bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Early Modern Kidney—Nephrology in and about the Nineteenth Century (Part 2)
Authors: Eknoyan Garabed 
Published: March 2014

AbstractTwo basic science specialties that matured in the nineteenth century were instrumental in the transformation of medicine into a scientific discipline and in the process of establishing the evidentiary basis of the fundamental role of the kidney in maintaining homeostasis, whose continued exploration would lead to the emergence of nephrology in the following century. The first specialty was that of chemistry, which progressed from a descriptive to an analytical, organic, biological, and physical science that progressively eroded the animism of the “vital” forces of old and replaced it with the physicochemical forces and laws of chemical reactions that govern the “matters of life”. The second specialty was that of cell biology, which established the cell as the structural and functional unit of living organisms, be they plant or animal. Refined microscopic technologies then helped to identify the structural components of the cell, amongst which the plasma membrane emerged as the most important in regulating the separation of the intracellular machinery from its external environment and thereby maintaining the internal milieu of cells. The interaction of these two specialties (chemistry, cell biology) clarified the functions of the cell in health and disease and extended it to the study of epithelial cell transport. This transforming turn of events established the role of the renal tubules in the vital function of the kidney of maintaining body homeostasis, a function well beyond that of the passive excretory filter of wastes and excess fluids it had been considered theretofore.
Genetic variants of 17q21 are associated with childhood‐onset asthma and related phenotypes in a northeastern Han Chinese population: a case–control study
Authors: Yu X. , Yu C. , Ren Z. , Deng Y. , Song J. , Zhang H. , Zhou H. 
Published: March 2014

AbstractA genome‐wide association study (GWAS) suggested that variants on chromosome 17q21 were associated with childhood‐onset asthma in white populations. Two replication studies had been conducted in southern Han Chinese population in 2009 and 2012. However, these two Chinese replication results were inconsistent. To further confirm the role of 17q21 common variants, an association study of 17q21 single nucleotide polymorphisms (SNPs) with the risk of childhood‐onset asthma was performed in a Han population from northeastern China. In this study, rs3894194, rs12603332 and rs11650680 were genotyped in 435 asthmatic children and 601 healthy controls by using a SNaPshot method. Our data showed that the allelic frequency of rs12603332 and rs11650680 showed significant differences between asthmatic cases and healthy controls, with an odds ratio (OR) of 1.36 [95% confidence interval (CI) 1.12–1.65, P = 0.002] and an OR of 1.36 (95% CI 1.07–1.74, P = 0.01). Genotype distribution analysis also showed the significant associations of the above two loci with childhood asthma under dominant, recessive and additive model (dominant OR = 1.57, 95% CI 1.04–2.36, P = 0.032; recessive OR = 1.41, 95% CI 1.09–1.83, P = 0.009; additive OR = 1.97, 95% CI 1.24–3.14, P = 0.004; recessive OR = 1.50, 95% CI 1.13–1.98, P = 0.005). Besides, linear regression analysis showed that rs3894194 and rs12603332 were also significantly associated with asthma phenotypes such as log10‐transformed immunoglobulin E (IgE) level (IU/ml) and log10‐transformed eosinophil percentage (dominant, P = 0.04; additive, P = 0.01; recessive, P = 0.04; recessive, P = 0.03; additive, P = 0.02). Collectively, our findings suggest that orosomucoid 1‐like 3 (ORMDL3) locus on chromosome 17q21 is a risk factor for childhood‐onset asthma in northeastern Han Chinese population. Further studies will be needed to elucidate the pathogenesis that ORMDL3 locus predisposes to childhood‐onset asthma.
Development of a simple microarray for genotyping HIV‐1 drug resistance mutations in the reverse transcriptase gene in rural Tanzania
Authors: Masimba Pax , Gare Janet , Klimkait Thomas , Tanner Marcel , Felger Ingrid 
Published: March 2014

AbstractObjectiveAiming at a simple, inexpensive and robust tool for HIV‐1 drug resistance genotyping during antiretroviral therapy (ART) we developed and validated a microarray‐based detection of 25 drug resistance mutations most relevant for the Tanzanian ART regimen.MethodsA reverse transcriptase gene fragment was reverse‐transcribed and amplified by reverse transcription–polymerase chain reaction (RT–PCR). Primers for mini‐sequencing were designed based on alignments of the most prevalent local HIV‐1 variants. Tagged primers were extended by fluorochrome‐labelled dideoxynuclotide triphosphate (ddNTPs) to indicate the single‐nucleotide polymorphism (SNP) allele of the sample tested, followed by hybridisation on treated microarray slides. Images were analysed with a laser scanner and genotype calling was performed using in‐house developed software.ResultsThe microarray was validated with four cloned HIV‐1 genome fragments from a Swiss HIV‐1 cohort and 102 HIV‐1 sequences amplified from the Tanzanian target population (field samples). Results were concordant with the Sanger sequencing SNP profile in 92.7% of 2550 SNP data points compared. Lack of signals in small number of SNPs was due to either failure in the extension reaction or hybridisation owing to mismatches between PCR product and extension primer.ConclusionOur study demonstrates the feasibility of hybridisation‐based genotyping of drug resistance mutations of HIV, even though our microarray, which was designed for population studies, achieved only correct assignment of 92% of all SNPs in the tested samples.
Taenia solium metacestode fasciclin‐like protein is reactive with sera of chronic neurocysticercosis
Authors: Bae Young‐An , Yeom Joon‐Sup , Wang Hu , Kim Seon‐Hee , Ahn Chun‐Seob , Kim Jin‐Taek , Yang Hyun‐Jong , Kong Yoon 
Published: March 2014

AbstractObjectivesNeurocysticercosis (NC), an infection of the central nervous system with Taenia solium metacestodes (TsM), invokes a formidable neurological disease. A bundle of antigens is applicable for serodiagnosis of active cases, while they demonstrate fairly low reactivity against sera of chronic NC. Identification of sensitive biomarkers for chronic NC is critical for appropriate management of patients.MethodsProteome analysis revealed several isoforms of 65‐ and 83‐kDa TsM fasciclin‐like proteins (TsMFas) to be highly reactive with sera of chronic NC. A cDNA encoding one of the 83‐kDa TsMFas (TsMFas1) was isolated from a cDNA library. We expressed a recombinant protein (rTsMFas1) and evaluated its diagnostic potential employing sera from chronic NC (n = 80), tissue‐invasive cestodiases (n = 169) and trematodiases (n = 80) and those of normal controls (n = 50).ResultsSecretory TsMFas1 was composed of 766 amino acid polypeptide and harboured fasciclin and fasciclin‐superfamily domains. The protein was constitutively expressed in metacestode and adult stages, with preferential locality in the scolex. Bacterially expressed rTsMFas1 exhibited 78.8% sensitivity (63/80 cases) and 93% specificity (278/299 samples) in diagnosing chronic NC. Some cross‐reactivity was observed with sera of cystic echinococcosis (10/56, 17.8%) and sparganosis (4/50, 8%). Positive and negative predictive values were 75% and 95.5%, respectively.ConclusionTsM fasciclin‐like protein may be useful for differential diagnosis of chronic NC in clinical settings, especially where both NC and other infectious cerebral granulomatoses are prevalent.
Adjusting the HIV prevalence for non‐respondents using mortality rates in an open cohort in northwest Tanzania
Authors: Tenu Filemon , Isingo Raphael , Zaba Basia , Urassa Mark , Todd Jim 
Published: March 2014

AbstractObjectiveTo estimate HIV prevalence in adults who have not tested for HIV using age‐specific mortality rates and to adjust the overall population HIV prevalence to include both tested and untested adults.MethodsAn open cohort study was established since 1994 with demographic surveillance system (DSS) and five serological surveys conducted. Deaths from Kisesa DSS were used to estimate mortality rates and 95% confidence intervals by HIV status for 3‐ 5‐year periods (1995–1999, 2000–2004, and 2005–2009). Assuming that mortality rates in individuals who did not test for HIV are similar to those in tested individuals, and dependent on age, sex and HIV status and HIV, prevalence was estimated.ResultsIn 1995–1999, mortality rates (per 1000 person years) were 43.7 (95% CI 35.7–53.4) for HIV positive, 2.6 (95% CI 2.1–3.2) in HIV negative and 16.4 (95% CI 14.4–18.7) in untested. In 2000–2004, mortality rates were 43.3 (95% CI 36.2–51.9) in HIV positive, 3.3 (95% CI 2.8–4.0) in HIV negative and 11.9 (95% CI 10.5–13.6) in untested. In 2005–2009, mortality rates were 30.7 (95% CI 24.8–38.0) in HIV positive, 4.1 (95% CI 3.5–4.9) in HIV negative and 5.7 (95% CI 5.0–6.6) in untested residents. In the three survey periods (1995–1999, 2000–2004, 2005–2009), the adjusted period prevalences of HIV, including the untested, were 13.5%, 11.6% and 7.1%, compared with the observed prevalence in the tested of 6.0%, 6.8 and 8.0%. The estimated prevalence in the untested was 33.4%, 21.6% and 6.1% in the three survey periods.ConclusionThe simple model was able to estimate HIV prevalence where a DSS provided mortality data for untested residents.
Rhabdomyosarcoma associated with the lead wire of a pacemaker generator implant
Authors: Thieman Mankin Kelley M. , Dunbar Mark D. , Toplon David , Ginn Pamela , Maisenbacher Herbert W. , Risselada Marije 
Published: March 2014

AbstractAn 11‐year‐old female spayed Labrador Retriever was presented for a draining, painful subcutaneous mass palpated over a previously implanted pacemaker generator. Infection was suspected and the mass was removed surgically. On cut surface, the mass was friable and mottled tan to brown with firm pale tan nodules, surrounding the pacemaker lead wire adjacent to the pacemaker generator. Cytologic interpretation of impression smears was consistent with a sarcoma, and suggestive of a rhabdomyosarcoma due to the presence of strap‐like cells. On histopathologic examination, a highly invasive nodular mass surrounded the pacemaker lead, composed of pleomorphic round, spindle and strap cells, and multinucleated giant cells. The population exhibited microscopic invasion into the deep portion of the fibrous capsule surrounding the pacemaker generator. There were tumor emboli within small to medium subcutaneous veins adjacent to the mass. Immunohistochemically, the neoplastic cells stained positive for α‐sarcomeric actin and vimentin, and negative for α‐smooth muscle actin, consistent with a rhabdomyosarcoma arising at the site of the pacemaker generator. To our knowledge, this is the first report of a rhabdomyosarcoma associated with the lead wire of a pacemaker generator in a dog.
Ion beam tracking using ultrasound motion detection
Authors: Prall M. , Kaderka R. , Saito N. , Graeff C. , Bert C. , Durante M. , Parodi K. , Schwaab J. , Sarti C. , Jenne J. 
Published: March 2014

Purpose:The use of motion mitigation techniques such as tracking and gating in particle therapy requires real‐time knowledge of tumor position with millimeter precision. The aim of this phantom‐based study was to evaluate the option of diagnostic ultrasound (US) imaging (sonography) as real‐time motion detection method for scanned heavy ion beam irradiation of moving targets.Methods:For this pilot experiment, a tumor surrogate was moved inside a water bath along two‐dimensional trajectories. A rubber ball was used for this purpose. This ball was moved by a robotic arm in two dimensions lateral to the heavy ion beam. Trajectories having a period of 3 s and peak to peak amplitude of 20 mm were used. Square radiation fields of were irradiated on radiosensitive films with a 200 MeV/u beam of calcium ions having a FWHM of 6 mm. Pencil beam scanning and beam tracking were employed. The films were attached on the robotic arm and thus moved with the rubber ball. The position of the rubber ball was continuously measured by a US tracking system (Mediri GmbH, Heidelberg) and sent to the GSI therapy control system (TCS). This position was used as tracking vector. Position reconstruction from the US tracking system and data communication introduced a delay leading to a position error of several millimeters. An artificial neural network (ANN) was implemented in the TCS to predict motion from US measurements and thus to compensate for the delay.Results:Using ANN delay compensation and large motion amplitudes, the authors could produce irradiation patterns with a few percent inhomogeneity and about 1 mm geometrical conformity.Conclusions:This pilot experiment suggests that diagnostic US should be further investigated as dose‐free, high frame‐rate, and model‐independent motion detection method for scanning heavy ion beam irradiation of moving targets.
Feasibility of using intermediate x‐ray energies for highly conformal extracranial radiotherapy
Authors: Dong Peng , Yu Victoria , Nguyen Dan , Demarco John , Woods Kaley , Boucher Salime , Low Daniel A. , Sheng Ke 
Published: March 2014

Purpose:To investigate the feasibility of using intermediate energy 2 MV x‐rays for extracranial robotic intensity modulated radiation therapy.Methods:Two megavolts flattening filter free x‐rays were simulated using the Monte Carlo code MCNP (v4c). A convolution/superposition dose calculation program was tuned to match the Monte Carlo calculation. The modeled 2 MV x‐rays and actual 6 MV flattened x‐rays from existing Varian Linacs were used in integrated beam orientation and fluence optimization for a head and neck, a liver, a lung, and a partial breast treatment. A column generation algorithm was used for the intensity modulation and beam orientation optimization. Identical optimization parameters were applied in three different planning modes for each site: 2, 6 MV, and dual energy 2/6 MV.Results:Excellent agreement was observed between the convolution/superposition and the Monte Carlo calculated percent depth dose profiles. For the patient plans, overall, the 2/6 MV x‐ray plans had the best dosimetry followed by 2 MV only and 6 MV only plans. Between the two single energy plans, the PTV coverage was equivalent but 2 MV x‐rays improved organs‐at‐risk sparing. For the head and neck case, the 2MV plan reduced lips, mandible, tongue, oral cavity, brain, larynx, left and right parotid gland mean doses by 14%, 8%, 4%, 14%, 24%, 6%, 30% and 16%, respectively. For the liver case, the 2 MV plan reduced the liver and body mean doses by 17% and 18%, respectively. For the lung case, lung V20, V10, and V5 were reduced by 13%, 25%, and 30%, respectively. V10 of heart with 2 MV plan was reduced by 59%. For the partial breast treatment, the 2 MV plan reduced the mean dose to the ipsilateral and contralateral lungs by 27% and 47%, respectively. The mean body dose was reduced by 16%.Conclusions:The authors showed the feasibility of using flattening filter free 2 MV x‐rays for extracranial treatments as evidenced by equivalent or superior dosimetry compared to 6 MV plans using the same inverse noncoplanar intensity modulated planning method.
Image quality in thoracic 4D cone‐beam CT: A sensitivity analysis of respiratory signal, binning method, reconstruction algorithm, and projection angular spacing
Authors: Shieh Chun‐Chien , Kipritidis John , O'Brien Ricky T. , Kuncic Zdenka , Keall Paul J. 
Published: March 2014

Purpose:Respiratory signal, binning method, and reconstruction algorithm are three major controllable factors affecting image quality in thoracic 4D cone‐beam CT (4D‐CBCT), which is widely used in image guided radiotherapy (IGRT). Previous studies have investigated each of these factors individually, but no integrated sensitivity analysis has been performed. In addition, projection angular spacing is also a key factor in reconstruction, but how it affects image quality is not obvious. An investigation of the impacts of these four factors on image quality can help determine the most effective strategy in improving 4D‐CBCT for IGRT.Methods:Fourteen 4D‐CBCT patient projection datasets with various respiratory motion features were reconstructed with the following controllable factors: (i) respiratory signal (real‐time position management, projection image intensity analysis, or fiducial marker tracking), (ii) binning method (phase, displacement, or equal‐projection‐density displacement binning), and (iii) reconstruction algorithm [Feldkamp–Davis–Kress (FDK), McKinnon–Bates (MKB), or adaptive‐steepest‐descent projection‐onto‐convex‐sets (ASD‐POCS)]. The image quality was quantified using signal‐to‐noise ratio (SNR), contrast‐to‐noise ratio, and edge‐response width in order to assess noise/streaking and blur. The SNR values were also analyzed with respect to the maximum, mean, and root‐mean‐squared‐error (RMSE) projection angular spacing to investigate how projection angular spacing affects image quality.Results:The choice of respiratory signals was found to have no significant impact on image quality. Displacement‐based binning was found to be less prone to motion artifacts compared to phase binning in more than half of the cases, but was shown to suffer from large interbin image quality variation and large projection angular gaps. Both MKB and ASD‐POCS resulted in noticeably improved image quality almost 100% of the time relative to FDK. In addition, SNR values were found to increase with decreasing RMSE values of projection angular gaps with strong correlations (r ≈ −0.7) regardless of the reconstruction algorithm used.Conclusions:Based on the authors’ results, displacement‐based binning methods, better reconstruction algorithms, and the acquisition of even projection angular views are the most important factors to consider for improving thoracic 4D‐CBCT image quality. In view of the practical issues with displacement‐based binning and the fact that projection angular spacing is not currently directly controllable, development of better reconstruction algorithms represents the most effective strategy for improving image quality in thoracic 4D‐CBCT for IGRT applications at the current stage.
Implications of CT noise and artifacts for quantitative 99mTc SPECT/CT imaging
Authors: Hulme K. W. , Kappadath S. C. 
Published: March 2014

Purpose:This paper evaluates the effects of computed tomography (CT) image noise and artifacts on quantitative single‐photon emission computed‐tomography (SPECT) imaging, with the aim of establishing an appropriate range of CT acquisition parameters for low‐dose protocols with respect to accurate SPECT attenuation correction (AC).Methods:SPECT images of two geometric and one anthropomorphic phantom were reconstructed iteratively using CT scans acquired at a range of dose levels (CTDIvol = 0.4 to 46 mGy). Resultant SPECT image quality was evaluated by comparing mean signal, background noise, and artifacts to SPECT images reconstructed using the highest dose CT for AC. Noise injection was performed on linear‐attenuation (μ) maps to determine the CT noise threshold for accurate AC.Results:High levels of CT noise (σ ∼ 200–400 HU) resulted in low μ‐maps noise (σ ∼ 1%–3%). Noise levels greater than ∼10% in 140 keV μ‐maps were required to produce visibly perceptible increases of ∼15% in 99mTc SPECT images. These noise levels would be achieved at low CT dose levels (CTDIvol = 4 μGy) that are over 2 orders of magnitude lower than the minimum dose for diagnostic CT scanners. CT noise could also lower (bias) the expected μ values. The relative error in reconstructed SPECT signal trended linearly with the relative shift in μ. SPECT signal was, on average, underestimated in regions corresponding with beam‐hardening artifacts in CT images. Any process that has the potential to change the CT number of a region by ∼100 HU (e.g., misregistration between CT images and SPECT images due to motion, the presence of contrast in CT images) could introduce errors in μ140 keV on the order of 10%, that in turn, could introduce errors on the order of ∼10% into the reconstructed 99mTc SPECT image.Conclusions:The impact of CT noise on SPECT noise was demonstrated to be negligible for clinically achievable CT parameters. Because CT dose levels that affect SPECT quantification is low (CTDIvol ∼ 4 μGy), the low dose limit for the CT exam as part of SPECT/CT will be guided by CT image quality requirements for anatomical localization and artifact reduction. A CT technique with higher kVp in combination with lower mAs is recommended when low‐dose CT images are used for AC to minimize beam‐hardening artifacts.
Identification of an Emergent Porcine Circovirus-2 in Vaccinated Pigs from a Brazilian Farm during a Postweaning Multisystemic Wasting Syndrome Outbreak
Authors: Salgado Rafael L. , Vidigal Pedro M. P. , de Souza Luiz F. L. , Onofre Thiago S. , Gonzaga Natália F. , Eller Monique R. , Bressan Gustavo C. , Fietto Juliana L. R. , Almeida Márcia R. , Silva Júnior Abelardo 
Published: March 2014

ABSTRACT
Three porcine circovirus-2 strains were isolated from pigs on a Brazilian farm during an outbreak, indicating a vaccine failure. They present identical genomic sequences, with high identities to other isolates that were also related to vaccination failures, supporting the recent theory about an antigen drift being associated with vaccine failures throughout the world.
Draft Genome Sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), Ocular Methicillin-Resistant Isolates
Authors: Velusamy Nithya , Prakash Logambiga , Sivakumar Neelamegam , Antony Aju , Prajna Lalitha , Mohankumar Vidyarani , Devarajan Bharanidharan 
Published: March 2014

ABSTRACT

Sequence type 22 (ST22) and ST672 are the two major emerging clones of community-acquired methicillin-resistant
Staphylococcus aureus
in India. ST672 strains were found to cause severe ocular infections. We report the draft genome sequences of two emerging strains of methicillin-resistant
S. aureus
, AMRF1 (ST22) and AMRF2 (ST672), isolated from patients with ocular infections.
Draft Genome Sequence of Clostridium pasteurianum NRRL B-598, a Potential Butanol or Hydrogen Producer
Authors: Kolek Jan , Sedlář Karel , Provazník Ivo , Patáková Petra 
Published: March 2014

ABSTRACT

We present a draft genome sequence of
Clostridium pasteurianum
NRRL B-598. This strain ferments saccharides by two-stage acetone-butanol (AB) fermentation, is oxygen tolerant, and has high hydrogen yields.
Genomes of Two Clinical Isolates of Mycobacterium tuberculosis from Odisha, India
Authors: Majid Mohammad , Kumar Narender , Qureshi Asifa , Yerra Priyadarshini , Kumar Ashutosh , Kumar Mandala Kiran , Tiruvayipati Suma , Baddam Ramani , Shaik Sabiha , Srikantam Aparna , Ahmed Niyaz 
Published: March 2014

ABSTRACT

We report whole-genome sequences of two clinical isolates of
Mycobacterium tuberculosis
isolated from patients in Odisha, India. The sequence analysis revealed that these isolates are of an ancestral type and might represent some of the “pristine” isolates in India that have not admixed with other lineages.
Draft Genome Sequence of Paenibacillus pini JCM 16418
T
, Isolated from the Rhizosphere of Pine Tree
Authors: Yuki Masahiro , Oshima Kenshiro , Suda Wataru , Oshida Yumi , Kitamura Keiko , Iida Toshiya , Hattori Masahira , Ohkuma Moriya 
Published: March 2014

ABSTRACT

Paenibacillus pini
strain JCM 16418
T
is a cellulolytic bacterium isolated from the rhizosphere of pine trees. Here, we report the draft genome sequence of this strain. This genome information will be useful for studies of rhizosphere bacteria.