66 research outputs found
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New Methods Using Rigorous Machine Learning for Coarse-Grained Protein Folding and Dynamics
Artificial-intelligence-based molecular classification of diffuse gliomas using rapid, label-free optical imaging
Molecular classification has transformed the management of brain tumors by
enabling more accurate prognostication and personalized treatment. However,
timely molecular diagnostic testing for patients with brain tumors is limited,
complicating surgical and adjuvant treatment and obstructing clinical trial
enrollment. In this study, we developed DeepGlioma, a rapid ( seconds),
artificial-intelligence-based diagnostic screening system to streamline the
molecular diagnosis of diffuse gliomas. DeepGlioma is trained using a
multimodal dataset that includes stimulated Raman histology (SRH); a rapid,
label-free, non-consumptive, optical imaging method; and large-scale, public
genomic data. In a prospective, multicenter, international testing cohort of
patients with diffuse glioma () who underwent real-time SRH imaging, we
demonstrate that DeepGlioma can predict the molecular alterations used by the
World Health Organization to define the adult-type diffuse glioma taxonomy (IDH
mutation, 1p19q co-deletion and ATRX mutation), achieving a mean molecular
classification accuracy of . Our results represent how
artificial intelligence and optical histology can be used to provide a rapid
and scalable adjunct to wet lab methods for the molecular screening of patients
with diffuse glioma.Comment: Paper published in Nature Medicin
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank
Upsilon (1S+2S+3S) production in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and cold-nuclear matter effects
The three Upsilon states, Upsilon(1S+2S+3S), are measured in d+Au and p+p
collisions at sqrt(s_NN)=200 GeV and rapidities 1.2<|y|<2.2 by the PHENIX
experiment at the Relativistic Heavy-Ion Collider. Cross sections for the
inclusive Upsilon(1S+2S+3S) production are obtained. The inclusive yields per
binary collision for d+Au collisions relative to those in p+p collisions
(R_dAu) are found to be 0.62 +/- 0.26 (stat) +/- 0.13 (syst) in the gold-going
direction and 0.91 +/- 0.33 (stat) +/- 0.16 (syst) in the deuteron-going
direction. The measured results are compared to a nuclear-shadowing model,
EPS09 [JHEP 04, 065 (2009)], combined with a final-state breakup cross section,
sigma_br, and compared to lower energy p+A results. We also compare the results
to the PHENIX J/psi results [Phys. Rev. Lett. 107, 142301 (2011)]. The rapidity
dependence of the observed Upsilon suppression is consistent with lower energy
p+A measurements.Comment: 495 authors, 11 pages, 9 figures, 5 tables. Submitted to Phys. Rev.
C. Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Measurements of elliptic and triangular flow in high-multiplicity HeAu collisions at GeV
We present the first measurement of elliptic () and triangular ()
flow in high-multiplicity HeAu collisions at
GeV. Two-particle correlations, where the particles have a large separation in
pseudorapidity, are compared in HeAu and in collisions and
indicate that collective effects dominate the second and third Fourier
components for the correlations observed in the HeAu system. The
collective behavior is quantified in terms of elliptic and triangular
anisotropy coefficients measured with respect to their corresponding
event planes. The values are comparable to those previously measured in
Au collisions at the same nucleon-nucleon center-of-mass energy.
Comparison with various theoretical predictions are made, including to models
where the hot spots created by the impact of the three He nucleons on the
Au nucleus expand hydrodynamically to generate the triangular flow. The
agreement of these models with data may indicate the formation of low-viscosity
quark-gluon plasma even in these small collision systems.Comment: 630 authors, 9 pages, 4 figures, 2 tables. v2 is the version accepted
for publication by Physical Review Letters. Plain text data tables for the
points plotted in figures for this and previous PHENIX publications are (or
will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Measurement of long-range angular correlation and quadrupole anisotropy of pions and (anti)protons in central Au collisions at =200 GeV
We present azimuthal angular correlations between charged hadrons and energy
deposited in calorimeter towers in central Au and minimum bias
collisions at GeV. The charged hadron is measured at
midrapidity , and the energy is measured at large rapidity
(, Au-going direction). An enhanced near-side angular
correlation across 2.75 is observed in Au collisions.
Using the event plane method applied to the Au-going energy distribution, we
extract the anisotropy strength for inclusive charged hadrons at
midrapidity up to GeV/. We also present the measurement of
for identified and (anti)protons in central Au collisions,
and observe a mass-ordering pattern similar to that seen in heavy ion
collisions. These results are compared with viscous hydrodynamic calculations
and measurements from Pb at TeV. The magnitude of
the mass-ordering in Au is found to be smaller than that in Pb
collisions, which may indicate smaller radial flow in lower energy Au
collisions.Comment: 424 authors, 8 pages, and 4 figures. v2 is version accepted for
publication in Phys. Rev. Lett. Published version will be at
http://www.phenix.bnl.gov/phenix/WWW/info/pp1/161/ Plain text data tables
will be at http://www.phenix.bnl.gov/papers.htm
Cold-nuclear-matter effects on heavy-quark production at forward and backward rapidity in d+Au collisions at sqrt(s_NN)=200 GeV
The PHENIX experiment has measured open heavy-flavor production via
semileptonic decay muons over the transverse momentum range 1 < pT < 6 GeV/c at
forward and backward rapidity (1.4 < |y| < 2.0) in d+Au and p+p collisions at
?sNN = 200 GeV. In central d+Au collisions an enhancement (suppression) of
heavy-flavor muon production is observed at backward (forward) rapidity
relative to the yield in p+p collisions scaled by the number of binary
collisions. Modification of the gluon density distribution in the Au nucleus
contributes in terms of anti-shadowing enhancement and shadowing suppression;
however, the enhancement seen at backward rapidity exceeds expectations from
this effect alone. These results, implying an important role for additional
cold nuclear matter effects, serves as a key baseline for heavy-quark
measurements in A+A collisions and in constraining the magnitude of charmonia
breakup effects at the Relativistic Heavy Ion Collider and the Large Hadron
Collider.Comment: 424 authors, 69 insitutions, 8 pages, 4 figures. Submitted to
Physical Review Letters. Plain text data tables for the points plotted in
figures for this and previous PHENIX publications are (or will be) publicly
available at http://www.phenix.bnl.gov/papers.htm
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