bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate mass searching of individual lipid species candidates from high‐resolution mass spectra for shotgun lipidomics
Authors: Wang Miao , Huang Yingying , Han Xianlin 
Published: September 2014

RATIONALEWith the increased mass accuracy and resolution in commercialized mass spectrometers, new developments on shotgun lipidomics could be expected with increased speed, dynamic range, and coverage over lipid species and classes. However, we found that the major issue by using high mass accuracy/resolution instruments to search lipid species is the partial overlap between the two‐13C‐atom‐containing isotopologue of a species M (i.e., M+2 isotopologue) and the ion of a species with one less double bond than M (assigned here as L). This partial overlap alone could cause a mass shift of the species L to the lower mass end up to 12 ppm around m/z 750 as well as significant peak broadening.METHODSWe developed an approach for accurate mass searching by exploring one of the major features of shotgun lipidomics data that lipid species of a class are present in ion clusters where neighboring masses from different species differ by one or a few double bonds. In the approach, a mass‐searching window of 18 ppm (from –15 to 3 ppm) was first searched for an entire group of species of a lipid class. Then accurate mass searching of the plus one 13C isotopologue of individual species was used to eliminate the potential false positive.RESULTSThe approach was extensively validated through comparing with the species determined by the multi‐dimensional MS‐based shotgun lipidomics platform. The newly developed strategy of accurate mass searching enables the overlapped L species to be identified and the corresponding peak intensities to be acquired.CONCLUSIONSWe believe that this novel approach could substantially broaden the applications of high mass accurate/resolution mass spectrometry for shotgun lipidomics. Copyright © 2014 John Wiley & Sons, Ltd.
QoS provisioning by power control for video communication via satellite links
Authors: Ma Ting , Lee Yee Hui , Winkler Stefan , Ma Maode 
Published: September 2014

SummaryVideo transmissions over satellite links are sensitive to signal fades because of rain, especially in the tropics. We performed a video‐streaming experiment over a satellite link for 24 days distributed over 1 year to investigate the effects of rain fade. Based on the measurements, models for the relationships between rainfall rate, power level, packet loss, and video quality are proposed. Furthermore, for both uplink and downlink channel, an adaptive closed loop power control algorithm, with a Proportional–Integral–Derivative controller is designed. This is used for the mitigation of the rain‐induced attenuation in order to guarantee a certain level of Quality of Service and Quality of Experience. Simulation results show the effectiveness of the proposed power control solution and its ability to sustain video quality levels in spite of rain fades. Copyright © 2014 John Wiley & Sons, Ltd.
Practical key‐dependent message chosen‐ciphertext security based on decisional composite residuosity and quadratic residuosity assumptions
Authors: Chang Jinyong , Xue Rui 
Published: September 2014

AbstractAn encryption scheme is key‐dependent message chosen plaintext attack (KDM‐CPA) secure if it is secure even against an attacker who has access to encryptions of messages that depend on the secret key. Such situations naturally occur in some scenarios such as formal calculus, hard‐disk encryption, or multi‐party protocols. However, up to now, there are not many schemes that achieve KDM‐CPA security, let alone KDM chosen ciphertext attack (KDM‐CCA) security. The constructions proposed by Camenisch, Chandran, and Shoup (Eurocrypt 2009), and Hofheinz (Eurocrypt 2013) are the only two general constructions that can be proved to be KDM‐CCA secure in the standard model. Besides, Qin, Liu, and Huang (ACISP 2013) also presented another concrete implementation. In particular, they showed how to obtain KDM‐CCA security from the classic Cramer–Shoup cryptosystem (based on the decisional Diffie–Hellman assumption) w.r.t. a new ensemble of functions (we call QLH ensemble). Since the Cramer–Shoup scheme has short ciphertext size and higher computational efficiency, they obtain practical KDM‐CCA security w.r.t. a reasonably large ensemble.In this paper, we study the KDM‐CCA security of other cryptosystems proposed by Cramer and Shoup (Eurocrypt 2002). In particular, we prove that the schemes, based on decisional composite residuosity (DCR) and quadratic residuosity (QR) assumptions, respectively, also achieve KDM‐CCA security w.r.t. the QLH ensemble. On the one hand, because the DCR‐based and QR‐based schemes of Cramer et al. are fairly practical, we also obtain practical KDM‐CCA security based on DCR and QR assumptions, respectively. On the other hand, compared with the result of Qin et al., we need not tailor the original schemes of Cramer et al. because themselves have natural “compatibility” for the message space and the secret key space. Copyright © 2014 John Wiley & Sons, Ltd.
Wnt/β-Catenin Signaling Regulates Sequential Fate Decisions of Murine Cortical Precursor Cells
Authors: Draganova Kalina , Zemke Martina , Zurkirchen Luis , Valenta Tomas , Cantù Claudio , Okoniewski Michal , Schmid Marie-Theres , Hoffmans Raymond , Götz Magdalena , Basler Konrad , Sommer Lukas 
Published: September 2014

Abstract
The fate of neural progenitor cells (NPCs) is determined by a complex interplay of intrinsic programs and extrinsic signals, very few of which are known. β-Catenin transduces extracellular Wnt signals, but also maintains adherens junctions integrity. Here, we identify for the first time the contribution of β-catenin transcriptional activity as opposed to its adhesion role in the development of the cerebral cortex by combining a novel β-catenin mutant allele with conditional inactivation approaches. Wnt/β-catenin signaling ablation leads to premature NPC differentiation, but, in addition, to a change in progenitor cell cycle kinetics and an increase in basally dividing progenitors. Interestingly, Wnt/β-catenin signaling affects the sequential fate switch of progenitors, leading to a shortened neurogenic period with decreased number of both deep and upper-layer neurons and later, to precocious astrogenesis. Indeed, a genome-wide analysis highlighted the premature activation of a corticogenesis differentiation program in the Wnt/β-catenin signaling-ablated cortex. Thus, β-catenin signaling controls the expression of a set of genes that appear to act downstream of canonical Wnt signaling to regulate the stage-specific production of appropriate progenitor numbers, neuronal subpopulations, and astroglia in the forebrain. Stem Cells 2015;33:170–182
Mesenchymal Stromal Cells Express GARP/LRRC32 on Their Surface: Effects on Their Biology and Immunomodulatory Capacity
Authors: Carrillo-Galvez Ana Belén , Cobo Marién , Cuevas-Ocaña Sara , Gutiérrez-Guerrero Alejandra , Sánchez-Gilabert Almudena , Bongarzone Pierpaolo , García-Pérez Angélica , Muñoz Pilar , Benabdellah Karim , Toscano Miguel G. , Martín Francisco , Anderson Per 
Published: September 2014

Abstract
Mesenchymal stromal cells (MSCs) represent a promising tool for therapy in regenerative medicine, transplantation, and autoimmune disease due to their trophic and immunomodulatory activities. However, we are still far from understanding the mechanisms of action of MSCs in these processes. Transforming growth factor (TGF)-β1 is a pleiotropic cytokine involved in MSC migration, differentiation, and immunomodulation. Recently, glycoprotein A repetitions predominant (GARP) was shown to bind latency-associated peptide (LAP)/TGF-β1 to the cell surface of activated Foxp3+ regulatory T cells (Tregs) and megakaryocytes/platelets. In this manuscript, we show that human and mouse MSCs express GARP which presents LAP/TGF-β1 on their cell surface. Silencing GARP expression in MSCs increased their secretion and activation of TGF-β1 and reduced their proliferative capacity in a TGF-β1-independent manner. Importantly, we showed that GARP expression on MSCs contributed to their ability to inhibit T-cell responses in vitro. In summary, we have found that GARP is an essential molecule for MSC biology, regulating their immunomodulatory and proliferative activities. We envision GARP as a new target for improving the therapeutic efficacy of MSCs and also as a novel MSC marker. Stem Cells 2015;33:183–195
Daylight Vision Repair by Cell Transplantation
Authors: Santos-Ferreira Tiago , Postel Kai , Stutzki Henrike , Kurth Thomas , Zeck Günther , Ader Marius 
Published: September 2014

Abstract
Human daylight vision depends on cone photoreceptors and their degeneration results in visual impairment and blindness as observed in several eye diseases including age-related macular degeneration, cone-rod dystrophies, or late stage retinitis pigmentosa, with no cure available. Preclinical cell replacement approaches in mouse retina have been focusing on rod dystrophies, due to the availability of sufficient donor material from the rod-dominated mouse retina, leaving the development of treatment options for cone degenerations not well studied. Thus, an abundant and traceable source for donor cone-like photoreceptors was generated by crossing neural retina leucine zipper-deficient (Nrl−/−) mice with an ubiquitous green fluorescent protein (GFP) reporter line resulting in double transgenic tg(Nrl−/−; aGFP) mice. In Nrl−/− retinas, all rods are converted into cone-like photoreceptors that express CD73 allowing their enrichment by CD73-based magnetic activated cell sorting prior transplantation into the subretinal space of adult wild-type, cone-only (Nrl−/−), or cone photoreceptor function loss 1 (Cpfl1) mice. Donor cells correctly integrated into host retinas, acquired mature photoreceptor morphology, expressed cone-specific markers, and survived for up to 6 months, with significantly increased integration rates in the cone-only Nrl−/− retina. Individual retinal ganglion cell recordings demonstrated the restoration of photopic responses in cone degeneration mice following transplantation suggesting, for the first time, the feasibility of daylight vision repair by cell replacement in the adult mammalian retina. Stem Cells 2015;33:79–90
Concise Reviews: A Stem Cell Apostasy: A Tale of Four H Words
Authors: Quesenberry Peter J. , Goldberg Laura R. , Dooner Mark S. 
Published: September 2014

Abstract
The field of hematopoietic stem cell (HSC) biology has become increasingly dominated by the pursuit and study of highly purified populations of HSCs. Such HSCs are typically isolated based on their cell surface marker expression patterns and ultimately defined by their multipotency and capacity for self-generation. However, even with progressively more stringent stem cell separation techniques, the resultant HSC population remains heterogeneous with respect to both self-renewal and differentiation capacity. Critical studies on unseparated whole bone marrow have definitively shown that long-term engraftable HSCs are in active cell cycle and thus continually changing phenotype. Therefore, they cannot be purified by current approaches dependent on stable surface epitope expression because the surface markers are continually changing as well. These critical cycling cells are discarded with current stem cell purifications. Despite this, research defining such characteristics as self-renewal capacity, lineage-commitment, bone marrow niches, and proliferative state of HSCs continues to focus predominantly on this small subpopulation of purified marrow cells. This review discusses the research leading to the hierarchical model of hematopoiesis and questions the dogmas pertaining to HSC quiescence and purification. Stem Cells 2015;33:15–20
Sexual Assault Training in the Military: Evaluating Efforts to End the “Invisible War”
Authors: Holland Kathryn J. , Rabelo Verónica Caridad , Cortina Lilia M. 
Published: September 2014

AbstractSexual assault is an insidious problem in the United States military. In 2005 the Department of Defense (DoD) created the Sexual Assault Prevention and Response Office, which centralizes responsibility for sexual assault training. However, this training initiative has undergone little evaluation by outside researchers. Addressing this need, we analyzed responses from over 24,000 active duty personnel who completed the 2010 DoD Workplace and Gender Relations Survey. We assessed whether sexual assault training exposure (None, Minimal, Partial, or Comprehensive) predicted accurate knowledge of sexual assault resources and protocols. Using a social‐ecological framework, we investigated whether institutional and individual factors influenced Service members’ training exposure and judgment of training effectiveness. According to our results, exposure to comprehensive training predicted lower sexual assault incidence and superior knowledge. However, comprehensive training differed as a function of military branch, rank, gender, and sexual assault history. Judgments of training effectiveness also varied across these dimensions. Our results highlight the importance of considering context, gender, and victimization history when evaluating institutional efforts to end sexual violence. The DoD's 2010 annual report on military sexual assault concluded that “most Active Duty members receive effective training on sexual assault” (p. 104). Our results cast doubt on that assertion.
“How Should I Tell my Child?” Disclosing the Diagnosis of Sex Chromosome Aneuploidies
Authors: Dennis Anna , Howell Susan , Cordeiro Lisa , Tartaglia Nicole 
Published: September 2014

AbstractTo date, the disclosure of a sex chromosome aneuploidy (SCA) diagnosis to an affected individual has not been explored. This study aimed to assess the timing and content revealed to an affected child by his or her parent(s), resources accessed in preparation, parental feelings of preparedness, common parental concerns, and recommendations for disclosure approaches. Two online surveys were created: 1) for parents of a child with a diagnosis and 2) for individuals with a diagnosis. One‐hundred thirty‐nine parent surveys (XXY n = 68, XXX n = 21, XYY n = 9, other SCAs n = 41) and 67 individual surveys (XXY n = 58, XXX n = 9) were analyzed. Parents most frequently discussed the topics of learning disabilities (47 %) and genetics (45 %) with their child during the initial disclosure. A significantly greater proportion of parent respondents reported feeling prepared vs. unprepared for disclosure, regardless of their child's diagnosis (z‐test of proportions, all p's < 0.001). Both prepared and unprepared parents most frequently accessed resources such as websites, support groups, and discussion with the child's physician prior to disclosure, with unprepared parents accessing fewer resources (M = 2.0 ± 1.41) than prepared parents [M = 2. ± 1.56; t(101) =−2.02, p < 0.05]. Common parental concerns included making the conversation age‐appropriate, discussing infertility, and possible impact on the child's self‐esteem. Both parent and individual respondents endorsed being honest with the child, disclosing the diagnosis early and before puberty, and discussing the diagnosis gradually over time. These results provide recommendations for parents, and suggest benefits from additional resources and supports to alleviate concerns when approaching diagnosis disclosure.
Attention, locomotor activity and developmental milestones in rats prenatally exposed to ethanol
Authors: Brys Ivani , Pupe Stéfano , Bizarro Lisiane 
Published: September 2014

AbstractRationaleDecline of attentional performance as a function of time engaged on a task and hyperactivity are features shared by children and adults with fetal alcohol syndrome or attentional deficit and hyperactivity disorders.ObjectiveTo investigate the effects of prenatal exposure to two doses of ethanol on developmental milestones, locomotor activity and attention.MethodsWistar rats born from dams exposed to one of four maternal treatments during pregnancy were used: A35 – liquid diet with 35% ethanol‐derived calories; A10 – liquid diet with 10% ethanol‐derived calories; control – ethanol‐free liquid diet; chow – laboratory chow and water.ResultsA35 performed worse in grip strength than control and chow (postnatal day – 14, p < 0.05) but not in negative geotaxis (postnatal days 7–10); A35 also showed more locomotor activity than control and A10 (p < 0.05). Regarding attention, acquisition of the five choice reaction time task was similar between groups, but, the percentage of omission errors from A35 group was greater than other groups at baseline parameters, at shorter (2 s) and longer (7 s) inter‐trial intervals and at a shorter stimulus duration (0.5 s) (p < 0.05). The percentage of omissions was larger in A35 as the blocks progressed in sessions with either longer or shorter inter‐trial intervals (group × block p < 0.05). Animals from A10 group did not show any impairment in the tasks performed.ConclusionsOur study demonstrates that as well as developmental impairments, prenatal ethanol can produce deficits associated with an increase in attentional demand in rodents, analogous to those observed in fetal alcohol syndrome and attentional deficit and hyperactivity disorders.
HIV, other sexually transmitted infections, and risk behaviors among female sex workers in Liuzhou, China
Authors: Fan Yin‐Guang , Liu Jin‐Ji , Zhang Yu‐Jing , Dai Se‐Ying , Li Ming‐Qiang , Ye Dong‐Qing 
Published: September 2014

AbstractObjectiveTo determine the prevalence of infections with HIV and hepatitis C virus (HCV), and of syphilis among female sex workers (FSWs) in Liuzhou, China, along with levels of HIV‐related knowledge and frequencies of risk behaviors.MethodsA cross‐sectional survey was conducted between July 2012 and January 2013. FSWs (aged ≥ 16 years; reported receiving payment for sex in previous 6 months) working at 58 selected commercial sex establishments (level 1 [>¥300 per transaction], level 2 [¥100–300], or level 3 [<¥100]) completed a questionnaire and provided blood samples for testing.ResultsOf 622 participating FSWs, 7 (1.1%) had HIV infection, 67 (10.8%) syphilis, and 44 (7.1%) HCV infection. Consistent condom use during commercial sex encounters in the past month was reported by 412 (66.2%) FSWs. Inconsistent condom use was most likely in FSWs working in level 3 establishments (odds ratio [OR] 1.85; 95% CI 1.02–3.39), with a regular partner (OR 1.65; 95% CI 1.12–2.45), and who used illicit drugs (OR 2.10; 95% CI 1.24–3.54). Inconsistent condom use was least likely in FSWs with high HIV awareness (OR 0.29; 95% CI 0.18–0.48) and who had had a previous HIV test (OR 0.51; 95% CI 0.34–0.76).ConclusionFurther prioritized and combined programs aimed at FSWs are needed to prevent HIV transmission in China.
Pressure fluctuations produced by forward steps immersed in a turbulent boundary layer
Authors: Awasthi Manuj , Devenport William J. , Glegg Stewart A. L. , Forest Jonathan B. 
Published: September 2014

AbstractExperiments have been performed on the disturbance of a high-Reynolds-number turbulent boundary layer by three forward steps with sizes close to 3.8, 15 and 60 % of the boundary layer thickness. Particular attention is focused on the impact of the steps on the fluctuating surface pressure field. Measurements were made from 5 boundary layer thicknesses upstream to 22 boundary layer thicknesses downstream of the step, a distance equivalent to over 600 step heights for the smallest step size. Flow speeds of 30 and $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}60\ \mathrm{m}\ {\mathrm{s}}^{-1}$ were studied, corresponding to boundary layer momentum thickness Reynolds numbers of 15 500 and 26 600 and step size Reynolds numbers from 6640 to 213 000. The steps produce a disturbance to the boundary layer pressure spectrum that scales on step size and decays remarkably slowly with distance downstream. When normalized on step height and free-stream velocity, the disturbance is self-similar and appears to develop almost independently of the enveloping boundary layer. The disturbance is still clearly visible at 150 step heights downstream of the mid-size step. Pressure correlations show the disturbance to be characterized by organized quasiperiodic motions that become visible well downstream of reattachment. The coherence and scale of these motions, as seen in the wall pressure correlations, scales on the step height and thus their visibility relative to the boundary layer grows rapidly as the step size is increased.
Intermittency route to thermoacoustic instability in turbulent combustors
Authors: Nair Vineeth , Thampi Gireeshkumaran , Sujith R. I. 
Published: September 2014

AbstractThe dynamic transition from combustion noise to combustion instability was investigated experimentally in two laboratory-scale turbulent combustors (namely, swirl-stabilized and bluff-body-stabilized backward-facing-step combustors) by systematically varying the flow Reynolds number. We observe that the onset of combustion-driven oscillations is always presaged by intermittent bursts of high-amplitude periodic oscillations that appear in a near-random fashion amidst regions of aperiodic low-amplitude fluctuations. These excursions to periodic oscillations last longer in time as operating conditions approach instability and finally the system transitions completely into periodic oscillations. A continuous measure to quantify this bifurcation in dynamics can be obtained by defining an order parameter as the probability of the signal amplitude exceeding a predefined threshold. A hysteresis zone was observed in the bluff-body-stabilized configuration that was absent in the swirl-stabilized configuration. The recurrence properties of the dynamics of intermittent burst oscillations were quantified using recurrence plots and the distribution of the aperiodic phases was examined. From the statistics of these aperiodic phases, robust early-warning signals of an impending combustion instability may be obtained.
Three-dimensional boundary layers with short spanwise scales
Authors: Hewitt Richard E. , Duck Peter W. 
Published: September 2014

AbstractWe investigate three-dimensional (laminar) boundary layers that include a spanwise scale comparable to the boundary-layer thickness. A forcing of short spanwise scales requires viscous dissipation to be retained in the two-dimensional cross-section, perpendicular to the external flow direction, and in this respect the flows are related to previous work on corner boundary layers. We use two examples to highlight the main features of this category of boundary layer: (i) a flat plate of narrow (spanwise) width, and (ii) a narrow (spanwise) gap cut into an otherwise infinite flat plate; in both cases the plate is aligned with a uniform oncoming stream. We find that a novel feature arises in connection with the external flow; the presence of a narrow gap/plate (or indeed any comparable short-scale feature of long streamwise extent) necessarily modifies the streamwise mass flux in that vicinity, which in turn induces an associated boundary-layer transpiration on the same short spanwise length scale. This (short-scale) transpiration region leads to a half-line-source/sink correction to the outer inviscid, irrotational flow. Crucially, the volumetric flux associated with this line-source/sink must be explicitly included as part of the computational procedure for the leading-order boundary layer, and as such there is a weak interaction between the outer (inviscid) flow and the boundary layer. This is a generic feature of boundary layers that are forced through the presence of short-scale spanwise variations.