A mutation-induced drug resistance database (MdrDB).

Mutation-induced drug resistance is a significant challenge to the clinical treatment of many diseases, as structural changes in proteins can diminish drug efficacy. Understanding how mutations affect protein-ligand binding affinities is crucial for developing new drugs and therapies. However, the lack of a large-scale and high-quality database has hindered the research progresses in this area. To address this issue, we have developed MdrDB, a database that integrates data from seven publicly available datasets, which is the largest database of its kind. By integrating information on drug sensitivity and cell line mutations from Genomics of Drug Sensitivity in Cancer and DepMap, MdrDB has substantially expanded the existing drug resistance data. MdrDB is comprised of 100,537 samples of 240 proteins (which encompass 5119 total PDB structures), 2503 mutations, and 440 drugs. Each sample brings together 3D structures of wild type and mutant protein-ligand complexes, binding affinity changes upon mutation (ΔΔG), and biochemical features. Experimental results with MdrDB demonstrate its effectiveness in significantly enhancing the performance of commonly used machine learning models when predicting ΔΔG in three standard benchmarking scenarios. In conclusion, MdrDB is a comprehensive database that can advance the understanding of mutation-induced drug resistance, and accelerate the discovery of novel chemicals.

TenCirChem: An Efficient Quantum Computational Chemistry Package for the NISQ Era.

TenCirChem is an open-source Python library for simulating variational quantum algorithms for quantum computational chemistry. TenCirChem shows high-performance in the simulation of unitary coupled-cluster circuits, using compact representations of quantum states and excitation operators. Additionally, TenCirChem supports noisy circuit simulation and provides algorithms for variational quantum dynamics. TenCirChem's capabilities are demonstrated through various examples, such as the calculation of the potential energy curve of H2O with a 6-31G(d) basis set using a 34-qubit quantum circuit, the examination of the impact of quantum gate errors on the variational energy of the H2 molecule, and the exploration of the Marcus inverted region for charge transfer rate based on variational quantum dynamics. Furthermore, TenCirChem is capable of running real quantum hardware experiments, making it a versatile tool for both simulation and experimentation in the field of quantum computational chemistry.

Shortcuts to adiabaticity for open systems in circuit quantum electrodynamics.

Shortcuts to adiabaticity are powerful quantum control methods, allowing quick evolution into target states of otherwise slow adiabatic dynamics. Such methods have widespread applications in quantum technologies, and various shortcuts to adiabaticity protocols have been demonstrated in closed systems. However, realizing shortcuts to adiabaticity for open quantum systems has presented a challenge due to the complex controls in existing proposals. Here, we present the experimental demonstration of shortcuts to adiabaticity for open quantum systems, using a superconducting circuit quantum electrodynamics system. By applying a counterdiabatic driving pulse, we reduce the adiabatic evolution time of a single lossy mode from 800 ns to 100 ns. In addition, we propose and implement an optimal control protocol to achieve fast and qubit-unconditional equilibrium of multiple lossy modes. Our results pave the way for precise time-domain control of open quantum systems and have potential applications in designing fast open-system protocols of physical and interdisciplinary interest, such as accelerating bioengineering and chemical reaction dynamics.

Rapid and unconditional parametric reset protocol for tunable superconducting qubits.

Qubit initialization is a critical task in quantum computation and communication. Extensive efforts have been made to achieve this with high speed, efficiency and scalability. However, previous approaches have either been measurement-based and required fast feedback, suffered from crosstalk or required sophisticated calibration. Here, we report a fast and high-fidelity reset scheme, avoiding the issues above without any additional chip architecture. By modulating the flux through a transmon qubit, we realize a swap between the qubit and its readout resonator that suppresses the excited state population to 0.08% ± 0.08% within 34 ns (284 ns if photon depletion of the resonator is required). Furthermore, our approach (i) can achieve effective second excited state depletion, (ii) has negligible effects on neighboring qubits, and (iii) offers a way to entangle the qubit with an itinerant single photon, useful in quantum communication applications.

A scoping literature review of studies assessing effectiveness and cost-effectiveness of prosthetic and orthotic interventions.

Purpose: Approximately 1.5% of the world's population (∼100 million people) need a prosthesis/orthosis. The objective of the study was to establish an overview of the literature that has examined prosthetic and orthotic interventions with a view to inform policy development.Methods: Fourteen databases were searched from 1995-2015. Studies reporting primary research on the effectiveness or cost-effectiveness of prosthetic and orthotic interventions were examined. Metadata and information on study characteristics were extracted from the included studies.Results: The searches resulted in a total of 28,958 articles, a focus on studies with the words "randomized" OR "randomized" OR "cost" OR "economic" in their citation reduced this total to 2644. Research has predominantly been conducted in Australia, Canada, Germany, Netherlands, UK and USA. A total of 346 randomized controlled trials were identified, with only four randomized controlled trials examining prosthetic interventions. The majority of research examined lower limb orthoses in the adult population and used a wide range of outcome measures.Conclusions: While various international organizations have highlighted the value of providing prosthetic and orthotic services, both to the user and society as a whole, the availability of scientific research to inform policy is limited. Future structured evaluation of prosthetic and orthotic interventions/services is warranted to inform future policy developments.Implications for rehabilitationResearch into prosthetic and orthotic interventions has grown substantially in the last 20 years, with most of this research conducted in a small number of countries and focusing on the use of lower limb orthotics in adult populations.Research to date has utilized an extensive range of outcome measures, the development of agreed standardized sets of outcomes would allow comparison and combination of results in future research.This study highlights the need for further research in this area, especially studies which examine the cost-effectiveness of prosthetic and orthotic provision.

Quantum communication beyond the localization length in disordered spin chains.

We study the effects of localization on quantum state transfer in spin chains. We show how to use quantum error correction and multiple parallel spin chains to send a qubit with high fidelity over arbitrary distances, in particular, distances much greater than the localization length of the chain.