bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new formulation of vector weights in localized particle filters
Authors: Shen Zheqi , Tang Youmin , Li Xiaojing 
Published: October 2017

Particle filters (PFs) constitute a sequential data assimilation method based on the Monte Carlo approximation of Bayesian estimation theory. Standard PFs use scalar weights derived from the likelihood of the approximate posterior probability density functions (PDFs) of observations and use resampling schemes to generate posterior particles. However, the scalar weights approach interferes with the localization algorithm and often results in filter degeneracy.Recently, a localized particle filter (LPF) was developed by extending the scalar weights of PFs to vector weights, which produces various (local) posterior PDFs for different model grids and variables. With a sampling and merging approach in the resampling, a LPF can effectively solve the filter degeneracy problem and offer a practical, efficient algorithm for localization. However, this algorithm assumes the variations in the weights of a state variable of neighbouring grids to be continuous and uses a spatially linear interpolation of PF weights to determine the local weights.In this paper, we first analyse the possible concerns associated with the linear continuity of PF weights. This assumption is found to challenge the theoretical properties of nonlinear and non‐Gaussian variations in weights and alleviate the intrinsic spatial variations of PF weights. On this basis, we propose a new algorithm to produce vector weights for PFs for neighbouring grids. Numerical experiments using the Lorenz 96 model show that our new LPF performs better than the existing LPF algorithm, indicating the advantages and potential applications of this new algorithm of vector weights in the field of data assimilation.
Application of the broadband collision‐induced dissociation (bbCID) mass spectrometry approach for protein glycosylation and phosphorylation analysis
Authors: Couto Narciso , Davlyatova Liliya , Evans Caroline A. , Wright Phillip C. 
Published: October 2017

RationaleAnalysis of post‐translationally modified peptides by mass spectrometry (MS) remains incomplete, in part due to incomplete sampling of all peptides which is inherent to traditional data‐dependent acquisition (DDA). An alternative MS approach, data‐independent acquisition (DIA), enables comprehensive recording of all detectable precursor and product ions, independent of precursor intensity. The use of broadband collision‐induced dissociation (bbCID), a DIA method, was evaluated for the identification of protein glycosylation and phosphorylation.MethodsbbCID was applied to identify glycopeptides and phosphopeptides generated from standard proteins using a high‐resolution Bruker maXis 3G mass spectrometer. In bbCID, precursor and product ion spectra were obtained by alternating low and high collision energy. Precursor ions were assigned manually based on the detection of diagnostic ions specific to either glycosylation or phosphorylation. The composition of the glycan modification was resolved in the positive ion mode, while the level of phosphorylation was investigated in the negative ion mode.ResultsThe results demonstrate for the first time that the use of a bbCID approach is suitable for the identification of glycopeptides and phosphopeptides based on the detection of specific diagnostic and associated precursor ions. The novel use of bbCID in negative ion mode allowed the discrimination of singly and multiply phosphorylated peptides based on the detection of phosphate diagnostic ions. The results also demonstrate the ability of this approach to allow the identification of glycan composition in N‐ and O‐linked glycopeptides, in positive ion mode.ConclusionsWe contend that bbCID is a valuable addition to the existing toolkit for PTM discovery. Moreover, this technique could be employed to direct targeted proteomics methods, particularly where there is no a priori information on glycosylation or phosphorylation status. This technique is immediately relevant to the characterisation of individual proteins or biological samples of low complexity, as demonstrated for the analysis of the glycosylation status of a therapeutic protein.
Structural investigation by tandem mass spectrometry analysis of a heterogeneous mixture of Lipid An isolated from the lipopolysaccharide of Aeromonas hydrophila SJ‐55Ra
Authors: Almostafa Mervt , Fridgen Travis D. , Banoub Joseph H. 
Published: October 2017

RationaleWe report herein the electrospray ionization mass spectrometry (ESI‐MS) negative ion mode and low‐energy collision‐induced dissociation tandem mass spectrometry (CID‐MS/MS) analysis of a mixture of lipid An isolated from the lipopolysaccharide (LPS) of a rough‐resistant wild strain of the Gram‐negative bacteria Aeromonas hydrophila grown in the presence of phages (SJ‐55Ra). This investigation indicates that the presence of a mixture of lipid A acylated disaccharides, whose molecular structures were not relatively conserved, resulted from the incomplete LPS biosynthesis caused by the phage treatment.MethodsThe heterogeneous lipid An mixture from the LPS‐SJ55Ra was obtained following growth of the Gram‐negative bacteria Aeromonas hydrophila (SJ‐55R) in the presence of phages and isolation by the aqueous phenol method. Following hydrolysis and purification of the lipopolysaccharide, ESI‐MS and low‐energy CID‐MS/MS analyses were performed on a triple‐quadrupole (QqQ) and a Fourier transform ion cyclotron resonance (FTICR) instrument.ResultsESI‐MS analysis suggested that this lipid An mixture contained eight molecular disaccharide anions and three monosaccharide anions. This series of lipid An was asymmetrically substituted with ((R)‐14:0(3‐OH)) fatty acids located at O‐3 and N‐2 and with branched fatty acids: (Cl4:0(3‐(R)‐O‐C14:0)) and (C12:0(3‐(R)‐O‐(14:0)) at the O‐3′ and N‐2′ positions.ConclusionsTandem mass spectrometric analyses allowed the exact determination of the fatty acid acylation locations on the D‐GlcpN disaccharide. The MS/MS results established that it was possible to selectively cleave C–O, C–N, and C–C bonds, together with glycosidic C–O and cross‐ring cleavages, affording excellent structural analysis of lipid A biomolecules.
Development of a physical shoulder simulator for the training of basic arthroscopic skills
Authors: McCracken Laura C. , Trejos Ana Luisa , LeBel Marie‐Eve , Poursartip Behnaz , Escoto Abelardo , Patel Rajni V. , Naish Michael D. 
Published: October 2017

AbstractBackgroundOrthopaedic training programs are incorporating arthroscopic simulations into their residency curricula. There is a need for a physical shoulder simulator that accommodates lateral decubitus and beach chair positions, has realistic anatomy, allows for an objective measure of performance and provides feedback to trainees.MethodsA physical shoulder simulator was developed for training basic arthroscopic skills. Sensors were embedded in the simulator to provide a means to assess performance. Subjects of varying skill level were invited to use the simulator and their performance was objectively assessed.ResultsNovice subjects improved their performance after practice with the simulator. A survey completed by experts recognized the simulator as a valuable tool for training basic arthroscopic skills.ConclusionsThe physical shoulder simulator helps train novices in basic arthroscopic skills and provides objective measures of performance. By using the physical shoulder simulator, residents could improve their basic arthroscopic skills, resulting in improved patient safety.
When dinosaurs fly: The role of firm capabilities in the ‘avianization’ of incumbents during disruptive technological change
Authors: Roy Raja , Lampert Curba M. , Stoyneva Irina 
Published: October 2017

Research Summary: Prior research suggests that large incumbents will become victims of disruptive technological change. We investigate the image sensor industry in which the emergence of CMOS sensors challenged the manufacturers of CCD sensors. Although this disruptive technological change led to the demise of CCD technology, it also led to avianization—or strategic renewal—for some incumbents, similar to how some dinosaurs survived the mass Cretaceous‐Tertiary extinction by evolving into birds. We find that CCD manufacturers that did avianize were preadapted to the disruptive CMOS technology in that they possessed relevant complementary technologies and access to in‐house users that allowed them to strategically renew themselves.Managerial Summary: We investigate the transition from CCD to CMOS image sensors in the digital image sensor industry. Although the emergence of CMOS sensors was disruptive to CCD sensors, we find that CCD sensor manufacturers such as Sony and Sharp successfully transitioned to manufacturing CMOS sensors. Contrary to popular press and prior academic research characterizing disruptive change as being a source of failure for large firms, our research reveals that firms that possess relevant complementary technologies and have access to in‐house users are able to strategically renew themselves in the face of a disruptive threat.
Added value of chromosomal microarray analysis over karyotyping in early pregnancy loss: systematic review and meta‐analysis
Authors: Pauta M. , Grande M. , Rodriguez‐Revenga L. , Kolomietz E. , Borrell A. 
Published: October 2017

ABSTRACTObjectiveTo estimate the increased test success rate and incremental yield of chromosomal microarray analysis (CMA) over conventional karyotyping in detection of pathogenic copy number variants (CNVs) and variants of unknown significance (VOUS) in early pregnancy loss.MethodThis was a systematic review conducted in accordance with PRISMA criteria. All articles identified in PubMed, Ovid MEDLINE and Web of Science, between January 2000 and April 2017, that described CNVs in early pregnancy losses (up to 20 weeks) were included. Risk differences were pooled to estimate the incremental yield of CMA over karyotyping overall, and after stratification. In addition, test success rate, defined as the proportion of informative results, was compared in series in which CMA and karyotyping were performed concurrently.ResultsTwenty‐three studies, reporting on 5507 pregnancy losses up to 20 weeks with full data available, met the inclusion criteria for analysis. In the series in which CMA and karyotyping were performed concurrently, CMA showed a significant improvement in success rate, providing informative results in 95% (95% CI, 94–96%) of cases compared with karyotyping in which informative results were provided in 68% (95% CI, 66–70%) of cases. Combined data from reviewed studies revealed that incremental yields of CMA over karyotyping were 2% (95% CI, 1–2%) for pathogenic CNVs and 4% (95% CI, 3–6%) for VOUS. The most common pathogenic CNVs reported were 22q11.21 and 1p36.33 deletion.ConclusionIn comparison with conventional karyotyping, CMA provides a significant increase in test success rate and incremental diagnostic yield in early pregnancy loss. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Effect of clomiphene citrate on endometrial thickness, ovulation, pregnancy and live birth in anovulatory women: systematic review and meta‐analysis
Authors: Gadalla M. A. , Huang S. , Wang R. , Norman R. J. , Abdullah S. A. , El Saman A. M. , Ismail A. M. , van Wely M. , Mol B. W. J. 
Published: October 2017

ABSTRACTObjectivesTo compare the impact of clomiphene citrate (CC) vs other drug regimens on mid‐cycle endometrial thickness (EMT), ovulation, pregnancy and live birth rates in women with World Health Organization (WHO) group II ovulatory disorders.MethodsWe searched MEDLINE, EMBASE, Scopus, Web of Science, The Cochrane Central Register of Clinical Trials (CENTRAL) and the non‐MEDLINE subset of PubMed from inception to December 2016 and cross‐checked references of relevant articles. We included only randomized controlled trials (RCTs) comparing CC used alone vs other drug regimens for ovulation induction in women with WHO group II anovulation. Outcomes were mid‐cycle EMT, ovulation, pregnancy and live birth rates. We pooled weighted mean differences (WMD) with 95% confidence intervals (CI) for continuous variables (EMT) and risk ratios (RR) with 95% CI for binary variables (ovulation, pregnancy and live birth rates).ResultsWe retrieved 1718 articles of which 33 RCTs (4349 women, 7210 ovulation induction cycles) were included. In 15 RCTs that compared CC with letrozole, EMT was lower in the CC group (1957 women, 3892 cycles; WMD, −1.39; 95% CI, −2.27 to −0.51; I2 = 100%), ovulation rates after CC and letrozole were comparable (1710 women, 3217 cycles; RR, 0.97; 95% CI, 0.90–1.04; I2 = 47%), while CC led to a lower pregnancy rate (1957 women, 3892 cycles; RR, 0.78; 95% CI, 0.63–0.95; I2 = 43%) and a lower live birth rate (RR, 0.70; 95% CI, 0.49–0.98; I2 = 35%). In two RCTs that compared CC with CC plus metformin, EMT, ovulation and pregnancy rates were comparable (101 women, 140 cycles; WMD, −0.23; 95% CI, −0.92 to 0.45; I2 = 78%; RR, 0.84; 95% CI, 0.67–1.06; I2 = 0%; and RR, 0.79; 95% CI, 0.33–1.87; I2 = 0%). In three studies that compared CC with CC plus N‐acetyl cysteine (NAC), EMT was lower in the CC group (340 women, 300 cycles; WMD, −1.51; 95% CI, −1.98 to −1.04; I2 = 45%). In two studies that compared CC with CC + nitric oxide (NO) donor, EMT was lower in the CC group (120 women, 304 cycles; WMD, −1.75; 95% CI, −2.08 to −1.41; I2 = 0%). Compared with CC plus NO donor or NAC, CC showed statistically significant lower ovulation and pregnancy rates. Compared with tamoxifen in three studies, CC showed a tendency towards lower EMT (571 women, 844 cycles; WMD, −1.34; 95% CI, −2.70 to 0.01; I2 = 96%) with comparable ovulation and pregnancy rates.ConclusionsIn women with WHO group II ovulatory disorders, ovulation induction with CC might result in lower EMT than other ovulation induction regimens. Whether the lower EMT caused the lower pregnancy and live birth rates remains to be elucidated. Letrozole seems to be beneficial for these women. However, our findings should be interpreted with caution as the quality of evidence was very low. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Gonadotropin‐releasing hormone agonists for ovarian protection during cancer chemotherapy: systematic review and meta‐analysis
Authors: Senra J. C. , Roque M. , Talim M. C. T. , Reis F. M. , Tavares R. L. C. 
Published: October 2017

ABSTRACTObjectiveTo evaluate the effectiveness of gonadotropin‐releasing hormone agonist (GnRHa) administration before and/or during cancer chemotherapy for the protection of ovarian reserve in premenopausal women without prior diagnosis of infertility.MethodsThis was a systematic review and meta‐analysis of randomized controlled trials (RCTs) comparing administration of GnRHa before and/or during chemotherapy vs chemotherapy alone. Eligible participants were premenopausal women at any stage of cancer, without previous diagnosis of infertility. An electronic database search in MEDLINE, CENTRAL, LILACS and
ClinicalTrials.gov was performed. After selecting eligible studies, the relative risk (RR) was assessed for primary ovarian insufficiency (POI)/amenorrhea and for spontaneous pregnancy after completion of treatment.ResultsThirteen RCTs comparing concurrent use of GnRHa and chemotherapy (609 participants) with chemotherapy alone (599 participants) were eligible for meta‐analysis. All trials were open‐label and patients had been treated for breast cancer (n = 1099) or lymphoma (n = 109). GnRHa had a significant benefit on the risk of POI/amenorrhea (RR, 0.60; 95% CI, 0.45–0.79), which persisted in subgroup analysis for breast cancer (RR, 0.57; 95% CI, 0.43–0.77) but not for lymphoma patients (RR, 0.70; 95% CI, 0.20–2.47). The rate of spontaneous pregnancy after completion of treatment was higher in women receiving GnRHa plus chemotherapy compared with those receiving chemotherapy alone (RR, 1.43; 95% CI, 1.01–2.02). Overall, the quality of evidence was low due to the unclear risk of bias, short follow‐up and lack of objective assessment of ovarian function and reserve.ConclusionsEvidence, albeit of low quality, supports the use of GnRHa before and/or during chemotherapy to reduce the risk of POI and increase the probability of spontaneous pregnancy in the short term. Further high quality RCTs with more accurate assessment of ovarian reserve are needed to support definitive recommendations for clinical practice. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Outcome of assisted reproduction in women with congenital uterine anomalies: a prospective observational study
Authors: Prior M. , Richardson A. , Asif S. , Polanski L. , Parris‐Larkin M. , Chandler J. , Fogg L. , Jassal P. , Thornton J. G. , Raine‐Fenning N. J. 
Published: October 2017

ABSTRACTObjectivesTo assess the prevalence of congenital uterine anomalies, including arcuate uterus, and their effect on reproductive outcome in subfertile women undergoing assisted reproduction.MethodsConsecutive women referred for subfertility between May 2009 and November 2015 who underwent assisted reproduction were included in the study. As part of the initial assessment, each woman underwent three‐dimensional transvaginal sonography. Uterine morphology was classified using the modified American Fertility Society (AFS) classification of congenital uterine anomalies proposed by Salim et al. If the external contour of the uterus was uniformly convex or had an indentation of < 10 mm, but there was a cavity indentation, it was defined as arcuate or septate. Arcuate uterus was further defined as the presence of a concave fundal indentation with a central point of indentation at an obtuse angle. Subseptate uterus was defined as the presence of a septum, not extending to the cervix, with the central point of the septum at an acute angle; if the septum extended to the internal cervical os, the uterus was defined as septate. Reproductive outcomes, including live birth, clinical pregnancy and preterm birth, were compared between women with a normal uterus and those with a congenital uterine anomaly. Subgroup analysis by type of uterine morphology and logistic regression analysis adjusted for age, body mass index, levels of anti‐Müllerian hormone, antral follicle count and number and day of embryo transfer were performed.ResultsA total of 2375 women were included in the study, of whom 1943 (81.8%) had a normal uterus and 432 (18.2%) had a congenital uterine anomaly. The most common anomalies were arcuate (n = 387 (16.3%)) and subseptate (n = 16 (0.7%)) uterus. The rate of live birth was similar between women with a uterine anomaly and those with a normal uterus (35% vs 37%; P = 0.47). The rates of clinical pregnancy, mode of delivery and sex of the newborn were also similar between the two groups. Preterm birth before 37 weeks' gestation was more common in women with uterine anomalies than in controls (22% vs 14%, respectively; P = 0.03). Subgroup analysis by type of anomaly showed no difference in the incidence of live birth and clinical pregnancy for women with an arcuate uterus, but indicated worse pregnancy outcome in women with other major anomalies (P = 0.042 and 0.048, respectively).ConclusionsCongenital uterine anomalies as a whole, when defined using the modified AFS classification, do not affect clinical pregnancy or live‐birth rates in women following assisted reproduction, but do increase the incidence of preterm birth. The presence of uterine abnormalities more severe than arcuate uterus significantly worsens all pregnancy outcomes. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Environmental humanities and climate change: understanding humans geologically and other life forms ethically
Authors: Robin Libby 
Published: October 2017

The task of reconceptualizing planetary change for the human imagination calls on a wide range of disciplinary wisdom. Environmental studies were guided by the natural sciences in the 1960s, and in the 1970s broadened to include policy and the social sciences. By the 1990s, with global environmental changes well‐documented, various humanist initiatives emerged, expanding the idea of ethics, responsibility and justice within the transdisciplinary mode of environmental studies. Shared problems, places, and scales form the basis for collaborative work in the environmental humanities, sometimes in partnerships with natural sciences and the creative arts. Experiential learning and trust in judgments based on different methods typically guide humanities interventions. Shifting the frameworks of environmental research to be more consciously inclusive and diverse is enabling concepts of the physical world that better include humans and taking ethics beyond humans to consider more‐than‐human Others. This review considers historically how the environment and the humanities became conceptualized together. It then explores three emerging fields in transdisciplinary environmental scholarship where environmental humanities are playing major leadership roles: (1) climate and biodiversity justice, both for humans and for other forms of life; (2) the Anthropocene as a metaphor for living with planetary changes and (3) life after ‘the end of nature,’ including rewilding and restoration. While environmental humanities also work in many other fields, these cases exemplify the crucial tasks of situating the human in geological and ecological terms and other life forms (the ‘more‐than‐human’) in ethical terms.WIREs Clim Change2018, 9:e499. doi: 10.1002/wcc.499This article is categorized under:Climate, History, Society, Culture > Disciplinary Perspectives
The fission yeast MAPK Spc1 senses perturbations in Cdc25 and Wee1 activities and targets Rad24 to restore this balance
Authors: Paul Madhurima , Ghosal Agamani , Bandyopadhyay Sushobhana , G. Prakadeeswari , Selvam Upasna , Rai Neeraj , Sundaram Geetanjali 
Published: October 2017

AbstractMitogen‐activated protein kinases (MAPKs) play vital roles in multiple cellular processes and represent prominently pursued targets for development of therapeutic regimes. The MAPK Spc1 (p38 homologue) is known to be very important for both mitotic promotion and delay in Schizosaccharomyces pombe. However, the mechanism responsible for mitotic inhibition has remained elusive. Cdc25 (Cdc2 activator) and Wee1 (Cdc2 inhibtor) are important determinants of mitotic timing in all eukaryotes. Our results show that Spc1 can sense the perturbations in the balance of Cdc25 and Wee1 activities in S. pombe and that its function as a mitotic inhibitor is very important for controlling the same. An Spc1–Srk1–Rad24‐dependent pathway for mitotic inhibition has been reported earlier.Here we report the presence of an alternative mechanism wherein Spc1 targets the 14–3–3 protein, Rad24, independently of Srk1, leading to relocalization of Cdc25 and mitotic inhibition. Our observations suggest that this pathway can serve as a backup mechanism for Cdc2 inactivation in the absence of Wee1.