bluuebunny/crossref_metadata_2025_split huggingface dataset:
A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence
Authors: Lypaczewski Patrick , Hoshizaki Johanna , Zhang Wen-Wei , McCall Laura-Isobel , Torcivia-Rodriguez John , Simonyan Vahan , Kaur Amanpreet , Dewar Ken , Matlashewski Greg 
Published: November 2018

AbstractLeishmania donovaniis responsible for visceral leishmaniasis, a neglected and lethal parasitic disease with limited treatment options and no vaccine. The study ofL.donovanihas been hindered by the lack of a high-quality reference genome and this can impact experimental outcomes including the identification of virulence genes, drug targets and vaccine development. We therefore generated a complete genome assembly by deep sequencing using a combination of second generation (Illumina) and third generation (PacBio) sequencing technologies. Compared to the currentL.donovaniassembly, the genome assembly reported within resulted in the closure over 2,000 gaps, the extension of several chromosomes up to telomeric repeats and the re-annotation of close to 15% of protein coding genes and the annotation of hundreds of non-coding RNA genes. It was possible to correctly assemble the highly repetitive A2 and Amastin virulence gene clusters. A comparative sequence analysis using the improved reference genome confirmed 70 published and identified 15 novel genomic differences between closely related visceral and atypical cutaneous disease-causingL.donovanistrains providing a more complete map of genes associated with virulence and visceral organ tropism. Bioinformatic tools including protein variation effect analyzer and basic local alignment search tool were used to prioritize a list of potential virulence genes based on mutation severity, gene conservation and function. This complete genome assembly and novel information on virulence factors will support the identification of new drug targets and the development of a vaccine forL.donovani.
Contrasting streamflow regimes induced by melting glaciers across the Tien Shan – Pamir – North Karakoram
Authors: Luo Yi , Wang Xiaolei , Piao Shilong , Sun Lin , Ciais Philippe , Zhang Yiqing , Ma Changkun , Gan Rong , He Chansheng 
Published: November 2018

AbstractThe glacierized Tien Shan – Pamir – Karakoram mountain complex supplies water to about 42 million people. Yet, the knowledge about future glacial runoff in response to future climate is limited. Here, we address this issue using a hydrological model, that includes the three components of glacial runoff: ice melt, snowmelt and the runoff of rainfall over ice. The model is forced by climate projections of the CMIP5 models. We find that the three components exhibit different long-term trajectories, sometimes opposite in sign to the long-term trend in glacier impacts. For the eastern slope basins, streamflow is projected to increase by 28% (ranging from 9 to 44%, from climate model variation (CMV)) by the late 21st century, under the representative concentration pathway, RCP8.5. Ice melt contributes 39% (25 to 65%, CMV) of the total streamflow increase. However, streamflow from the western slopes is projected to decrease by 5% (−24 to 16%, CMV), due to the smaller contribution of ice melt, less precipitation and higher evapotranspiration. Increasing water supply from the eastern slopes suggests more water availability for currently degraded downstream ecosystems in the Xinjiang province of China, while the likely decreasing streamflow in Central Asian rivers on the western slopes indicates new regulations will be needed.
Derivation and Numerical analysis of an Attenuation Operator for non-relativistic waves
Authors: Manzetti Sergio 
Published: November 2018

AbstractQuantum mechanical models for particles are strictly dependent on the Schrödinger equation, where the solutions and the Hermitian polynomials form a mathematical foundation to derive expectation values for observables. As for all quantum systems, the solutions are derived in discrete energy levels, and yield probability density, the kinetic energy and average momentum. In this study however, an attenuation Hamiltonian is derived by the algebraic relation of the momentum and position operators, and the derived equation, where the attenuation of kinetic energy is the eigenvalue, is studied numerically. The numerical solutions suggest that the change in kinetic energy from one transition to the next proceeds in an undular fashion, and not in a definite manner. This suggests that any sub-atomic particle which experiences a transition from one level to the next, does so by both gaining and losing energy in an undular manner before reaching an equilibrium with a new and stabilized kinetic energy. The results show also that the phase of the change in kinetic energy between transitions differs between high and low momenta and that higher levels of momentum attenuate more smoothly than transitions between lower energy levels. The investigated attenuation operator may be important for future pinning and quasipinning approaches and play a role in future quantum information processing. Future research is required on the spectrum of the operator and on its potential analytical solutions.
A practical protocol for measurements of spinal cord functional connectivity
Authors: Barry Robert L. , Conrad Benjamin N. , Smith Seth A. , Gore John C. 
Published: November 2018

AbstractResting state functional magnetic resonance imaging (fMRI) has been used to study human brain function for over two decades, but only recently has this technique been successfully translated to the human spinal cord. The spinal cord is structurally and functionally unique, so resting state fMRI methods developed and optimized for the brain may not be appropriate when applied to the cord. This report therefore investigates the relative impact of different acquisition and processing choices (including run length, echo time, and bandpass filter width) on the detectability of resting state spinal cord networks at 3T. Our results suggest that frequencies beyond 0.08 Hz should be included in resting state analyses, a run length of ~8–12 mins is appropriate for reliable detection of the ventral (motor) network, and longer echo times – yet still shorter than values typically used for fMRI in the brain – may increase the detectability of the dorsal (sensory) network. Further studies are required to more fully understand and interpret the nature of resting state spinal cord networks in health and in disease, and the protocols described in this report are designed to assist such studies.
Structural, electronic and magnetic properties of MnxGa/Co2MnSi (x = 1, 3) bilayers
Authors: Chen Ting , Wang Junhao , Cheng Zhenxiang , Wang Xiaotian , Chen Hong 
Published: November 2018

AbstractDirectly coupled hard and soft ferromagnets were popularly used as the hybridized electrodes to enhance tunnel magnetoresistance (TMR) ratio in the perpendicular magnetic tunnel junction (pMTJ). In this paper, we employ the density functional theory (DFT) with general gradient approximation (GGA) to investigate the interfacial structure and magnetic behavior of tetragonal Heusler-type MnGa (MG)/L21-Co2MnSi (CMS) Heusler alloy bilayers with the MnGa being D022-MnGa alloy (Mn3Ga) and L10-MnGa alloy (MnGa). The MM-MS_B interface with the bridge (B) connection of MnMn termination (MM) of D022- and L10-MnGa layers to MnSi termination (MS) of CMS layers is found to be most stable in the energy point of view. Also, a strong antiferromagnetic coupling and relatively higher spin polarization can be observed in the MM-MS_B interface. Further, a remarkable potential difference to derive electrons to transfer from MG layer to CMS layer appears at the interface. These theoretical results indicate that the MG/CMS bilayers are promising candidates as coupled composites, and moreover, the D022-MG/CMS bilayer is better than L10-MG/CMS bilayer due to its larger spin polarization and built-in field at the interface.
High carnivore population density highlights the conservation value of industrialised sites
Authors: Loock Daan J. E. , Williams Samual T. , Emslie Kevin W. , Matthews Wayne S. , Swanepoel Lourens H. 
Published: November 2018

AbstractAs the environment becomes increasingly altered by human development, the importance of understanding the ways in which wildlife interact with modified landscapes is becoming clear. Areas such as industrial sites are sometimes presumed to have little conservation value, but many of these sites have areas of less disturbed habitats around their core infrastructure, which could provide ideal conditions to support some species, such as mesocarnivores. We conducted the first assessments of the density of serval (Leptailurus serval) at the Secunda Synfuels Operations plant, South Africa, using camera trap surveys analysed within a spatially explicit capture recapture framework. We show that servals occurred at densities of 76.20–101.21 animals per 100 km², which are higher than previously recorded densities for this species, presumably due to high abundance of prey and the absence of persecution and/or competitor species. Our findings highlight the significant conservation potential of industrialised sites, and we suggest that such sites could help contribute towards meeting conservation goals.
K-variant BCHE and pesticide exposure: Gene-environment interactions in a case–control study of Parkinson’s disease in Egypt
Authors: Rösler Thomas W. , Salama Mohamed , Shalash Ali S. , Khedr Eman M. , El-Tantawy Abdelhalim , Fawi Gharib , El-Motayam Amal , El-Seidy Ehab , El-Sherif Mohamed , El-Gamal Mohamed , Moharram Mohamed , El-Kattan Mohammad , Abdel-Naby Muhammad , Ashour Samia , Müller Ulrich , Dempfle Astrid , Kuhlenbäumer Gregor , Höglinger Günter U. 
Published: November 2018

AbstractPesticide exposure is associated with increased risk of Parkinson’s disease (PD). We investigated in Egypt whether common variants in genes involved in pesticide detoxification or transport might modify the risk of PD evoked by pesticide exposure. We recruited 416 PD patients and 445 controls. Information on environmental factors was collected by questionnaire-based structured interviews. Candidate single-nucleotide polymorphisms (SNPs) in 15 pesticide-related genes were genotyped. We analyzed the influence of environmental factors and SNPs as well as the interaction of pesticide exposure and SNPs on the risk of PD. The risk of PD was reduced by coffee consumption [OR = 0.63, 95% CI: 0.43–0.90, P = 0.013] and increased by pesticide exposure [OR = 7.09, 95% CI: 1.12–44.01, P = 0.036]. The SNP rs1126680 in the butyrylcholinesterase gene BCHE reduced the risk of PD irrespective of pesticide exposure [OR = 0.38, 95% CI: 0.20–0.70, P = 0.002]. The SNP rs1803274, defining K-variant BCHE, interacted significantly with pesticide exposure (P = 0.007) and increased the risk of PD only in pesticide-exposed individuals [OR = 2.49, 95% CI: 1.50–4.19, P = 0.0005]. The K-variant BCHE reduces serum activity of butyrylcholinesterase, a known bioscavenger for pesticides. Individuals with K-variant BCHE appear to have an increased risk for PD when exposed to pesticides.
Retinal micro-vascular and aortic macro-vascular changes in postmenopausal women with primary hyperparathyroidism
Authors: Pepe Jessica , Cipriani Cristiana , Tedeschi Massimiliano , Curione Mario , Parravano Mariacristina , Varano Monica , Biamonte Federica , Colangelo Luciano , Minisola Salvatore 
Published: November 2018

AbstractAim of the study was to evaluate the micro and macro-vascular changes in patients with primary hyperparathyroidism (PHPT) compared to controls. 30 postmenopausal PHPT women (15 hypertensive and 15 normotensive) and 30 normotensive controls underwent biochemical evaluation of mineral metabolism and measurements of arterial stiffness by 24 hour ambulatory blood pressure monitoring. Retinal microcirculation was imaged by a Retinal Vessel Analyzer. PHPT patients also underwent bone mineral density measurements and kidney ultrasound. PHPT patients had higher mean calcium and parathyroid hormone values compared to controls. Evaluating macro-vascular compartment, we found higher values of 24 hours-systolic, diastolic blood pressure, aortic pulse wave velocity (aPWV) and aortic augmentation index (Aix) in hypertensive PHPT, but not in normotensive PHPT compared to controls. The eye examination showed narrowing arterial and venular diameters of retinal vessels in both hypertensive and normotensive PHPT compared to controls. In hypertensive PHPT, 24 hours systolic blood pressure was associated only with parathyroid hormone (PTH) levels (beta = 0.36, p = 0.04). aPWV was associated with retinal diameter (beta = −0.69, p = 0.003), but not with PTH. Retinal artery diameter was associated with PTH (beta = −0.6, p = 0.008). In the normotensive PHPT, only PTH was associated with retinal artery diameter (beta = −0.60, p = 0.01) and aortic AIx (beta = 0.65, p = 0.02). In conclusion, we found macro-vascular impairment in PHPT and that micro-vascular impairment is negatively associated with PTH, regardless of hypertension in PHPT.
Tetanus toxin C-fragment protects against excitotoxic spinal motoneuron degeneration in vivo
Authors: Netzahualcoyotzi Citlalli , Tapia Ricardo 
Published: November 2018

AbstractThe tetanus toxin C-fragment is a non-toxic peptide that can be transported from peripheral axons into spinal motoneurons. Inin vitroexperiments it has been shown that this peptide activates signaling pathways associated with Trk receptors, leading to cellular survival. Because motoneuron degeneration is the main pathological hallmark in motoneuron diseases, and excitotoxicity is an important mechanism of neuronal death in this type of disorders, in this work we tested whether the tetanus toxin C-fragment is able to protect MN in the spinal cordin vivo. For this purpose, we administered the peptide to rats subjected to excitotoxic motoneuron degeneration induced by the chronic infusion of AMPA in the rat lumbar spinal cord, a well-established model developed in our laboratory. Because the intraspinal infusion of the fragment was only weakly effective, whereas the i.m. administration was remarkably neuroprotective, and because the i.m. injection of an inhibitor of Trk receptors diminished the protection, we conclude that such effects require a retrograde signaling from the neuromuscular junction to the spinal motoneurons. The protection after a simple peripheral route of administration of the fragment suggests a potential therapeutic use of this peptide to target spinal MNs exposed to excitotoxic conditionsin vivo.
Wideband Absorbance and 226-Hz Tympanometry in the Prediction of Optimal Distortion Product Otoacoustic Emission Primary Tone Levels
Authors: Marcrum Steven C. , Steffens Thomas , Zeman Florian , Kummer Peter 
Published: November 2018

PurposeDistortion product otoacoustic emission (DPOAE) amplitude is sensitive to the primary tone level separation effective within the cochlea. Despite potential for middle ear sound transmission characteristics to affect this separation, no primary tone level optimization formula accounts for its influence. This study was conducted to determine if inclusion of ear- and frequency-specific immittance features improves primary tone level optimization formula performance beyond that achieved using a univariate,L2-based formula.MethodFor 30 adults with normal hearing, DPOAE, wideband absorbance, and 226-Hz tympanometry measures were completed. A mixed linear modeling technique, incorporating both primary tone and acoustic immittance features, was used to generate a multivariable formula for the middle ear–specific recommendation of primary tone level separations forf2= 1–6 kHz. The accuracy with whichL1OPT, or theL1observed to maximize DPOAE level for each givenL2, could be predicted using the multivariable formula was then compared with that of a traditional,L2-based univariate formula for each individual ear.ResultsUse of the multivariable formulaL1= 0.47L2+ 2.40A+f2param+ 38 [dB SPL] resulted in significantly more accurateL1OPTpredictions than did the univariate formulaL1= 0.49L2+ 41 [dB SPL]. Although average improvement was small, meaningful improvements were identified within individual ears, especially forf2= 1 and 6 kHz.ConclusionIncorporation of a wideband absorbance measure into a primary tone level optimization formula resulted in a minor average improvement inL1OPTprediction accuracy when compared with a traditional univariate optimization formula. Further research is needed to identify characteristics of ears that might disproportionately benefit from the additional measure.
Orthographic Learning in Children Who Are Deaf or Hard of Hearing
Authors: Wass Malin , Ching Teresa Y. C. , Cupples Linda , Wang Hua-Chen , Lyxell Björn , Martin Louise , Button Laura , Gunnourie Miriam , Boisvert Isabelle , McMahon Catherine , Castles Anne 
Published: November 2018

Purpose
The purpose of the current study was to investigate the relationship between orthographic learning and language, reading, and cognitive skills in 9-year-old children who are deaf or hard of hearing (DHH) and to compare their performance to age-matched typically hearing (TH) controls.

Method
Eighteen children diagnosed with moderate-to-profound hearing loss who use hearing aids and/or cochlear implants participated. Their performance was compared with 35 age-matched controls with typical hearing. Orthographic learning was evaluated using a spelling task and a recognition task. The children were assessed on measures of reading ability, language, working memory, and paired-associate learning.

Results
On average, the DHH group performed more poorly than the TH controls on the spelling measure of orthographic learning, but not on the recognition measure. For both groups of children, there were significant correlations between orthographic learning and phonological decoding and between visual–verbal paired-associate learning and orthographic learning.

Conclusions
Although the children who are DHH had lower scores in the spelling test of orthographic learning than their TH peers, measures of their reading ability revealed that they acquired orthographic representations successfully. The results are consistent with the self-teaching hypothesis in suggesting that phonological decoding is important for orthographic learning.
Predicting Reading Problems 6 Years Into the Future: Dynamic Assessment Reduces Bias and Increases Classification Accuracy
Authors: Petersen Douglas B. , Gragg Shelbi L. , Spencer Trina D. 
Published: November 2018

Purpose
The purpose of this study was to examine how well a kindergarten dynamic assessment of decoding predicts future reading difficulty at 2nd, 3rd, 4th, and 5th grade and to determine whether the dynamic assessment improves the predictive validity of traditional static kindergarten reading measures.

Method
With a small variation in sample size by grade, approximately 370 Caucasian and Hispanic students were administered a 3-min dynamic assessment of decoding and static measures of letter identification and phonemic awareness at the beginning of kindergarten. Oral reading fluency was then assessed at the end of Grades 2–5. In this prospective, longitudinal study, predictive validity was estimated for the Caucasian and Hispanic students by examining the amount of variance the static and dynamic assessments explained and by referring to area under the curve and sensitivity and specificity values.

Results
The dynamic assessment accounted for variance in reading ability over and above the static measures, with fair to good area under the curve values and sensitivity and specificity. Classification accuracy worsened when the static measures were included as predictor measures. The results of this study indicate that a very brief dynamic assessment can predict with approximately 75%–80% accuracy, which kindergarten students will have difficulty in learning to decode up to 6 years into the future.

Conclusions
Dynamic assessment of decoding is a promising approach to identifying future reading difficulty of young kindergarten students, mitigating the cultural and linguistic bias found in traditional static early reading measures.
Parallel current‐fed resonant converter with balance current sharing and no input ripple current
Authors: Lin Bor‐Ren , Lin Yue 
Published: November 2018

This studies a parallel current‐fed resonant converter with the advantages of the balance current sharing and no input ripple current. The basic structure of the developed circuit includes a boost converter and half‐bridge resonant converter with the same power switches to reduce switch counts. Two boost‐type converters with an interleaved pulse with modulation are used in the front stage to eliminate input ripple current and reduce the size of boost inductor. Parallel resonant converter with magnetic coupling current balancing cell is adopted in the rear stage to automatically balance two resonant circuits and realise the zero‐voltage turn‐on switching for power devices. The voltage doubler circuit is employed on the secondary‐side to achieve high‐voltage output. The developed converter can be used for current‐type input source and voltage‐type output. Finally, experiments with 1 kW laboratory prototype are provided to confirm the feasibility of the proposed converter.
So Now My Patient Has Squamous Cell Cancer: Diagnosis, Staging, and Treatment of Squamous Cell Carcinoma of the Anal Canal and Anal Margin
Authors: Kin Cindy 
Published: November 2018

AbstractSquamous cell carcinomas of the anal canal and the anal margin are rare malignancies that are increasing in incidence. Patients with these tumors often experience delayed treatment due to delay in diagnosis or misdiagnosis of the condition. Distinguishing between anal canal and anal margin tumors has implications for staging and treatment. Chemoradiation therapy is the mainstay of treatment for anal canal squamous cell, with abdominoperineal resection reserved for salvage treatment in cases of persistent or recurrent disease. Early anal margin squamous cell carcinoma can be treated with wide local excision, but more advanced tumors require a combination of chemoradiation therapy and surgical excision.
Vasoactive Inotropic Score and Outcome Assessment in Cyanotic Infants after Cardiovascular Surgery
Authors: Talwar Sachin , Bansal Ashwani , Sahu Manoj , Singh Sarvesh , Choudhary Shiv , Airan Balram 
Published: November 2018

Abstract
Objective Prospective assessment of vasoactive inotropic score (VIS) for predicting postoperative outcomes in cyanotic infants following open-heart surgery.
Methods In this prospective observational study, postoperative outcomes were analyzed in 100 cyanotic infants operated between September 2014 and April 2016. Inotropic score and VIS were calculated at 1 hour, 24 hours, and 48 hours following surgery.
Results Mean age at surgery was 7.39 ± 4.4 months (3 days–12 months, median 9 months). Surgical procedures included repair of total anomalous pulmonary venous connection (n = 40), tetralogy of Fallot (n = 24), double outlet right ventricle with pulmonary stenosis (n = 4), bidirectional superior cavopulmonary anastomosis (n = 19), and miscellaneous (n = 13). On regression analysis, prolonged intensive care unit and hospital stay correlated best with VIS at 48-hour interval (R
2 = 0.67 and 0.50 respectively, p > 0.001). Low birth weight (< 2.5 kg), preoperative ventilation and high first-hour VIS score (> 25) were predictive of higher postoperative mortality. Maximum VIS at 24 and 48 hours were positively correlated with adverse postoperative outcomes (p < 0.001).
Conclusion In cyanotic infants undergoing open-heart surgery, higher 48-hour VIS was associated with poor postoperative outcome indicating its utility as a valuable tool in predicting postoperative outcomes.