bluuebunny/crossref_metadata_2025_split huggingface dataset:
The efficacy of plasma biomarkers in early diagnosis of Alzheimer's disease
Authors: Wang Tao , Xiao Shifu , Liu Yuanyuan , Lin Zhiguang , Su Ning , Li Xia , Li Guanjun , Zhang Mingyuan , Fang Yiru 
Published: December 2013

BackgroundEarly diagnosis of Alzheimer's disease (AD) is imperative for the prevention of disease progression and the development of effective treatments.ObjectiveClinically, AD diagnosis has been based on adherence to clinical criteria. It has recently been proposed that diagnostic criteria should also incorporate biomarker findings. However, the most studied candidates or group of candidates for AD biomarkers, including pathological processes and proteins, needs further research. The current study aimed to investigate the capabilities of the following plasma proteins in the diagnosis of AD and amnesia mild cognitive impairment (aMCI): peripheral interleukin (IL) 10, IL‐6, amyloid‐β (Aβ) 40, Aβ42, phosphorylated tau 181, and total tau.MethodsIn addition to 122 normal control (NC) group, 97 AD patients and 54 aMCI patients were recruited for this study. An enzyme‐linked immunosorbent assay was used to analyze the concentration of the following blood plasma biomarkers: IL‐10, IL‐6, Aβ40, Aβ42, phosphorylated tau 181, and total tau.ResultsA one‐way analysis of variance (one‐factor analysis of variance) of Aβ40 and IL‐10 levels revealed a statistically significant difference between the three groups (p < 0.001 and p = 0.020). Using Aβ40 ≥ 42.70 pg/ml as the cut‐off point, the sensitivity of the ability of Aβ40 to discriminate between AD and NC groups was 80.0%, and specificity was 69.6%.ConclusionsThe plasma Aβ40 biomarker was able to distinguish between AD and NC groups. However, the plasma biomarkers in the present research were not able to distinguish between aMCI and NC groups. Copyright © 2013 John Wiley & Sons, Ltd.
Interventions to reduce the number of falls among older adults with/without cognitive impairment: an exploratory meta‐analysis
Authors: Guo Jong‐Long , Tsai Yi‐Ying , Liao Jung‐Yu , Tu Hsiu‐Mei , Huang Chiu‐Mieh 
Published: December 2013

ObjectiveThis exploratory meta‐analysis aimed to examine and compare the effective interventions to prevent falls among institutionalized/non‐institutionalized older adults without cognitive impairment with interventions to prevent falls for older adults with cognitive impairment.DesignA database search identified 111 trials published between January 1992 and August 2012 that evaluated fall‐prevention interventions among institutionalized/non‐institutionalized older adults with and without cognitive impairment as measured by valid cognition scales.ResultsExercise alone intervention was similar effective on reducing the numbers of falls among older adults without cognitive impairment regardless of setting (non‐institutionalized: OR = 0.783, 95% confidence interval (CI) = 0.656–0.936; p = 0.007 institutionalized: OR = 0.799, 95% CI = 0.646–0.988, p = 0.038). Vitamin D/calcium supplementation had a positive effect on the reduction of numbers of falls among non‐institutionalized older adults without cognitive impairment (OR = 0.789, 95% CI = 0.631–0.985, p = 0.036), as did home visits and environment modification (OR = 0.751, 95% CI = 0.565–0.998, p = 0.048). Exercise alone, exercise‐related multiple interventions, and multifactorial interventions were associated with positive outcomes among both institutionalized and non‐institutionalized older adults with cognitive impairment, but studies are limited.ConclusionsSingle exercise interventions can significantly reduce numbers of falls among older adults with and without cognitive impairment in institutional or non‐institutional settings. Vitamin D and calcium supplementation, home visits, and environment modification can reduce the risk of falls among older adults in non‐institutional settings. Exercise‐related multiple interventions and multifactorial interventions may only be effective for preventing falls in older adults with cognitive impairment. Copyright © 2013 John Wiley & Sons, Ltd.
Drug resistance mutations and genetic diversity in adults treated for HIV type 1 infection in Mauritania
Authors: Fall‐Malick F‐Zahra , Tchiakpé Edmond , Ould Soufiane Sid'Ahmed , Diop‐Ndiaye Halimatou , Mouhamedoune Baye Abderrahmane , Ould Horma Babana Abdallah , Kane Coumba Touré , Lo Baidy , Mboup Souleymane 
Published: December 2013

AbstractThe aim of this cross‐sectional study was to evaluate the drug resistance mutationprofile observed in patients receiving antiretroviral therapy with virological failure and to document the HIV‐1 genetic diversity in Mauritania. Eighty‐six subjects were included and 65 samples were amplified successfully and sequenced. HIV‐1 genotyping was performed using the Agence Nationale de Recherche sur le SIDA AC11 resistance procedure. The median treatment duration was 32 months (range: 6–88) and the median viral load, 5 log10 copies/ml (range: 3.13–7). Fifty‐nine patients (90.8%) were on first line regimens including 32.0% (19/59) on triomune fixed‐dose and six on second‐line therapy with NonNucleoside Reverse Transcriptase plus a protease inhibitor. Forty‐seven patients (72.3%) had at least one drug resistance mutation including 73.0% (43/59) on first‐line therapy. For the second‐line, one out of six patients presented resistance mutations and only one presented PI DRM. Overall, the most common DRMs detected were M184V/I (n = 32; 49.2%), K103N (n = 28; 43%), and Y181C (n = 13; 20%). Thymidine Analog Mutations (TAMs) were found in 26.0% (n = 17) of strains and the most common was T215Y (n = 11, 16.9%). Phylogenetic analysis revealed 17 HIV‐1 variants with the predominance of CRF02_AG (n = 42; 64.6%). A high rate of DRM was found in this study and shows the potential need for a structured virological surveillance including viral load quantification and genotyping. Further studies may also be needed in regards to the great variability of HIV‐1 strains in Mauritania. J. Med. Virol. 86:404–410, 2014. © 2013 Wiley Periodicals, Inc.
Hepatic resection for colorectal metastases
Authors: Frankel Timothy L. , D'Angelica Michael I. 
Published: December 2013

AbstractThe liver represents a common site for metastasis in colorectal cancer. Improvements in patient selection and surgical techniques has resulted in improved outcomes following hepatic metastasectomy with large series reporting 5‐ and 10‐year overall survival rates of 40% and 20%, respectively. In recent years, criteria for resectability has expanded with the use of forced liver hypertrophy and staged resection. The role of perioperative chemotherapy remains controversial with a slight increase in survival and operative morbidity. J. Surg. Oncol. 2014 109:2–7. © 2013 Wiley Periodicals, Inc.
Pretreatment selection of regimen according to genetic analysis improves the efficacy of chemotherapy in the first line treatment of metastatic colorectal cancer
Authors: Kim Do Yoon , Paek Tae Yoon , Oh Seung Yeop , Kim Young Bae , Lee Je Hee , Lee Mi Young , Choi Zi Sun , Suh Kwang Wook 
Published: December 2013

Background and ObjectivesMetastatic colon cancer patients are treated with the chemotherapy regimens, FOLFOX and FOLFIRI, in either order. So far, we cannot predict the response of chemotherapeutic agent, so it is necessary to find which regimen is adequate before starting chemotherapy.MethodsEnrolled patients are randomized into either conventional treatment or planned treatment preceded by pretreatment genetic analysis. Blood samples of patients in planned treatment group (N = 53) were analyzed for the genetic polymorphism before selection of chemotherapeutic agents. Target genes were XPD‐751, GSTP‐1‐105, XRCC1‐399 for oxaliplatin, UGT1A1 for irinotecan. The response was measured by computed tomographic scan after completion of three cycles of chemotherapy.ResultsOverall response rate was significantly higher in planned group (67.9% vs. 46.3%, P = 0.020). In FOLFOX group, response rate was significantly improved in the planned patients(77.1% vs. 50%, P = 0.018). In FOLFIRI group, the difference didn't reach statistical significance (50% vs. 42.5%, P = 0.776).ConclusionsWe found significantly improved response rates in the chemotherapy of metastatic colon cancer by pretreatment genetic analysis, especially in FOLFOX group. J. Surg. Oncol. 2014 109:250–254. © 2013 Wiley Periodicals, Inc.
Factors associated with response, survival, and limb salvage in patients undergoing isolated limb infusion
Authors: Steinman Jonathan , Ariyan Charlotte , Rafferty Brian , Brady Mary S. 
Published: December 2013

AbstractBackgroundIsolated limb infusion (ILI) is a percutaneous method of delivering regional chemotherapy to patients with recurrent tumors of the extremity. This study determines predictors of response, survival, and limb salvage.MethodsSingle institution data from a prospective clinical trial and subsequent ILI experience were reviewed. Limb tumor burden was assessed in melanoma patients with “high” (≥10 lesions or one lesion >3 cm) or “low” burden (<10 lesions and no lesion >3 cm). Response was assessed at 3 months from ILI.ResultsBetween 1999 and 2011, 62 patients underwent ILI (58 melanoma, 2 Merkel cell carcinoma (MCC), 2 soft tissue sarcoma (STS)). Low tumor burden patients had more complete responses (CR) (11/23, 48%) than high tumor burden (3/32, 9%, P < 0.001); they had higher 5‐year survival (69% vs. 29%, P = .007). Five‐year survival rates based on response: 91% CR, 53% partial response (PR), 25% less than PR (P = 0.042, CR vs. PR).7 patients (11%) underwent amputation due to disease progression; 3 had prior CR or PR.ConclusionsLow tumor burden is a significant predictor of response in melanoma patients. Response to ILI is a significant predictor of survival. Progression of limb disease requiring amputation is not associated with any factors. J. Surg. Oncol. 2014 109:405–409. © 2013 Wiley Periodicals, Inc.
Prenatal ultrasound evaluation of fetal Hb Bart's disease among pregnancies at risk at 11 to 14 weeks of gestation
Authors: Sirichotiyakul Supatra , Luewan Suchaya , Srisupundit Kasemsri , Tongprasert Fuanglada , Tongsong Theera 
Published: December 2013

ABSTRACTObjectiveThe objective of this article is to evaluate the efficacy of the first trimester sonomarkers (11–14 weeks) in predicting hemoglobin (Hb) Bart's disease among fetuses at riskMaterials and MethodsProspective analysis was conducted on pregnancies at risk of fetal Hb Bart's disease at 11 to 14 weeks of gestation. Sonographic markers including cardiothoracic (CT) ratio, peak systolic velocity of the middle cerebral artery (MCA‐PSV), placental thickness, and nuchal translucency were prospectively assessed and recorded. The definite diagnosis of fetal Hb Bart's disease was based on DNA analysis (chorionic villus sampling) or subsequent fetal Hb typing (high‐performance liquid chromatography; cordocentesis).ResultsAmong 104 pregnancies at risk with complete sonographic assessment at 11 to 14 weeks of gestation, 30 fetuses were finally proven to be affected. The CT ratio gave the highest sensitivity, 93.3%, with specificity of 93.2%, followed by placental thickness and MCA‐PSV, respectively. Nuchal translucency had a very low sensitivity of 16.7%. The combination of CT ratio and MCA‐PSV increased the sensitivity to 96.7% but somewhat compromise specificity.ConclusionsAt 11 to 14 weeks of gestation, sonographic markers can effectively differentiate affected from unaffected pregnancies. The most sensitive marker was CT ratio plus MCA‐PSV. Of couples at risk with no any sonographic markers, the risk of having an affected fetus is nearly eliminated. © 2013 John Wiley & Sons, Ltd.
Relation between light trapping and surface topography of plasma textured crystalline silicon wafers
Authors: Souren F. M. M. , Rentsch J. , van de Sanden M. C. M. 
Published: December 2013

AbstractCurrently, in the photovoltaic industry, wet chemical etching technologies are used for saw damage removal and surface texturing. Alternative to wet chemical etching is plasma etching. However, as for example, the linear microwave plasma technique, developed by Roth&Rau, has not been implemented in the photovoltaic industry for etching, because of the very low etch rate (<1 µm/min) and the high cost of ownership related to the etching process. In this study, different front surface textured crystalline silicon wafers obtained by means of the linear microwave plasma technique and the expanding thermal plasma technique are investigated in terms of weighted reflection by using reflectometry (250–1200 nm) to study the optical properties of the textures in detail. In addition, atomic force microscopy is used to measure the surface topography to determine statistical roughness parameters, as presented in this paper. Effective light trapping can be obtained by multiple reflections as well as by a graded layer, which leads to a diffuse front surface, or a combination of both. A graded layer can be described as a smooth transition with increasing refractive index from air to silicon with typical thickness of (200 ± 50) nm. We have found that the average plane tilt angle correlates to the measured weighted reflection. Moreover, we can determine from the aspect ratio whether the light trapping is effective by multiple reflections. From the roughness exponent, which is a measure for the micro roughness, we can determine whether the light trapping is effective by a graded layer. Copyright © 2013 John Wiley & Sons, Ltd.
Activated 5′flanking region of NANOGP8 in a self‐renewal environment is associated with increased sphere formation and tumor growth of prostate cancer cells
Authors: Zhang Kai , Fowler Marcie , Glass Jonathan , Yin Hong 
Published: December 2013

AbstractINTRODUCTIONNANOGP8 is a retrogene which encodes a full‐length protein similar to the NANOG1 gene. The expression of NANOGP8 has been documented in several cancers and is related to cell proliferation and tumor development. However, the regulation of NANOGP8 expression has not been investigated. Therefore, the role of NANOGP8 in cell proliferation has not been completely understood.METHODSWe evaluate the expression of NANOG1 and NANOGP8 in prostate cancer cell lines and primary cultures of prostate tissues. We investigate clonogenicity, sphere formation, and xenograft tumor growth of prostate cancer cells with an activated 5′flanking region of NANOGP8. We examine the role of NANOGP8 in cell cycle progression.RESULTSIn the prostate cells the NANOG RNA was transcribed from NANOGP8 and not from NANOG1. Cells with the activated 5′flanking region of NANOGP8 exhibited enhanced clonogenicity, sphere formation, and xenograft tumor growth. The sphere culture and tumor initiation mouse mode promoted the activation of the 5′flanking region of NANOGP8. Forced expression of NANOGP8 increased the entry into the cell cycle.DISCUSSIONIn prostate cells NANOGP8 is a predominant molecule of NANOG. The activation of 5′flanking sequence of NANOGP8 could play a role in the regulation of the stem‐like properties of cancer stem cells and prostate tumor initiation and development. The microenvironment favoring cancer stem cells could promote the activation of the 5′flanking region of NANOGP8. Prostate 74:381–394, 2014. © 2013 Wiley Periodicals, Inc.
Diagnostic Performance of Ultrasound for Macroscopic Hematuria in the Era of Multidetector Computed Tomography Urography
Authors: Rhéaume-Lanoie Julien , Lepanto Luigi , Fradet Vincent , Billiard Jean-Sébastien , Tang An 
Published: December 2013

Purpose The objective of this study was to evaluate the diagnostic performance of ultrasound for detecting urinary tract neoplasm in the setting of macroscopic hematuria by using multidetector computed tomography urography (MDCTU) and cystoscopy as the reference standard. Methods This retrospective study was approved by our institutional review board. Patients with macroscopic hematuria who were investigated with an abdominal or renal ultrasound, an MDCTU, and a cystoscopy between January 2007 and December 2009, were eligible (95 patients). Exclusion criteria were time interval >12 months between index and reference tests or the absence of histopathologic proof of malignancy. Ultrasound results of the remaining 86 patients were collected and compared with the reference standard test, which was the combination of MDCTU for the assessment of upper urinary tract and cystoscopy for assessment of the lower urinary tract. The final diagnosis of neoplasm was based on pathologic findings. Results Urinary tract neoplasm was diagnosed in 20% of the patients (17/86). Sensitivity, specificity, positive and negative predictive values, and positive and negative likelihood ratios of ultrasound for detecting urinary tract neoplasms were 35.3% (6/17), 89.9% (62/69), 46.2% (6/13), 84.9% (62/73), 3.48 (95% confidence interval, 1.34-9.02), and 0.72 (95% confidence interval, 0.5-1.3), respectively. Conclusion Sensitivity of ultrasound for the evaluation of macroscopic hematuria in the era of MDCTU is lower than expected. Results of our study suggest that patients with macroscopic hematuria should undergo MDCTU as first-line imaging modality, with little added benefit from ultrasound.
Quaternary structural partitioning within the rigid Tarim plate inferred from magnetostratigraphy and sedimentation rate in the eastern Tarim Basin in China
Authors: Chang Hong , An Zhisheng , Liu Weiguo , Ao Hong , Qiang Xiaoke , Song Yougui , Lai Zhongping 
Published: December 2013

AbstractIt has been proposed that within the Tarim Basin tectonic activity has been limited since Triassic time. However, on the basis of magnetostratigraphy from the eastern Tarim Basin, which defines the chronology of sedimentation and structural evolution of the basin, we show that the basin interior has been uplifted and partitioned during Quaternary. The magnetostratigraphy was constructed from 2228 samples that yielded acceptable inclination values. Characteristic remnant magnetization (ChRM) with both normal (N1–N11) and reversed (R1–R11) polarity was isolated by thermal demagnetization. The data correlate best with polarity chrons C3r to C1n, which range from 5.39 Ma to recent on the geological time scale 2004 (GTS2004). An abrupt decrease in the sedimentation rate is observed at 1.77 Ma in the Ls1 core. This change does not overlap with known Pleistocene climate-change events. We attribute this sedimentation rate decrease to a structurally controlled local decrease in accommodation space where basin basement uplifts occur. This period of sedimentary environmental change reveals that structural partitioning in the basement of the Tarim Basin occurred since ~ 1.77 Ma, and we speculate that tilting of the Southeast Uplift (a sub-basin unit) within the Tarim Basin began in early Pleistocene time.
Dispersion characteristics of surface plasmon polariton modes in a metallic slab waveguide with nonlinear magnetic cladding
Authors: Ajith R. , Mathew Vincent 
Published: December 2013

We investigate the propagation characteristics of surface plasmon polaritons along a slab waveguide with a nonlinear magnetic cladding characterized by permeability μ =μl+μnlH2 and a linear substrate. The dispersion relation for the surface plasmon polariton modes supported by the structure was derived and numerically solved. The dependance of mode behavior on input power was studied. As the input power increases, the propagation constant of the modes increases. The effect of self focussed peak on the mode confinement near the interface and the resulting propagation characteristics of the plasmon modes were investigated. Increase in metal film thickness lifts the degeneracy of nonlinear plasmon modes supported by the waveguide. It has been observed that the propagation length is not a single valued function of input power which is crucial in understanding optical nano-switches.
RNA-seq differential expression studies: more sequence or more replication?
Authors: Liu Yuwen , Zhou Jie , White Kevin P. 
Published: December 2013

Abstract
Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources.
Results: We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF7, adding more sequencing depth after 10 M reads gives diminishing returns on power to detect DE genes, whereas adding biological replicates improves power significantly regardless of sequencing depth. We also propose a cost-effectiveness metric for guiding the design of large-scale RNA-seq DE studies. Our analysis showed that sequencing less reads and performing more biological replication is an effective strategy to increase power and accuracy in large-scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies.
Availability and implementation: The code used in this paper is provided on: http://home.uchicago.edu/∼jiezhou/replication/. The expression data is deposited in the Gene Expression Omnibus under the accession ID GSE51403.
Contact: kpwhite@uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data
Authors: Lartillot Nicolas 
Published: December 2013

Abstract
Motivation: Correlation between life history or ecological traits and genomic features such as nucleotide or amino acid composition can be used for reconstructing the evolutionary history of the traits of interest along phylogenies. Thus far, however, such ancestral reconstructions have been done using simple linear regression approaches that do not account for phylogenetic inertia. These reconstructions could instead be seen as a genuine comparative regression problem, such as formalized by classical generalized least-square comparative methods, in which the trait of interest and the molecular predictor are represented as correlated Brownian characters coevolving along the phylogeny.
Results: Here, a Bayesian sampler is introduced, representing an alternative and more efficient algorithmic solution to this comparative regression problem, compared with currently existing generalized least-square approaches. Technically, ancestral trait reconstruction based on a molecular predictor is shown to be formally equivalent to a phylogenetic Kalman filter problem, for which backward and forward recursions are developed and implemented in the context of a Markov chain Monte Carlo sampler. The comparative regression method results in more accurate reconstructions and a more faithful representation of uncertainty, compared with simple linear regression. Application to the reconstruction of the evolution of optimal growth temperature in Archaea, using GC composition in ribosomal RNA stems and amino acid composition of a sample of protein-coding genes, confirms previous findings, in particular, pointing to a hyperthermophilic ancestor for the kingdom.
Availability and implementation: The program is freely available at www.phylobayes.org.
Contact: nicolas.lartillot@univ-lyon1.fr
Supplementary information: Supplementary data are available at Bioinformatics online.