the levee and creates the flood.
Flood inundation map was prepared using GIS techniques from 70 m base level to 81.5 m high level, which indicate the inundated area with every 1-2.5 m rise in the Rapti river water level. Rating curves and flood frequency curves have been prepared to identify the recurrence interval for major floods. It is concluded that prolong heavy precipitation, discharge variability of the river, siltation in the river bed, artificial levee, and anthropogenic impacts on younger river terraces and river valley leads to flood. Its affect is devastating when water level, discharge and sediment loads are above 77 m, 5000 m3/sec, and 5 metric tones respectively. The flood inundation map and recurrence interval are useful parameters for flood risk management, whereas the upland terrace is flood-free surface suitable for settlement. This study can be used as a model for other flood prone regions.
Mineralogy and Geochemistry of Fenitized Nephelinites of the Amba Dongar Complex, Gujarat
Authors: Viladkar S. G. 
Published: May 2015

Abstract
In the Amba Dongar sub-volcanic complex, nephelinite plugs and dikes of phonolites were emplaced before the carbonatites. The fenitizing fluids released from carbonatite magma caused extensive fenitization in nephelinites with intensity varying from mild carbonatization (CO2 metasomatism accompanied by hematitization) in the distal outcrops, to a high degree of K-fenitization (feldspathization, phlogopitization) in outcrops closer to the carbonatite bodies. The intensely fenitized rocks are the xenoliths of nephelinites within the sövite. The primary texture of the nephelinites is mostly preserved, but the highly feldspathised nephelinites look more like nepheline syenite with water clear poikilitic K-feldspar in the groundmass. Invariably, nepheline is largely replaced by hydromuscovite and to lesser extent by zeolite (mainly natrolite and phillipsite). Cancrinite is also noticed in some thin sections. Pyroxene has been partially or totally replaced by phlogopite while the groundmass has been feldspathised with formation of poikilitic Kfeldspar (Or&gt;90%). On the basis of mineralogical study, back scattered electron images and elemental mapping on microprobe, three processes of fenitization, namely, K-metasomatism (formation of hydromuscovite, phlogopite and Kfeldspar), zeolitization and CO2-metasomatism along with hematitization are identified. K-feldspar in the norms of fenitized nephelinite varies from 9% to 36%. Fenitized nephelinites show enrichment in trace and rare earth elements over the unfenitized nephelinites.
Treatment of stress urinary incontinence with a generic transobturator tape
Authors: Abougamrah Amgad , Ibrahim Moustafa , Elsabaa Haitham , Ellaithy Mohamed , Sweed Mohamed 
Published: May 2015

AbstractObjectiveTo evaluate the efficacy and safety of using a generic tape tailored from type 1 monofilamentous, macroporous polypropylene mesh during transobturator tape (TOT) surgery.MethodsA prospective study was performed in a tertiary center in Cairo, Egypt, between July 2004 and December 2013. Women with stress urinary incontinence scheduled for TOT surgery using the outside‐in technique were recruited. Monarc tape was used in all patients until November 2005, after which it was used for patients who could afford it only; generic tape was used in the other patients. The primary outcome measures were the objective and subjective cure rates.ResultsOverall, 431 women were included in analyses. After 5 years of follow‐up, objective cure was achieved in 143 (94.1%) of 152 women who received Monarc tape and 249 (89.2%) of 279 who received the generic tape (P = 0.135). Subjective cure was achieved in 121 (79.6%) women who received the Monarc tape and 236 (84.6%) women who received the generic tape (P = 0.229). There were no significant between‐group differences in postoperative urgency, de novo urgency, urge incontinence, voiding dysfunction, urinary retention, vaginal erosion, or the frequency of TOT‐related reoperation or repeat anti‐incontinence procedures.ConclusionThe TOT outside‐in procedure can be easily, safely, and effectively performed in low‐resource settings using a generic polypropylene tape.
Participatory Methodologies with Victims: An Emancipatory Approach to Transitional Justice Research
Authors: Robins Simon , Wilson Erik 
Published: May 2015

Abstract
Transitional justice seeks to address legacies of violence around political transition from authoritarianism and armed conflict. It does so in ways driven by a global discourse that is prescriptive and often remote from the contexts in which it is articulated and the populations it claims to serve. Transitional justice is also embedded in teleological liberal approaches to transition, with a perceived endpoint of liberal democracy. Critical approaches to transitional justice have used qualitative methodologies to understand the agendas of those—notably victims of violence—that transitional justice foregrounds, and to demonstrate that transitional justice mechanisms often serve elite agendas, while minimizing the agency of socially excluded populations. An alternative, minimally explored route to victim engagement with such processes has been the mobilization of victims and victim organizations, an emancipatory approach that seeks to provide a space for victims to engage in transitional justice debates on their own terms. Here, a research engagement with a victims’ organization through a Participatory Action Research modality is described in which researchers support victim engagement in peer research to catalyze a social movement of victims in post-conflict Nepal.
Towards a New Study of the So-CalledTārīkh al-fattāsh
Authors: Nobili Mauro , Mathee Mohamed Shahid 
Published: May 2015

AbstractThis article advances a new theory about the composition of the chronicle generally referred to asTārīkh al-fattāsh.TheTārīkh al-fattāsh, allegedly written in the sixteenth-seventeenth century, is one of the most famous chronicles on which scholars have relied for information about West Africa’s pre-colonial history. However, there are still many puzzling issues and unsolved problems associated with this work, as edited by Octave V. Houdas and Maurice Delafosse in the early twentieth century. This analysis uses unexplored manuscripts that were either unknown or unavailable to previous scholars, and advances a new theory on the genesis and authorship of the chronicle: that the edited text in fact conflates two texts, a seventeenth-century chronicle and a nineteenth century one.