113 research outputs found
A simpler and more efficient algorithm for the next-to-shortest path problem
Given an undirected graph with positive edge lengths and two
vertices and , the next-to-shortest path problem is to find an -path
which length is minimum amongst all -paths strictly longer than the
shortest path length. In this paper we show that the problem can be solved in
linear time if the distances from and to all other vertices are given.
Particularly our new algorithm runs in time for general
graphs, which improves the previous result of time for sparse
graphs, and takes only linear time for unweighted graphs, planar graphs, and
graphs with positive integer edge lengths.Comment: Partial result appeared in COCOA201
Role of Nebulin on Actomyosin Interaction Studied in situ in Demembranated Skeletal Muscle Fibers from Newborn Mice
Dispersive properties of quasi-phase-matched optical parametric amplifiers
The dispersive properties of non-degenerate optical parametric amplification
in quasi-phase-matched (QPM) nonlinear quadratic crystals with an arbitrary
grating profile are theoretically investigated in the no-pump-depletion limit.
The spectral group delay curve of the amplifier is shown to be univocally
determined by its spectral power gain curve through a Hilbert transform. Such a
constraint has important implications on the propagation of spectrally-narrow
optical pulses through the amplifier. In particular, it is shown that anomalous
transit times, corresponding to superluminal or even negative group velocities,
are possible near local minima of the spectral gain curve. A possible
experimental observation of such effects using a QPM Lithium-Niobate crystal is
suggested.Comment: submitted for publicatio
Jastrow-type calculations of one-nucleon removal reactions on open - shell nuclei
Single-particle overlap functions and spectroscopic factors are calculated on
the basis of Jastrow-type one-body density matrices of open-shell nuclei
constructed by using a factor cluster expansion. The calculations use the
relationship between the overlap functions corresponding to bound states of the
-particle system and the one-body density matrix for the ground state of
the -particle system. In this work we extend our previous analyses of
reactions on closed-shell nuclei by using the resulting overlap functions for
the description of the cross sections of reactions on the open -
shell nuclei Mg, Si and S and of S
reaction. The relative role of both shell structure and short-range
correlations incorporated in the correlation approach on the spectroscopic
factors and the reaction cross sections is pointed out.Comment: 11 pages, 5 figures, to be published in Phys. Rev.
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
A review of spatial causal inference methods for environmental and epidemiological applications
The scientific rigor and computational methods of causal inference have had
great impacts on many disciplines, but have only recently begun to take hold in
spatial applications. Spatial casual inference poses analytic challenges due to
complex correlation structures and interference between the treatment at one
location and the outcomes at others. In this paper, we review the current
literature on spatial causal inference and identify areas of future work. We
first discuss methods that exploit spatial structure to account for unmeasured
confounding variables. We then discuss causal analysis in the presence of
spatial interference including several common assumptions used to reduce the
complexity of the interference patterns under consideration. These methods are
extended to the spatiotemporal case where we compare and contrast the potential
outcomes framework with Granger causality, and to geostatistical analyses
involving spatial random fields of treatments and responses. The methods are
introduced in the context of observational environmental and epidemiological
studies, and are compared using both a simulation study and analysis of the
effect of ambient air pollution on COVID-19 mortality rate. Code to implement
many of the methods using the popular Bayesian software OpenBUGS is provided
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.
Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy
Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.
BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362
Desmin: molecular interactions and putative functions of the muscle intermediate filament protein
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival
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