bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outer rotation curve of the Galaxy with VERA. III. Astrometry of IRAS 07427−2400 and test of the density-wave theory
Authors: Sakai Nobuyuki , Nakanishi Hiroyuki , Matsuo Mitsuhiro , Koide Nagito , Tezuka Daisuke , Kurayama Tomoharu , Shibata Katsunori M. , Ueno Yuji , Honma Mareki 
Published: August 2015

Abstract
We report the trigonometric parallax of IRAS 07427−2400 with VERA to be 0.185 ± 0.027 mas, corresponding to a distance of 5.41$^{+0.92}_{-0.69}\:$kpc. The result is consistent with the previous result of 5.32$^{+0.49}_{-0.42}\:$kpc obtained by Choi et al. (2014, ApJ, 790, 99) within error. To remove the effect of internal maser motions (e.g., random motions), we observed six maser features associated with IRAS 07427−2400 and determined systematic proper motions of the source by averaging proper motions of the six maser features. The obtained proper motions are (μαcos δ, μδ) = (−1.79 ± 0.32, 2.60 ± 0.17) mas yr−1 in equatorial coordinates, while Choi et al. (2014) showed (μαcos δ, μδ) = (−2.43 ± 0.02, 2.49 ± 0.09) mas yr−1 with one maser feature. Our astrometry results place the source in the Perseus arm, the nearest main arm in the Milky Way. Using our result with previous astrometry results obtained from observations of the Perseus arm, we conducted direct (quantitative) comparisons between 27 astrometry results and an analytic gas dynamics model based on the density-wave theory, obtaining two results. First is the pitch angle of the Perseus arm determined by VLBI astrometry, 11 $_{.}^{\circ}$1 ± 1 $_{.}^{\circ}$4, differing from what is determined by the spiral potential model (probably traced by stars), ∼ 20°. The second is an offset between a dense gas region and the bottom of the spiral potential model. The dense gas region traced by VLBI astrometry is located downstream of the spiral potential model, which was previously confirmed in the nearby grand-design spiral galaxy M 51 in Egusa, Koda, and Scoville (2011, ApJ, 726, 85).
Study of infrared excess from circumstellar disks in binaries with Spitzer/IRAC
Authors: Itoh Yusuke , Fukagawa Misato , Shibai Hiroshi , Sumi Takahiro , Yamamoto Kodai 
Published: August 2015

Abstract
The presence of excess emission in the 3.6–8.0 μm region was investigated in a sample of 27 binary star systems located in two nearby star-forming regions, Taurus and Ophiuchus, by using Spitzer/Infrared Array Camera (IRAC) archival data. Angular (Projected) separations of the binaries are greater than 2″ (∼ 280 au), which enables us to perform spatially resolved photometry of individual primary and secondary sources. The measured occurrence of infrared excess suggests that binarity plays a role in the evolution of circumstellar disks, even at such wide binary separations. Most of the binaries have excess emission from both the circumprimary and circumsecondary disks, or show photospheric levels for both components at all four wavelengths of IRAC. On the other hand, four binary systems ($17^{+11}_{-8}$%, designated by “mixed” systems) exhibit the excess emission from a single binary component. This ratio is significantly smaller than that predicted by the random pairing of single stars, suggesting that circumprimary and circumsecondary disks are synchronously dispersed. In addition, the excess frequencies (EFs) of primary and secondary sources with a projected distance of ap ≃ 280–450 au are $100^{+0}_{-17}$% and $91^{+8}_{-18}$%, respectively, and significantly higher than that of single stars (70% ± 5%). We made a simple model describing the EF distribution as a function of the disk outer radius, Rout. Comparisons with observations using the Kolmogorov–Smirnov test show that the observational data are consistent with the model when the EF ≃ 100% region is found at Rout ∼ 30–100 au. This disk radius is smaller than that typically estimated for single stars. The high EF of circumstellar disks with these radii may indicate a prolonged lifetime of dust in binary systems, possibly because the smaller disks counteract mass loss by photoevaporation.
Chemoradiation for High-grade Neuroendocrine Carcinoma of the Rectum and Anal Canal
Authors: Voong K. Ranh , Rashid Asif , Crane Christopher H. , Minsky Bruce D. , Krishnan Sunil , Yao James C. , Wolff Robert A. , Skibber John M. , Feig Barry W. , Chang George J. , Das Prajnan 
Published: August 2015

Objectives:
We evaluated outcomes in patients with high-grade neuroendocrine (HGNE) carcinoma of the anorectum treated with pelvic chemoradiation.

Materials and Methods:
Between January 1, 2000 and February 17, 2013, 10 patients were confirmed to have HGNE carcinoma of the rectum or anal canal and treated with pelvic chemoradiation (radiation dose ≥45 Gy). Overall survival (OS), locoregional control (LRC), progression-free survival (PFS), and patterns of failure were evaluated.

Results:
Eight had pure HGNE carcinoma and 2 had HGNE carcinoma with minor component of adenocarcinoma. Median age was 62 years. Median follow-up was 15 months (range, 3 to 128 mo). Tumor stages included TxN0M0 (1), II (1), III (4), and IV (4) including 2 with only inguinal involvement. Median tumor size was 5.5 cm (range, 3 to 7 cm). Patients received postoperative chemoradiation (1), preoperative chemoradiation (2), and chemoradiation without surgery (7). Median dose was 50.4 Gy (range, 45 to 60 Gy). All patients received chemotherapy before or after chemoradiation. Seven had pelvic LRC; 2 had possible and 1 had confirmed local progression. Both patients who had preoperative chemoradiation only had microscopic focus of residual carcinoma at surgery. Seven had disease progression; of which all developed distant progression, with distant progression occurring as the first event in 6 (liver, lung, bone, and abdominal nodes). Actuarial 2-year PFS and OS were 30% and 46%, respectively. One patient received prophylactic cranial irradiation; only one of the other 9 patient developed brain metastasis.

Conclusions:
Pelvic chemoradiation provided LRC for the majority of the patients’ lifetime. Most patients had distant failure, but patterns of distant failure do not support routine prophylactic cranial irradiation.
Survival Outcomes Improved in Contemporary Cohort of Patients With Pelvic or Abdominal Recurrence After Treatment for Stage I/II Endometrial Carcinoma
Authors: Xu Melody J. , Chu Christina , Rubin Stephen , Lin Lilie L. 
Published: August 2015

Objectives:
Pelvic and abdominal recurrences in stage I/II endometrial carcinoma are associated with poor outcomes, yet prognostic factors for survival after recurrence are not well described. Herein, we identify patients with pelvic or abdominal recurrence after surgery for stage I/II endometrial carcinoma and describe symptoms at presentation, prognostic factors, and salvage treatment toxicity.

Materials and Methods:
This is a retrospective cohort of 20 consecutively treated patients with recurrence after treatment for stage I/II endometrial carcinoma followed by our Institution’s Radiation Oncology Department from 1998 to 2015.

Results:
The median time to pelvic or abdominal recurrence was 18.1 months (range, 4.2 to 59.6 mo), with 50% of recurrences at extranodal locations. Two-year progression-free survival (PFS) was 44% and 2-year overall survival (OS) was 82%. Salvage treatments varied widely, including chemotherapy and radiotherapy (RT) (7), surgery and RT (3), and surgery, chemotherapy, and RT (3). On univariate analysis of PFS, symptoms at recurrence (P=0.04) and extranodal recurrences (P<0.01) were found to be statistically significant negative prognosticators for PFS. On univariate analysis of OS, increasing age at recurrence and presence of symptoms were found to have a trend toward statistically significant association with negative OS outcomes (P=0.08 and P=0.10, respectively).

Conclusions:
Our study demonstrates that long-term survival for pelvic or abdominal recurrences is possible with curative salvage therapy. The presence of symptoms is a negative prognostic factor in treatment outcome, and imaging may be effective for diagnosis in symptomatic and asymptomatic patients. Larger studies need to be performed to confirm these findings.
Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life
Authors: Corvaglia Luigi , Tonti Giacomo , Martini Silvia , Aceti Arianna , Mazzola Giuseppe , Aloisio Irene , Di Gioia Diana , Faldella Giacomo 
Published: August 2015

ABSTRACTObjectives:The effect of intrapartum antibiotic prophylaxis (IAP) for group B Streptococcus (GBS) on bacterial colonization of the infant's gut has not been investigated extensively. We aimed to evaluate the effect of IAP on gut microbiota in healthy term infants, also exploring the influence of type of feeding.Methods:Healthy term infants, whose mothers had been screened for GBS in late gestation, were divided into 2 groups: infants born to GBS‐positive mothers who had received IAP versus controls. Neonatal fecal samples were collected at 7 and 30 days of life; DNA was extracted, and quantification of selected microbial groups (Lactobacillus spp, Bifidobacterium spp, and Bacteroides fragilis group) was performed by real‐time PCR.Results:A total of 84 infant–mother pairs were recruited. Bifidobacteria count was significantly lower in the IAP group at 7 days of life (median [interquartile range] 6.01 Log colony‐forming unit per gram [5.51–6.98] vs 7.80 [6.61–8.26], P = 0.000). No differences in Bifidobacteria count at 30 days or in Lactobacilli and B fragilis counts at any time point were documented. Furthermore, at 7 days of life, infants who had not received IAP and were exclusively human milk–fed had higher counts of Bifidobacteria. Regardless of IAP treatment, infants fed exclusively human milk had higher Lactobacillus spp counts both at 7 and 30 days of life.Conclusions:IAP alters gut microflora by reducing the count of Bifidobacteria, which is further affected in infants receiving formula feeding. Whether these alterations could have long‐term consequences on health and disease requires further investigation.
Impact and Culture Change After the Implementation of a Preprocedural Checklist in an Interventional Radiology Department
Authors: Wong Sydney Sek Ning , Cleverly Sue , Tan Kong Teng , Roche-Nagle Graham 
Published: August 2015

Objective
It has been accepted that the implementation of the a preprocedural surgical checklist can reduce perioperative morbidity and mortality in the operating suite. From this success, there has been focus on applying this intervention to other clinical areas. The objective of this study was to evaluate the acceptance and culture change after the implementation of a preprocedural checklist in the interventional radiology suite.

Methods
A preimplementation audit was performed to identify the need for a checklist in the department. A checklist was then developed, based on the surgical model. At 1 and 12 months after implementation, a survey was distributed to the staff at 3 separate teaching centers.

Results
Results showed that opinion of the checklist was generally positive, with staff agreement that it served as an important communication tool was in the patient's best interest, and presented a good opportunity for the team to identify important issues.

Conclusions
The checklist was regarded as having little effect on delay between cases. In our setting, the checklist has become a useful and consistent safety measure to ensure that relevant patient data are brought to the forefront before intervention. As a secondary benefit, it also serves as an important communication tool and improves collaboration among team members.
Formation and maintenance of robust long-term information storage in the presence of synaptic turnover
Authors: Fauth Michael , Wörgötter Florentin , Tetzlaff Christian 
Published: August 2015

AbstractA long-standing problem is how memories can be stored for very long times despite the volatility of the underlying neural substrate, most notably the high turnover of dendritic spines and synapses. To address this problem, here we are using a generic and simple probabilistic model for the creation and removal of synapses. We show that information can be stored for several months when utilizing the intrinsic dynamics of multi-synapse connections. In such systems, single synapses can still show high turnover, which enables fast learning of new information, but this will not perturb prior stored information (slow forgetting), which is represented by the compound state of the connections. The model matches the time course of recent experimental spine data during learning and memory in mice supporting the assumption of multi-synapse connections as the basis for long-term storage.Author SummaryIt is widely believed that information is stored in the connectivity, i.e. the synapses of neural networks. Yet, the morphological correlates of excitatory synapses, the dendritic spines, have been found to undergo a remarkable turnover on daily basis. This poses the question, how information can be retained on such a variable substrate.In this study, using connections with multiple synapses, we show that connections which follow the experimentally measured bimodal distribution in the number of synapses can store information orders of magnitude longer than the lifetime of a single synapse. This is a consequence of the underlying bistable collective dynamic of multiple synapses: Single synapses can appear and disappear without disturbing the memory as a whole.Furthermore, increasing or decreasing neural activity changes the distribution of the number of synapses of multi-synaptic connections such that only one of the peaks remains. This leads to a desirable property: information about these altered activities can be stored much faster than it is forgotten. Remarkably, the resulting model dynamics match recent experimental data investigating the long-term effect of learning on the dynamics of dendritic spines.
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis
Authors: Ezawa Kiyoshi , Graur Dan , Landan Giddy 
Published: August 2015

AbstractBackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. Recently, such probabilistic models are mostly based on either hidden Markov models (HMMs) or transducer theories, both of which give the indel component of the probability of a given sequence alignment as a product of either probabilities of column-to-column transitions or block-wise contributions along the alignment. However, it is nota prioriclear how these models are related with anygenuinestochastic evolutionary model, which describes the stochastic evolution of anentiresequence along the time-axis. Moreover, none of these models can fully accommodate biologically realistic features, such as overlapping indels, power-law indel-length distributions, and indel rate variation across regions.ResultsHere, we theoretically tackle theab initiocalculation of the probability of a given sequence alignment under agenuineevolutionary model, more specifically, a general continuous-time Markov model of the evolution of anentiresequence via insertions and deletions. Our model allows general indel rate parameters including length distributions but does not impose any unrealistic restrictions on indels. Using techniques of the perturbation theory in physics, we expand the probability into a series over different numbers of indels. Our derivation of this perturbation expansion elegantly bridges the gap between Gillespie’s (1977) intuitive derivation of his own stochastic simulation method, which is now widely used in evolutionary simulators, and Feller’s (1940) mathematically rigorous theorems that underpin Gillespie′s method. We find a sufficient and nearly necessary set of conditions under which the probability can be expressed as the product of an overall factor and the contributions from regions separated by gapless columns of the alignment. The indel models satisfying these conditions include those with some kind of rate variation across regions, as well as space-homogeneous models. We also prove that, though with a caveat, pairwise probabilities calculated by the method of Miklós et al. (2004) are equivalent to those calculated by ourab initioformulation, at least under a space-homogenous model.ConclusionsOur ab initio perturbative formulation provides a firm theoretical ground that other indel models can rest on.[This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend theab initioperturbative formulation of a general continuous-time Markov model of indels.]
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part II: Perturbation analyses
Authors: Ezawa Kiyoshi , Graur Dan , Landan Giddy 
Published: August 2015

AbstractBackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. In a separate paper (Ezawa, Graur and Landan 2015a), we established a theoretical basis of ourab initioperturbative formulation of agenuineevolutionary model, more specifically, a continuous-time Markov model of the evolution of anentiresequence via insertions and deletions. And we showed that, under some conditions, theab initioprobability of an alignment can be factorized into the product of an overall factor and contributions from regions (or local alignments) separated by gapless columns.ResultsThis paper describes how ourab initioperturbative formulation can be concretely used to approximately calculate the probabilities of all types of local pairwise alignments (PWAs) and some typical types of local multiple sequence alignments (MSAs). For each local alignment type, we calculated the fewest-indel contribution and the next-fewest-indel contribution to its probability, and we compared them under various conditions. We also derived a system of integral equations that can be numerically solved to give “exact solutions” for some common types of local PWAs. And we compared the obtained “exact solutions” with the fewest-indel contributions. The results indicated that even the fewest-indel terms alone can quite accurately approximate the probabilities of local alignments, as long as the segments and the branches in the tree are of modest lengths. Moreover, in the light of our formulation, we examined parameter regions where other indel models can safely approximate the correct evolutionary probabilities. The analyses also suggested some modifications necessary for these models to improve the accuracy of their probability estimations.ConclusionsAt least under modest conditions, ourab initioperturbative formulation can quite accurately calculate alignment probabilities under biologically realistic indel models. It also provides a sound reference point that other indel models can be compared to. [This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend theab initioperturbative formulation of a general continuous-time Markov model of indels.]
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations
Authors: Ezawa Kiyoshi , Graur Dan , Landan Giddy 
Published: August 2015

AbstractBackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. In a separate paper (Ezawa, Graur and Landan 2015a), we established the theoretical basis of ourab initioperturbative formulation of a continuous-time Markov model of the evolution of anentiresequence via insertions and deletions along time axis. In other separate papers (Ezawa, Graur and Landan 2015b,c), we also developed various analytical and computational methods to concretely calculate alignment probabilities via our formulation. In terms of frequencies, however, substitutions are usually more common than indels. Moreover, many experiments suggest that other mutations, such as genomic rearrangements and recombination, also play some important roles in sequence evolution.ResultsHere, we extend ourab initioperturbative formulation of agenuineevolutionary model so that it can incorporate other mutations. We give a sufficient set of conditions that the probability of evolution via both indels and substitutions is factorable into the product of an overall factor and local contributions. We also show that, under a set of conditions, the probability can be factorized into two sub-probabilities, one via indels alone and the other via substitutions alone. Moreover, we show that our formulation can be extended so that it can also incorporate genomic rearrangements, such as inversions and duplications. We also discuss how to accommodate some other types of mutations within our formulation.ConclusionsOurab initioperturbative formulation thus extended could in principle describe the stochastic evolution of anentiresequence along time axis via major types of mutations.[This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend theab initioperturbative formulation of a general continuous-time Markov model of indels.]
The constant philopater hypothesis: a new life history invariant for dispersal evolution
Authors: Rodrigues António M. M. , Gardner Andy 
Published: August 2015

AbstractLife history invariants play a pivotal role in the study of social adaptation: they provide theoretical hypotheses that can be empirically tested, and benchmark frameworks against which new theoretical developments can be understood. Here we derive a novel invariant for dispersal evolution: the “constant philopater hypothesis” (CPH). Specifically, we find that, irrespective of variation in maternal fecundity, all mothers are favoured to produce exactly the same number of philopatric offspring, with high-fecundity mothers investing proportionally more, and low-fecundity mothers investing proportionally less, into dispersing offspring. This result holds for female and male dispersal, under haploid, diploid and haplodiploid modes of inheritance, irrespective of the sex ratio, local resource availability, and whether mother or offspring controls the latter’s dispersal propensity. We explore the implications of this result for evolutionary conflicts of interest – and the exchange and withholding of contextual information – both within and between families, and we show that the CPH is the fundamental invariant that underpins and explains a wider family of invariance relationships that emerge from the study of social evolution.