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CERES is a new computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for copy number effects and variable sgRNA activity. Applying CERES to new genome-scale CRISPR–Cas9 essentiality screen data from 342 cancer cell lines and other published data sets shows that CERES decreases false-positive results and provides consistent estimates of sgRNA activity. The CRISPR–Cas9 system has revolutionized gene editing both at single genes and in multiplexed loss-of-function screens, thus enabling precise genome-scale identification of genes essential for proliferation and survival of cancer cells 1 , 2 . However, previous studies have reported that a gene-independent antiproliferative effect of Cas9-mediated DNA cleavage confounds such measurement of genetic dependency, thereby leading to false-positive results in copy number–amplified regions 3 , 4 . We developed CERES, a computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for the copy number–specific effect. In our efforts to define a cancer dependency map, we performed genome-scale CRISPR–Cas9 essentiality screens across 342 cancer cell lines and applied CERES to this data set. We found that CERES decreased false-positive results and estimated sgRNA activity for both this data set and previously published screens performed with different sgRNA libraries. We further demonstrate the utility of this collection of screens, after CERES correction, for identifying cancer-type-specific vulnerabilities.

Human neural stem cell transplantation (HuCNS-SC®) is a promising central nervous system (CNS) tissue repair strategy in patients with stable neurological deficits from chronic spinal cord injury (SCI). These immature human neural cells have been demonstrated to survive when transplanted in vivo, extend neural processes, form synaptic contacts, and improve functional outcomes after experimental SCI. A phase II single blind, randomized proof-of-concept study of the safety and efficacy of HuCNS-SC transplantation into the cervical spinal cord was undertaken in patients with chronic C5-7 tetraplegia, 4–24 months post-injury. In Cohort I (n = 6) dose escalation from 15,000,000 to 40,000,000 cells was performed to determine the optimum dose. In Cohort II an additional six participants were transplanted at target dose (40,000,000) and compared with four untreated controls. Within the transplant group, there were nine American Spinal Injury Association Impairment Scale (AIS) B and three AIS A participants with a median age at transplant of 28 years with an average time to transplant post-injury of 1 year. Immunosuppression was continued for 6 months post-transplant, and immunosuppressive blood levels of tacrolimus were achieved and well tolerated. At 1 year post-transplantation, there was no evidence of additional spinal cord damage, new lesions, or syrinx formation on magnetic resonance (MR) imaging. In summary, the incremental dose escalation design established surgical safety, tolerability, and feasibility in Cohort I. Interim analysis of Cohorts I and II demonstrated a trend toward Upper Extremity Motor Score (UEMS) and Graded Redefined Assessment of Strength, Sensibility, and Prehension (GRASSP) motor gains in the treated participants, but at a magnitude below the required clinical efficacy threshold set by the sponsor to support further development resulting in early study termination.

The rationale for implantation of autologous human Schwann cells (SCs) in persons with subacute spinal cord injury (SCI) is based on evidence that transplanted SCs are neuroprotective, support local axonal plasticity, and are capable of myelinating axons. A Phase I clinical trial was conducted to evaluate the safety of autologous human SC transplantation into the injury epicenter of six subjects with subacute SCI. The trial was an open-label, unblinded, non-randomized, non-placebo controlled study with a dose escalation design and standard medical rehabilitation. Participants were paraplegics with neurologically complete, trauma-induced spinal lesions. Autologous SCs were cultured in vitro from a sural nerve harvested from each participant and injected into the epicenter of the spinal lesion. Outcome measures for safety were protocol compliance, feasibility, adverse events, stability of neurological level, absence of detectable mass lesion, and the emergence of clinically significant neuropathic pain or muscle spasticity no greater than expected for a natural course cohort. One year post-transplantation, there were no surgical, medical, or neurological complications to indicate that the timing or procedure for the cell transplantation was unsafe. There were no adverse events or serious adverse events related to the cell therapy. There was no evidence of additional spinal cord damage, mass lesion, or syrinx formation. We conclude that it is feasible to identify eligible candidates, appropriately obtain informed consent, perform a peripheral nerve harvest to obtain SCs within 5–30 days of injury, and perform an intra-spinal transplantation of highly purified autologous SCs within 4–7 weeks of injury.

The use of fast surface redox storage (pseudocapacitive) mechanisms can enable devices that store much more energy than electrical double-layer capacitors (EDLCs) and, unlike batteries, can do so quite rapidly. Yet, few pseudocapacitive transition metal oxides can provide a high power capability due to their low intrinsic electronic and ionic conductivity. Here we demonstrate that two-dimensional transition metal carbides (MXenes) can operate at rates exceeding those of conventional EDLCs, but still provide higher volumetric and areal capacitance than carbon, electrically conducting polymers or transition metal oxides. We applied two distinct designs for MXene electrode architectures with improved ion accessibility to redox-active sites. A macroporous Ti 3 C 2 T x MXene film delivered up to 210 F g −1 at scan rates of 10 V s −1 , surpassing the best carbon supercapacitors known. In contrast, we show that MXene hydrogels are able to deliver volumetric capacitance of ∼1,500 F cm −3 reaching the previously unmatched volumetric performance of RuO 2 . Pseudocapacitors based on redox-active materials have relatively high energy density but suffer from low power capability. Here the authors report that two-dimensional transition metal carbides exhibit high gravimetric, volumetric and areal capacitance values at high charge/discharge rates.

It is generally accepted that solid–electrolyte interphase formed on the surface of lithium-battery electrodes play a key role in controlling their cycling performance. Although a large variety of surface-sensitive spectroscopies and microscopies were used for their characterization, the focus was on surface species nature rather than on the mechanical properties of the surface films. Here we report a highly sensitive method of gravimetric and viscoelastic probing of the formation of surface films on composite Li 4 Ti 5 O 12 electrode coupled with lithium ions intercalation into this electrode. Electrochemical quartz-crystal microbalance with dissipation monitoring measurements were performed with LiTFSI, LiPF 6 , and LiPF 6  + 2% vinylene carbonate solutions from which structural parameters of the surface films were returned by fitting to a multilayer viscoelastic model. Only a few fast cycles are required to qualify surface films on Li 4 Ti 5 O 12 anode improving in the sequence LiPF 6  < LiPF 6  + 2% vinylene carbonate << LiTFSI. The solid-electrolyte interphase formed on Li-battery electrodes strongly affects their cycling performance, however the mechanical properties of the surface films are not well-known. Here the authors report a sensitive gravimetric/viscoelastic method to probe surface film formation on composite electrodes, coupled with Li-ion intercalation.

Abstract BACKGROUND Human central nervous system stem cells (HuCNS-SC) are multipotent adult stem cells with successful engraftment, migration, and region-appropriate differentiation after spinal cord injury (SCI). OBJECTIVE To present data on the surgical safety profile and feasibility of multiple intramedullary perilesional injections of HuCNS-SC after SCI. METHODS Intramedullary free-hand (manual) transplantation of HuCNS-SC cells was performed in subjects with thoracic (n = 12) and cervical (n = 17) complete and sensory incomplete chronic traumatic SCI. RESULTS Intramedullary stem cell transplantation needle times in the thoracic cohort (20 M HuCNS-SC) were 19:30 min and total injection time was 42:15 min. The cervical cohort I (n = 6), demonstrated that escalating doses of HuCNS-SC up to 40 M range were well tolerated. In cohort II (40 M, n = 11), the intramedullary stem cell transplantation needle times and total injection time was 26:05 ± 1:08 and 58:14 ± 4:06 min, respectively. In the first year after injection, there were 4 serious adverse events in 4 of the 12 thoracic subjects and 15 serious adverse events in 9 of the 17 cervical patients. No safety concerns were considered related to the cells or the manual intramedullary injection. Cervical magnetic resonance images demonstrated mild increased T2 signal change in 8 of 17 transplanted subjects without motor decrements or emerging neuropathic pain. All T2 signal change resolved by 6 to 12 mo post-transplant. CONCLUSION A total cell dose of 20 M cells via 4 and up to 40 M cells via 8 perilesional intramedullary injections after thoracic and cervical SCI respectively proved safe and feasible using a manual injection technique.

Conventional electroanalytical and structure-analysis techniques provide limited information about ionic fluxes in electrochemical systems. A quartz crystal microbalance is now used as a gravimetric probe of the concentration and compositional changes in microporous activated carbon. Fast ionic transport in microporous activated-carbon electrodes is a prerequisite for the effective energy storage in electrochemical supercapacitors 1 , 2 . However, the quartz-crystal microbalance 3 , 4 , 5 , 6 , 7 , 8 (QCM), a direct tool to measure ionic fluxes in electrochemical systems, has not yet been used for studying transport phenomena in activated carbons (except for an early report on carbon nanotubes 9 ). Conventional electroanalytical 1 and suitable surface and structure-analysis techniques 10 , 11 , 12 provide limited prognostic information on this matter. It has been demonstrated herein that the QCM response of typical microporous activated carbons can serve as a gravimetric probe of the concentration and compositional changes in their pore volume. This allowed direct monitoring of the ionic fluxes, which depended strongly on the electrode’s point of zero change, pore width, ion size and cycling conditions (polarization amplitude, charge/discharge depth and so on). The information on the nature of ionic fluxes into activated carbons is critical for promoting improvements in the performance of electrochemical supercapacitors, membrane technologies and (electro/bio)chemical sensors.

Peripheral T-cell lymphomas (PTCL), a heterogeneous group of mature aggressive non-Hodgkin’s lymphomas, carry a worse prognosis for most subtypes when compared with their B-cell counterparts. Despite recent approval of newer therapies, the outlook for patients with relapsed/refractory (RR) PTCL remains poor and new treatment strategies are clearly needed. Targeting the profoundly immunosuppressive tumor microenvironment in PTCL is one such approach. To determine whether immune checkpoint blockade targeting program death receptor 1 would be effective in PTCL, we conducted an investigator-initiated phase 2 prospective study of single-agent nivolumab for RR PTCL. We report here results of the pre-specified interim analysis.MethodsThe primary objective was to assess the overall response rate (ORR). Secondary objectives were to assess safety and tolerability of nivolumab in PTCL and to assess progression-free survival (PFS), duration of response (DOR) and overall survival (OS). Hyperprogressive disease (HPD) was defined as time-to-treatment failure of less than or equal to one month from initiation of therapy.ResultsTwelve patients who received at least one cycle of nivolumab were included in this interim analysis. Half (6/12) of the patients had angioimmunoblastic T-cell lymphoma (AITL), 3/12 had PTCL, not otherwise specified. Most (11/12) were advanced stage, had extranodal disease (97.1%) and had received a prior autologous stem cell transplant (50%). The ORR was 33% (95% CI: 12.3 to 63.7%) with two complete response and two partial response. The median PFS was however short at 2.7 months (95% CI: 1.5 to NE); and the median OS was 6.7 months (95% CI: 3.4 to NE). The median DOR was also short at 3.6 months (95% CI: 1.9 to NE). HPD occurred in four patients, three of whom had AITL. Observed grade 3 and higher adverse events (AEs) were non-hematologic in 5/12 (42%), while hematologic AEs were seen in 3/12 (25%).ConclusionsNivolumab had modest clinical activity in R/R PTCL. Due to a high number of hyperprogression and short DOR, a decision was made to halt the study. These findings likely reflect the distinct biology of PTCL and should be considered when designing future studies using checkpoint inhibitors in these diseases.Trial registration numberNCT03075553.

Background Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in modeling gene regulatory networks. In the Boolean network model, the transcriptional state of each gene is represented by 0 (inactive) or 1 (active), and the relationship among genes is represented by logical gates updated at discrete time points. However, the Boolean gene states are never observed directly, but only indirectly and incompletely through noisy measurements based on expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays. The Partially-Observed Boolean Dynamical System (POBDS) signal model is distinct from other deterministic and stochastic Boolean network models in removing the requirement of a directly observable Boolean state vector and allowing uncertainty in the measurement process, addressing the scenario encountered in practice in transcriptomic analysis. Results BoolFilter is an R package that implements the POBDS model and associated algorithms for state and parameter estimation. It allows the user to estimate the Boolean states, network topology, and measurement parameters from time series of transcriptomic data using exact and approximated (particle) filters, as well as simulate the transcriptomic data for a given Boolean network model. Some of its infrastructure, such as the network interface, is the same as in the previously published R package for Boolean Networks BoolNet , which enhances compatibility and user accessibility to the new package. Conclusions We introduce the R package BoolFilter for Partially-Observed Boolean Dynamical Systems (POBDS). The BoolFilter package provides a useful toolbox for the bioinformatics community, with state-of-the-art algorithms for simulation of time series transcriptomic data as well as the inverse process of system identification from data obtained with various expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays.

This work summarizes the results of our studies devoted to Mg ions mobility in Chevrel phases (CPs), M x Mo 6 T 8 (M – metal, T = S, Se) and presents our vision of the problem of multivalent ions’ diffusion in intercalation compounds. A simplified analysis of the main factors, which affect the activation energy barriers, as well as experimental data of Mg ions insertion into different hosts, show that low Mg ions mobility in common transition metal oxides or sulfides cannot be explained only by strong ionic interactions, but it is rather caused by a hard redistribution of the bivalent cations charge in inorganic materials. In contrast to these hosts, CPs allow for a high mobility of multivalent cations, because their unusual crystal structure with octahedral Mo 6 -clusters enables a fast and efficient attainment of local electro-neutrality upon insertion of cations of high charge density. Analysis of diffusion pathways based on the detailed structural determinations sheds light on important aspects of the electrochemical behavior of CPs, such as partial Mg ions trapping in the course of reversible Mg insertion and the ways to avoid it.