Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture identification. 
*Results:* We first formulate the problem of PMF protein mixture identification as an optimization problem. Then, we show that the use of some simple heuristics enables us to find good solutions. As a result, we obtain much better identification results than previous methods. Moreover, the result on real MS data can be comparable with that of the peptide sequencing method. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF method in protein mixtures. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures

Communication between levels of transcriptional control improves robustness and adaptivity

Regulation of eukaryotic gene expression depends on groups of related proteins acting at the levels of chromatin organization, transcriptional initiation, RNA processing, and nuclear transport. However, a unified understanding of how these different levels of transcriptional control interact has been lacking. Here, we combine genome-wide protein–DNA binding data from multiple sources to infer the connections between functional groups of regulators in Saccharomyces cerevisiae. Our resulting transcriptional network uncovers novel biological relationships; supporting experiments confirm new associations between actively transcribed genes and Sir2 and Esc1, two proteins normally linked to silencing chromatin. Analysis of the regulatory network also reveals an elegant architecture for transcriptional control. Using communication theory, we show that most protein regulators prefer to form modules within their functional class, whereas essential proteins maintain the sparse connections between different classes. Moreover, we provide evidence that communication between different regulatory groups improves the robustness and adaptivity of the cell

Topological Superconductivity in Multifold Fermion Metals

Recently, multifold fermions characterized by band crossings with multifold degeneracy and Fermi surfaces with nontrivial Chern numbers have been discovered experimentally in AlPt[arXiv:1812.03310] and XSi(X=Rh,Co)[arXiv:1812.04466][arXiv:1901.03358][arXiv:1809.01312]. In this work, we largely expand the family of multifold fermion materials by pointing out that several well-studied noncentrosymmetric superconductors are indeed multifold fermion metals. Importantly, their normal state topological properties, which have been ignored in previous studies, play an important role in the superconducting properties. Taking Li$_2$Pd$_3$B and Li$_2$Pt$_3$B as examples, we found a large number of unconventional degenerate points, such as double spin-1, spin-3/2, Weyl and double Weyl topological band crossing points near the Fermi energy, which result in finite Chern numbers on Fermi surfaces. Long Fermi arc states in Li$_2$Pd$_3$B, originating from the nontrivial band topology were found. Importantly, it has been shown experimentally that Li$_2$Pd$_3$B and Li$_2$Pt$_3$B are fully gapped and gapless superconductors, respectively. By analyzing the possible pairing symmetries, we suggest that Li$_2$Pd$_3$B can be a DIII class topological superconductor with Majorana surface states, even though the spin-orbit coupling in Li$_2$Pd$_3$B is negligible. Interestingly, Li$_2$Pt$_3$B, being gapless, is likely to be a nodal topological superconductor with dispersionless surface Majorana modes. We further identified that several noncentrosymmetric superconductors, such as Mo$_3$Al$_2$C, PdBiSe, Y$_2$C$_3$ and La$_2$C$_3$, are multifold fermion superconductors whose normal state topological properties have been ignored in previous experimental and theoretical studies

Electron Correlation and the c-axis Dispersion of Cu d_z^2: a New Band Structure for High Temperature Superconductors

Previously we showed the major effect of electron correlation in the cuprate superconductors is to lower the energy of the Cu d_x^2-y^2/O p_sigma (x^2-y^2) band with respect to the Cu d_z^2/O' p_z (z^2) band. In our 2D Hubbard model for La_1.85Sr_0.15CuO_4 (LaSCO), the z^2 band is narrow and crosses the standard x^2-y^2 band just below the Fermi level. In this work, we introduce c-axis dispersion to the model and find the z^2 band to have considerable anisotropic 3D character. An additional hole-like surface opens up in the z^2 band at (0,0,2pi/c) which expands with doping. At sufficient doping levels, a symmetry allowed x^2-y^2/z^2 band crossing along the (0,0)-(pi,pi) direction of the Brillouin zone appears at the Fermi level. At this point, Cooper pairs between the two bands (e.g. (k uparrow x^2-y^2/k downarrow z^2)) can form, providing the basis for the Interband Pairing Theory of superconductivity in these materials.Comment: submitted to Phys. Rev. Lett. Related publications: Phys. Rev. B 58, 12303 (1998); Phys. Rev. B 58, 12323 (1998); cond-mat/9903088; cond-mat/990310

Dehazing Ultrasound using Diffusion Models

Echocardiography has been a prominent tool for the diagnosis of cardiac disease. However, these diagnoses can be heavily impeded by poor image quality. Acoustic clutter emerges due to multipath reflections imposed by layers of skin, subcutaneous fat, and intercostal muscle between the transducer and heart. As a result, haze and other noise artifacts pose a real challenge to cardiac ultrasound imaging. In many cases, especially with difficult-to-image patients such as patients with obesity, a diagnosis from B-Mode ultrasound imaging is effectively rendered unusable, forcing sonographers to resort to contrast-enhanced ultrasound examinations or refer patients to other imaging modalities. Tissue harmonic imaging has been a popular approach to combat haze, but in severe cases is still heavily impacted by haze. Alternatively, denoising algorithms are typically unable to remove highly structured and correlated noise, such as haze. It remains a challenge to accurately describe the statistical properties of structured haze, and develop an inference method to subsequently remove it. Diffusion models have emerged as powerful generative models and have shown their effectiveness in a variety of inverse problems. In this work, we present a joint posterior sampling framework that combines two separate diffusion models to model the distribution of both clean ultrasound and haze in an unsupervised manner. Furthermore, we demonstrate techniques for effectively training diffusion models on radio-frequency ultrasound data and highlight the advantages over image data. Experiments on both \emph{in-vitro} and \emph{in-vivo} cardiac datasets show that the proposed dehazing method effectively removes haze while preserving signals from weakly reflected tissue.Comment: 10 pages, 11 figures, preprint IEEE submissio

The Database of Macromolecular Motions: new features added at the decade mark

The database of molecular motions, MolMovDB (), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered on MolMovDB. In particular, we further developed the Morph Server to produce improved interpolations between two submitted structures. We added support for multiple chains to the original adiabatic mapping interpolation, allowing the analysis of subunit motions. We also added the option of using FRODA interpolation, which allows for more complex pathways, potentially overcoming steric barriers. We added an interface to a hinge prediction service, which acts on single structures and predicts likely residue points for flexibility. We developed tools to relate such points of flexibility in a structure to particular key residue positions, i.e. active sites or highly conserved positions. Lastly, we began relating our motion classification scheme to function using descriptions from the Gene Ontology Consortium

There's no place like home: 35-year patient survival on home hemodialysis.

The vast majority of maintenance dialysis patients suffer from poor long-term survival rates and lower levels of health-related quality of life. However, home hemodialysis is a historically significant dialysis modality that has been associated with favorable outcomes as well as greater patient autonomy and control, yet only represents a small minority of the total dialysis performed in the United States. Some potential disadvantages of home hemodialysis include vascular access complications, infection-related hospitalizations, patient fatigue, and attrition. In addition, current barriers and challenges in expanding the utilization of this modality include limited patient and provider education and technical expertise. Here we report a 65-year old male with end-stage renal disease due to Alport's syndrome who has undergone 35 years of uninterrupted thrice-weekly home hemodialysis (ie, every Sunday, Tuesday, and Thursday evening, each session lasting 3 to 3¼ hours in length) using a conventional hemodialysis machine who has maintained a high functional status allowing him to work 6-8 hours per day. The patient has been able to liberalize his dietary and fluid intake while only requiring 3-4 liters of ultrafiltration per treatment, despite having absence of residual kidney function. Through this case of extraordinary longevity and outcomes after 35 years of dialysis and a review of the literature, we illustrate the history of home hemodialysis, its significant clinical and psychosocial advantages, as well as the barriers that hinder its widespread adaptation

The Antiferromagnetic Band Structure of La2CuO4 Revisited

Using the Becke-3-LYP functional, we have performed band structure calculations on the high temperature superconductor parent compound, La2CuO4. Under the restricted spin formalism (rho(alpha) equal to rho(beta)), the R-B3LYP band structure agrees well with the standard LDA band structure. It is metallic with a single Cu x2-y2/O p(sigma) band crossing the Fermi level. Under the unrestricted spin formalism (rho(alpha) not equal to rho(beta)), the UB3LYP band structure has a spin polarized antiferromagnetic solution with a band gap of 2.0 eV, agreeing well with experiment. This state is 1.0 eV (per formula unit) lower than that calculated from the R-B3LYP. The apparent high energy of the spin restricted state is attributed to an overestimate of on-site Coulomb repulsion which is corrected in the unrestricted spin calculations. The stabilization of the total energy with spin polarization arises primarily from the stabilization of the x2-y2 band, such that the character of the eigenstates at the top of the valence band in the antiferromagnetic state becomes a strong mixture of Cu x2-y2/O p(sigma) and Cu z2/O' p(z). Since the Hohenberg-Kohn theorem requires the spin restricted and spin unrestricted calculations give exactly the same ground state energy and total density for the exact functionals, this large disparity in energy reflects the inadequacy of current functionals for describing the cuprates. This calls into question the use of band structures based on current restricted spin density functionals (including LDA) as a basis for single band theories of superconductivity in these materials.Comment: 13 pages, 8 figures, to appear in Phys. Rev. B, for more information see http://www.firstprinciples.co

Hepatitis C virus reinfection after successful treatment with direct-acting antiviral therapy in a large population-based cohort.

BACKGROUND & AIMS: Direct-acting antiviral therapies (DAA) are an important tool for hepatitis C virus (HCV) elimination. However, reinfection among people who inject drugs (PWID) may hamper elimination targets. Therefore, we estimated HCV reinfection rates among DAA-treated individuals, including PWID. METHODS: We analyzed data from the British Columbia Hepatitis Testers Cohort which included ∼1.7 million individuals screened for HCV in British Columbia, Canada. We followed HCV-infected individuals treated with DAAs who achieved a sustained virologic response (SVR) and had ≥1 subsequent HCV RNA measurement to April 22nd, 2018. Reinfection was defined as a positive RNA measurement after SVR. PWID were identified using a validated algorithm and classified based on recent (<3 years) or former (≥3 years before SVR) use. Crude reinfection rates per 100 person-years (PYs) were calculated. Poisson regression was used to model adjusted incidence rate ratios (IRRs) and 95% CIs. RESULTS: Of 4,114 individuals who met the inclusion criteria, most were male (n = 2,692, 65%), born before 1965 (n = 3,411, 83%) and were either recent (n = 875, 21%) or former PWID (n = 1,793, 44%). Opioid-agonist therapy (OAT) was received by 19% of PWID. We identified 40 reinfections during 2,767 PYs. Reinfection rates were higher among recent (3.1/100 PYs; IRR 6.7; 95% CI 1.9-23.5) and former PWID (1.4/100 PYs; IRR 3.7; 95% CI 1.1-12.9) than non-PWID (0.3/100 PYs). Among recent PWID, reinfection rates were higher among individuals born after 1975 (10.2/100 PYs) and those co-infected with HIV (5.7/100 PYs). Only one PWID receiving daily OAT developed reinfection. CONCLUSIONS: Population-level reinfection rates remain elevated after DAA therapy among PWID because of ongoing exposure risk. Engagement of PWID in harm-reduction and support services is needed to prevent reinfections. LAY SUMMARY: Direct-acting antivirals are an effective tool for the treatment of hepatitis C virus, enabling the elimination of the virus. However, some patients who have been successfully treated with direct-acting antivirals are at risk of reinfection. Our findings showed that the risk of reinfection was highest among people with recent injection drug use. Among people who inject drugs, daily use of opioid-agonist therapy was associated with a lower risk of reinfection

Precision grid and hand motion for accurate needle insertion in brachytherapy

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98741/1/MPH004749.pd