Molecular Dynamics and Other HPC Simulations for Drug Discovery

High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical systems with high precision in a short time, thanks to the use of sophisticated algorithms. It promotes the advancement of knowledge in fields that are inaccessible or difficult to access through experimentation and it contributes to accelerating the discovery of drugs for unmet medical needs while reducing costs. Herein, we report how computational performance has evolved over the past years, and then we detail three domains where HPC is essential. Molecular dynamics (MD) is commonly used to explore the flexibility of proteins, thus generating a better understanding of different possible approaches to modulate their activity. Modeling and simulation of biopolymer complexes enables the study of protein-protein interactions (PPI) in healthy and disease states, thus helping the identification of targets of pharmacological interest. Virtual screening (VS) also benefits from HPC to predict in a short time, among millions or billions of virtual chemical compounds, the best potential ligands that will be tested in relevant assays to start a rational drug design process.

In silico screening of SARS-CoV2 helicase using African natural products: Docking and molecular dynamics approaches

In the current medical era, there is an urgent necessity to identify new effective drugs to enrich the COVID-19's therapeutic arsenal. The SARS-COV-2 NSP13/helicase enzyme has been identified as a potential target for developing novel COVID-19 inhibitors. In this work, we aimed at endorsing effective natural products with potential inhibitory action towards the NSP13 through the virtual screening of 1012 natural products of botanical and marine origin from the South African Natural Compounds Database (SANCDB). The molecules were docked into the NTPase active site, and the best twelve compounds were chosen for further analysis. Thereafter, a combination of molecular dynamics simulations and MM-GBSA free energy calculations were carried out for a subset of best hits complexed with NSP13 helicase. We believe that the findings of this work will pave the way for additional research and experimental validation of some natural products as viable NSP13 helicase inhibitors.

Altered brain functional connectivity in vegetative state and minimally conscious state

Objectives

The pathological mechanism for a disorder of consciousness (DoC) is still not fully understood. Based on traditional behavioral scales, there is a high rate of misdiagnosis for subtypes of DoC. We aimed to explore whether topological characterization may explain the pathological mechanisms of DoC and be effective in diagnosing the subtypes of DoC.

Methods

Using resting-state functional magnetic resonance imaging data, the weighted brain functional networks for normal control subjects and patients with vegetative state (VS) and minimally conscious state (MCS) were constructed. Global and local network characteristics of each group were analyzed. A support vector machine was employed to identify MCS and VS patients.

Results

The average connection strength was reduced in DoC patients and roughly equivalent in MCS and VS groups. Global efficiency, local efficiency, and clustering coefficients were reduced, and characteristic path length was increased in DoC patients (p < 0.05). For patients of both groups, global network measures were not significantly different (p > 0.05). Nodal efficiency, nodal local efficiency, and nodal clustering coefficient were reduced in frontoparietal brain areas, limbic structures, and occipital and temporal brain areas (p < 0.05). The comparison of nodal centrality suggested that DoC causes reorganization of the network structure on a large scale, especially the thalamus. Lobal network measures emphasized that the differences between the two groups of patients mainly involved frontoparietal brain areas. The accuracy, sensitivity, and specificity of the classifier for identifying MCS and VS patients were 89.83, 78.95, and 95%, respectively.

Conclusion

There is an association between altered network structures and clinical symptoms of DoC. With the help of network metrics, it is feasible to differentiate MCS and VS patients.

Sex differences in externalizing and internalizing traits and ventral striatal responses to monetary loss

Ventral striatum (VS) processes rewarding and punishing stimuli. Women and men vary in externalizing and internalizing traits, which may influence neural responses to reward and punishment. To investigate sex differences in how individual traits influence VS responses to reward and punishment, we curated the data of the Human Connectome Project and identified 981 (473 men) subjects evaluated by the Achenbach Adult Self-Report Syndrome Scales. We processed the imaging data with published routines and extracted VS response (β) to win and to loss vs. baseline in a gambling task for correlation with externalizing and internalizing symptom severity. Men vs. women showed more severe externalizing symptoms and higher VS response to monetary losses (VS-loss β) but not to wins. Men but not women showed a significant, positive correlation between VS-loss β and externalizing traits, and the sex difference was confirmed by a slope test. The correlations of VS-loss vs. externalizing and of VS-win vs. externalizing and those of VS-loss vs. externalizing and of VS-loss vs. internalizing traits both differed significantly in slope, confirming its specificity, in men. Further, the sex-specific relationship between VS-loss β and externalizing trait did not extend to activities during exposure to negative emotion in the face matching task. To conclude, VS responses to loss but not to win and their correlation with externalizing rather than internalizing symptom severity showed sex differences in young adults. The findings highlight the relationship of externalizing traits and VS response to monetary loss and may have implications for psychological models of externalizing behaviors in men.

Tumor Biology and Microenvironment of Vestibular Schwannoma-Relation to Tumor Growth and Hearing Loss

Vestibular schwannoma is the most common benign neoplasm of the cerebellopontine angle. It arises from Schwann cells of the vestibular nerve. The first symptoms of vestibular schwannoma include hearing loss, tinnitus, and vestibular symptoms. In the event of further growth, cerebellar and brainstem symptoms, along with palsy of the adjacent cranial nerves, may be present. Although hearing impairment is present in 95% of patients diagnosed with vestibular schwannoma, most tumors do not progress in size or have low growth rates. However, the clinical picture has unpredictable dynamics, and there are currently no reliable predictors of the tumor's behavior. The etiology of the hearing loss in patients with vestibular schwannoma is unclear. Given the presence of hearing loss in patients with non-growing tumors, a purely mechanistic approach is insufficient. A possible explanation for this may be that the function of the auditory system may be affected by the paracrine activity of the tumor. Moreover, initiation of the development and growth progression of vestibular schwannomas is not yet clearly understood. Biallelic loss of the NF2 gene does not explain the occurrence in all patients; therefore, detection of gene expression abnormalities in cases of progressive growth is required. As in other areas of cancer research, the tumor microenvironment is coming to the forefront, also in vestibular schwannomas. In the paradigm of the tumor microenvironment, the stroma of the tumor actively influences the tumor's behavior. However, research in the area of vestibular schwannomas is at an early stage. Thus, knowledge of the molecular mechanisms of tumorigenesis and interactions between cells present within the tumor is crucial for the diagnosis, prediction of tumor behavior, and targeted therapeutic interventions. In this review, we provide an overview of the current knowledge in the field of molecular biology and tumor microenvironment of vestibular schwannomas, as well as their relationship to tumor growth and hearing loss.

Genome-wide association analysis identifies a susceptibility locus for sporadic vestibular schwannoma at 9p21

Vestibular schwannomas are benign nerve sheath tumours that arise on the vestibulocochlear nerves. Vestibular schwannomas are known to occur in the context of tumour predisposition syndromes NF2-related and LZTR1-related schwannomatosis. However, the majority of vestibular schwannomas present sporadically without identification of germline pathogenic variants. To identify novel genetic associations with risk of vestibular schwannoma development, we conducted a genome-wide association study in a cohort of 911 sporadic vestibular schwannoma cases collated from the neurofibromatosis type 2 genetic testing service in the North West of England, UK and 5,500 control samples from the UK Biobank resource. One risk locus reached genome-wide significance in our association analysis (9p21.3, rs1556516, P = 1.47e-13, odds ratio = 0.67, allele frequency = 0.52). 9p21.3 is a genome-wide association study association hotspot, and a number of genes are localised to this region, notably CDKN2B-AS1 and CDKN2A/B, also referred to as the INK4 locus. Dysregulation of gene products within the INK4 locus have been associated with multiple pathologies and the genes in this region have been observed to directly impact the expression of one another. Recurrent associations of the INK4 locus with components of well described oncogenic pathways provides compelling evidence that the 9p21.3 region is truly associated with risk of vestibular schwannoma tumourigenesis.

RAD51 Inhibitor and Radiation Toxicity in Vestibular Schwannoma

OBJECTIVE

To describe the RAD51 response (DNA repair) to radiation-induced DNA damage in patient-derived vestibular schwannoma (VS) cells and investigate the utility of RAD51 inhibitor (RI-1) in enhancing radiation toxicity.

STUDY DESIGN

Basic and translational science.

SETTING

Tertiary academic facility.

METHODS

VS tumors (n = 10) were cultured on 96-well plates and 16-well slides, exposed to radiation (0, 6, 12, or 18 Gy), and treated with RI-1 (0, 5, or 10 µM). Immunofluorescence was performed at 6 hours for γ-H2AX (DNA damage marker), RAD51 (DNA repair protein), and p21 (cell cycle arrest protein). Viability assays were performed at 96 hours, and capillary Western blotting was utilized to determine RAD51 expression in naïve VS tumors (n = 5).

RESULTS

VS tumors expressed RAD51. In cultured VS cells, radiation initiated dose-dependent increases in γ-H2AX and p21 expression. VS cells upregulated RAD51 to repair DNA damage following radiation. Addition of RI-1 reduced RAD51 expression in a dose-dependent manner and was associated with increased γ-H2AX levels and decreased viability in a majority of cultured VS tumors.

CONCLUSION

VS may evade radiation injury by entering cell cycle arrest and upregulating RAD51-dependent repair of radiation-induced double-stranded breaks in DNA. Although there was variability in responses among individual primary VS cells, RAD51 inhibition with RI-1 reduced RAD51-dependent DNA repair to enhance radiation toxicity in VS cells. Further investigations are warranted to understand the mechanisms of radiation resistance in VS and determine whether RI-1 is an effective radiosensitizer in patients with VS.

Facilitating SARS CoV-2 RNA-Dependent RNA polymerase (RdRp) drug discovery by the aid of HCV NS5B palm subdomain binders: In silico approaches and benchmarking

Corona Virus 2019 Disease (COVID-19) is a rapidly emerging pandemic caused by a newly discovered beta coronavirus, called Sever Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). SARS CoV-2 is an enveloped, single stranded RNA virus that depends on RNA-dependent RNA polymerase (RdRp) to replicate. Therefore, SARS CoV-2 RdRp is considered as a promising target to cease virus replication. SARS CoV-2 polymerase shows high structural similarity to Hepatitis C Virus-1b genotype (HCV-1b) polymerase.

Arising from the high similarity between SARS CoV-2 RdRp and HCV NS5B, we utilized the reported small-molecule binders to the palm subdomain of HCV NS5B (genotype 1b) to generate a high-quality DEKOIS 2.0 benchmark set and conducted a benchmarking analysis against HCV NS5B. The three highly cited and publicly available docking tools AutoDock Vina, FRED and PLANTS were benchmarked. Based on the benchmarking results and analysis via pROC-Chemotype plot, PLANTS showed the best screening performance and can recognize potent binders at the early enrichment. Accordingly, we used PLANTS in a prospective virtual screening to repurpose both the FDA-approved drugs (DrugBank) and the HCV-NS5B palm subdomain binders (BindingDB) for SARS CoV-2 RdRp palm subdomain. Further assessment by molecular dynamics simulations for 50 ns recommended diosmin (from DrugBank) and compound 3 (from BindingDB) to be the best potential binders to SARS CoV-2 RdRp palm subdomain. The best predicted compounds are recommended to be biologically investigated against COVID-19. In conclusion, this work provides in-silico analysis to propose possible SARS CoV-2 RdRp palm subdomain binders recommended as a remedy for COVID-19. Up-to-our knowledge, this study is the first to propose binders at the palm subdomain of SARS CoV2 RdRp. Furthermore, this study delivers an example of how to make use of a high quality custom-made DEKOIS 2.0 benchmark set as a procedure to elevate the virtual screening success rate against a vital target of the rapidly emerging pandemic.

Targeting multiple conformations of SARS-CoV2 Papain-Like Protease for drug repositioning: An in-silico study

Papain-Like Protease (PLpro) is a key protein for SARS-CoV-2 viral replication which is the cause of the emerging COVID-19 pandemic. Targeting PLpro can suppress viral replication and provide treatment options for COVID-19. Due to the dynamic nature of its binding site loop, PLpro multiple conformations were generated through a long-range 1 micro-second molecular dynamics (MD) simulation. Clustering the MD trajectory enabled us to extract representative structures for the conformational space generated. Adding to the MD representative structures, X-ray structures were involved in an ensemble docking approach to screen the FDA approved drugs for a drug repositioning endeavor. Guided by our recent benchmarking study of SARS-CoV-2 PLpro, FRED docking software was selected for such a virtual screening task. The results highlighted potential consensus binders to many of the MD clusters as well as the newly introduced X-ray structure of PLpro complexed with a small molecule. For instance, three drugs Benserazide, Dobutamine and Masoprocol showed a superior consensus enrichment against the PLpro conformations. Further MD simulations for these drugs complexed with PLpro suggested the superior stability and binding of dobutamine and masoprocol inside the binding site compared to Benserazide. Generally, this approach can facilitate identifying drugs for repositioning via targeting multiple conformations of a crucial target for the rapidly emerging COVID-19 pandemic.

Supporting SARS-CoV-2 Papain-Like Protease Drug Discovery: In silico Methods and Benchmarking

The coronavirus disease 19 (COVID-19) is a rapidly growing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Its papain-like protease (SARS-CoV-2 PLpro) is a crucial target to halt virus replication. SARS-CoV PLpro and SARS-CoV-2 PLpro share an 82.9% sequence identity and a 100% sequence identity for the binding site reported to accommodate small molecules in SARS-CoV. The flexible key binding site residues Tyr269 and Gln270 for small-molecule recognition in SARS-CoV PLpro exist also in SARS-CoV-2 PLpro. This inspired us to use the reported small-molecule binders to SARS-CoV PLpro to generate a high-quality DEKOIS 2.0 benchmark set. Accordingly, we used them in a cross-benchmarking study against SARS-CoV-2 PLpro. As there is no SARS-CoV-2 PLpro structure complexed with a small-molecule ligand publicly available at the time of manuscript submission, we built a homology model based on the ligand-bound SARS-CoV structure for benchmarking and docking purposes. Three publicly available docking tools FRED, AutoDock Vina, and PLANTS were benchmarked. All showed better-than-random performances, with FRED performing best against the built model. Detailed performance analysis via pROC-Chemotype plots showed a strong enrichment of the most potent bioactives in the early docking ranks. Cross-benchmarking against the X-ray structure complexed with a peptide-like inhibitor confirmed that FRED is the best-performing tool. Furthermore, we performed cross-benchmarking against the newly introduced X-ray structure complexed with a small-molecule ligand. Interestingly, its benchmarking profile and chemotype enrichment were comparable to the built model. Accordingly, we used FRED in a prospective virtual screen of the DrugBank database. In conclusion, this study provides an example of how to harness a custom-made DEKOIS 2.0 benchmark set as an approach to enhance the virtual screening success rate against a vital target of the rapidly emerging pandemic.

Ginsenoside Rh2 induces DNA damage and autophagy in vestibular schwannoma is dependent of LAMP2 transcriptional suppression

Ginsenoside Rh2 (G-Rh2), a component of ginseng extraction, exerted anti-tumor property in the occurrence and progress of human tumors. Vestibular schwannoma (VS) is a kind of benign tumor. Extraction of traditional Chinese herb has been applied to treat VS as adjuvant therapy. Nevertheless, G-Rh2-related molecular mechanisms in VS progress are not yet clear. The purpose of current study is to unveil the function and potential molecular mechanism of Rh2 in VS cellular functions. At first, the viability and apoptosis of VS cells treated with different concentrations of Rh2 were assessed. Autophagy and DNA damage response can be induced by multiple drugs. Here, we observed the changes of autophagy and DNA damage in Rh2-induced VS cells. Based on the experimental data, treatment with Rh2 contributed to cell apoptosis by inducing DNA damage and suppressing DNA damage. LAMP2 (lysosomal associated membrane protein 2), an autophagy inducer, was downregulated in Rh2-treated VS cells. Through mechanism study, we determined that Rh2 led to the transcriptional inactivation of LAMP2 by downregulating its transcription activator NR2F2 (nuclear receptor subfamily 2 group F member 2). In addition, NR2F2 overexpression recovered the role of Rh2 in cell functions, which was further rescued by the silence of LAMP2. Collectively, our study unveiled a novel NR2F2/LAMP2 axis in Rh2-mediated VS cells, which potentially contributes to the therapy for VS.

Behavioral Recovery and Early Decision Making in Patients with Prolonged Disturbance in Consciousness after Traumatic Brain Injury

The extent of behavioral recovery that occurs in patients with traumatic disorders of consciousness (DoC) following discharge from the acute care setting has been under-studied and increases the risk of overly pessimistic outcome prediction. The aim of this observational cohort study was to systematically track behavioral and functional recovery in patients with prolonged traumatic DoC following discharge from the acute care setting. Standardized behavioral data were acquired from 95 patients in a minimally conscious (MCS) or vegetative state (VS) recruited from 11 clinic sites and randomly assigned to the placebo arm of a previously completed prospective clinical trial. Patients were followed for 6 weeks by blinded observers to determine frequency of recovery of six target behaviors associated with functional status. The Coma Recovery Scale-Revised and Disability Rating Scale were used to track reemergence of target behaviors and assess degree of functional disability, respectively. Twenty percent (95% confidence interval [CI]: 13–30%) of participants (mean age 37.2; median 47 days post-injury; 69 men) recovered all six target behaviors within the 6 week observation period. The odds of recovering a specific target behavior were 3.2 (95% CI: 1.2–8.1) to 7.8 (95% CI: 2.7–23.0) times higher for patients in MCS than for those in VS. Patients with preserved language function (“MCS+”) recovered the most behaviors (p ≤ 0.002) and had the least disability (p ≤ 0.002) at follow-up. These findings suggest that recovery of high-level behaviors underpinning functional independence is common in patients with prolonged traumatic DoC. Clinicians involved in early prognostic counseling should recognize that failure to emerge from traumatic DoC before 28 days does not necessarily portend unfavorable outcome.

Computational Methods for Resting-State EEG of Patients With Disorders of Consciousness

Patients who survive brain injuries may develop Disorders of Consciousness (DOC) such as Coma, Vegetative State (VS) or Minimally Conscious State (MCS). Unfortunately, the rate of misdiagnosis between VS and MCS due to clinical judgment is high. Therefore, diagnostic decision support systems aiming to correct any differentiation between VS and MCS are essential for the characterization of an adequate treatment and an effective prognosis. In recent decades, there has been a growing interest in the new EEG computational techniques. We have reviewed how resting-state EEG is computationally analyzed to support differential diagnosis between VS and MCS in view of applicability of these methods in clinical practice. The studies available so far have used different techniques and analyses; it is therefore hard to draw general conclusions. Studies using a discriminant analysis with a combination of various factors and reporting a cut-off are among the most interesting ones for a future clinical application.

Real-Time Structural and Electrical Characterization of Metal-Insulator Transition in Strain-Modulated Single-Phase VO2 Wires with Controlled Diameters

Single-crystal VO2 wires have gained tremendous popularity for enabling the study of the fundamental properties of the metal-insulator transition (MIT); however, it remains tricky to precisely measure the intrinsic properties of the transitional phases with controlled wire-growth properties, such as diameter. Here, we report a facile method for growing VO2 wires with controlled diameters by separating the formation of the liquidus V2O5 seed droplets from the evolution of the VO2 wire using oxygen gas. The kinetic analyses suggest that the growth proceeds via the VS (vapor-solid) mechanism, whereas the droplet determines the size and the location of the wire. In situ Raman spectroscopy combined with analyses of the electrical properties of an individual wire allowed us to construct a diameter-temperature phase diagram from three initial phases (i.e., M1, T, and M2), which were created by misfit stress from the substrate and were preserved at room temperature. We also correlated this relation with resistivity-diameter and activation energy-diameter relations supported by theoretical modeling. These carefully designed approaches enabled us to elucidate the details of the phase transitions over a wide range of stress conditions, offering an opportunity to quantify relevant thermodynamic and electronic parameters (including resistivities, activation energies, and energy barriers of the key insulating phases) and to explain the intriguing behaviors of the T phase during the MIT.

Preservation of the bicuspid aortic valve associated with aneurysms of the aortic root and ascending aorta

INTRODUCTION AND OBJECTIVES

When the bicuspid aortic valve is associated with dilatation of the aorta, surgical repair requires correction of all the components of the aortic root. Here, we review our experience in this type of surgery.

METHODS

A descriptive and retrospective observational study was carried out to analyze morbidity and mortality in valve-sparing techniques and evaluate the medium-term durability of the aortic valve. We included all patients with a bicuspid aortic valve and dilatation of the aorta who underwent surgery with a valve-sparing technique in our center between 1999 and 2011.

RESULTS

A total of 151 patients underwent surgery. A valve-sparing technique was used in 51 patients. The mean (standard deviation) age of the patients was 51 (12) years and 92% were men. In 69% of the patients, aortic insufficiency was less than grade II and the aortic cusps showed little structural degeneration. Valve reimplantation was performed in 32 patients. There was no hospital mortality. With a median follow-up of 36 months (interquartile range, 18-45 months), none of the patients died or required reoperation, and all patients were free of aortic insufficiency greater than grade II.

CONCLUSIONS

Valve-preserving surgery in bicuspid aortic valves associated with dilatation of the aorta shows excellent short- and medium-term results in selected valves. The stabilization of all of the components of the aortic root improves the durability of the valve, and the techniques proposed are reproducible and stable in the medium-term.

Addressing case specific biogas plant tasks: industry oriented methane yields derived from 5L Automatic Methane Potential Test Systems in batch or semi-continuous tests using realistic inocula, substrate particle sizes and organic loading

The primary aim of the study was to develop and validate an in-house upscale of Automatic Methane Potential Test System II for studying real-time inocula and real-scale substrates in batch, codigestion and enzyme enhanced hydrolysis experiments, in addition to semi-continuous operation of the developed equipment and experiments testing inoculum functional quality. The successful upscale to 5L enabled comparison of different process configurations in shorter preparation times with acceptable accuracy and high-through put intended for industrial decision making. The adoption of the same scales, equipment and methodologies in batch and semi-continuous tests mirroring those at full scale biogas plants resulted in matching methane yields between the two laboratory tests and full-scale, confirming thus the increased decision making value of the approach for industrial operations.

Foam formation in a downstream digester of a cascade running full-scale biogas plant: Influence of fat, oil and grease addition and abundance of the filamentous bacterium Microthrix parvicella

The microbial community composition in a full-scale biogas plant fed with sewage sludge and fat, oil and grease (FOG) was investigated over a 15-month period, including two foam formation events. Addition of FOG as a substrate in the biogas plant together with high abundances of Microthrix parvicella were found to promote foam formation in the downstream digester of a cascade of two biogas digesters. Genetic fingerprinting and quantitative PCR (qPCR) indicated a higher abundance of M. parvicella in the digester, when the digestion process was accompanied by excessive foaming relative to the reference digesters without disturbance. The creation of foam depended on the introduced proportion of FOG and the abundance of M. parvicella. Furthermore, shifts in the abundance of M. parvicella in the biogas plant were observed within the 15-month monitoring period corresponding to its seasonal abundance in the sludge of the wastewater treatment plant (WWTP).

Energetic conversion of European semi-natural grassland silages through the integrated generation of solid fuel and biogas from biomass: energy yields and the fate of organic compounds

Twelve European habitat types were investigated to determine the influence of the IFBB technique (integrated generation of biogas and solid fuel from biomass) on the fate of organic compounds and energy yields of semi-natural grassland biomass. Concentration of organic compounds in silage and IFBB press cake (PC), mass flows within that system and methane yields of IFBB press fluids (PF) were determined. The gross energy yield of the IFBB technique was calculated in comparison to hay combustion (HC) and whole crop digestion (WCD). The IFBB treatment increased fibre and organic matter (OM) concentrations and lowered non-fibre carbohydrates and crude protein concentrations. The PF was highly digestible irrespective of habitat types, showing mean methane yields between 312.1 and 405.0 LN CH4 kg(-1) VS. Gross energy yields for the IFBB system (9.75-30.19MWh ha(-1)) were in the range of HC, outperformed WCD and were influenced by the habitat type.

Identification of novel drug scaffolds for inhibition of SARS-CoV 3-Chymotrypsin-like protease using virtual and high-throughput screenings

We have used a combination of virtual screening (VS) and high-throughput screening (HTS) techniques to identify novel, non-peptidic small molecule inhibitors against human SARS-CoV 3CLpro. A structure-based VS approach integrating docking and pharmacophore based methods was employed to computationally screen 621,000 compounds from the ZINC library. The screening protocol was validated using known 3CLpro inhibitors and was optimized for speed, improved selectivity, and for accommodating receptor flexibility. Subsequently, a fluorescence-based enzymatic HTS assay was developed and optimized to experimentally screen approximately 41,000 compounds from four structurally diverse libraries chosen mainly based on the VS results. False positives from initial HTS hits were eliminated by a secondary orthogonal binding analysis using surface plasmon resonance (SPR). The campaign identified a reversible small molecule inhibitor exhibiting mixed-type inhibition with a K(i) value of 11.1 μM. Together, these results validate our protocols as suitable approaches to screen virtual and chemical libraries, and the newly identified compound reported in our study represents a promising structural scaffold to pursue for further SARS-CoV 3CLpro inhibitor development.

Functional neuroanatomy of disorders of consciousness

Our understanding of the mechanisms of loss and recovery of consciousness, following severe brain injury or during anesthesia, is changing rapidly. Recent neuroimaging studies have shown that patients with chronic disorders of consciousness and subjects undergoing general anesthesia present a complex dysfunctionality in the architecture of brain connectivity. At present, the global hallmark of impaired consciousness appears to be a multifaceted dysfunctional connectivity pattern with both within-network loss of connectivity in a widespread frontoparietal network and between-network hyperconnectivity involving other regions such as the insula and ventral tegmental area. Despite ongoing efforts, the mechanisms underlying the emergence of consciousness after severe brain injury are not thoroughly understood. Important questions remain unanswered: What triggers the connectivity impairment leading to disorders of consciousness? Why do some patients recover from coma, while others with apparently similar brain injuries do not? Understanding these mechanisms could lead to a better comprehension of brain function and, hopefully, lead to new therapeutic strategies in this challenging patient population.

Applicability of dynamic membrane technology in anaerobic membrane bioreactors

This study investigated the applicability of dynamic membrane technology in anaerobic membrane bioreactors for the treatment of high strength wastewaters. A monofilament woven fabric was used as support material for dynamic membrane formation. An anaerobic dynamic membrane bioreactor (AnDMBR) was operated under a variety of operational conditions, including different sludge retention times (SRTs) of 20 and 40 days in order to determine the effect of SRT on both biological performance and dynamic membrane filtration characteristics. High COD removal efficiencies exceeding 99% were achieved during the operation at both SRTs. Higher filtration resistances were measured during the operation at SRT of 40 days in comparison to SRT of 20 days, applying a stable flux of 2.6 L/m(2) h. The higher filtration resistances coincided with lower extracellular polymeric substances concentration in the bulk sludge at SRT of 40 days, likely resulting in a decreased particle flocculation. Results showed that dynamic membrane technology achieved a stable and high quality permeate and AnDMBRs can be used as a reliable and satisfactory technology for treatment of high strength wastewaters.

Ischemia-induced depolarizations and associated hemodynamic responses in incomplete global forebrain ischemia in rats

Spontaneous depolarizations around the core are a consistent feature of focal cerebral ischemia, but the associated regional hemodynamic changes are heterogeneous. We determined how the features of depolarizations relate to subsequent cerebral blood flow (CBF) changes in global forebrain ischemia. Forebrain ischemia was produced in halothane-anesthetized rats (n=13) by common carotid artery occlusion and hypovolemic hypotension. Mean arterial blood pressure (MABP) was monitored via a femoral catheter. Specific illuminations allowed the capture of image sequences through a cranial window to visualize: changes in membrane potential (voltage-sensitive dye method); CBF (laser speckle contrast imaging); cerebral blood volume (intrinsic optical signal, IOS at 540-550nm); and hemoglobin deoxygenation (IOS at 620-640nm). A depolarization occurred (n=9) when CBF fell below 43.4±5% of control (41±4mmHg MABP), and propagated with a distinct wave front at a rate of 2.8mm/min. Depolarizations were either persistent (n=4), intermediate (n=3) or short, transient depolarization (n=2). Persistent and intermediate depolarizations were associated with sustained hypoperfusion (-11.7±5.1%) and transient hypoperfusion (-17.4±5.2, relative to CBF before depolarization). Short, transient depolarizations did not generate clear CBF responses. Depolarizations during incomplete global ischemia occurred at the lower limit of CBF autoregulation, propagated similar to spreading depolarization (SD), and the hemodynamic responses indicated inverse neurovascular coupling. Similar to SDs associated with focal stroke, the propagating event can be persistent or transient.

Urban mining: quality and quantity of recyclable and recoverable material mechanically and physically extractable from residual waste

The mechanically sorted dry fraction (MSDF) and Fines (<20mm) arising from the mechanical biological treatment of residual municipal solid waste (RMSW) contains respectively about 11% w/w each of recyclable and recoverable materials. Processing a large sample of MSDF in an existing full-scale mechanical sorting facility equipped with near infrared and 2-3 dimensional selectors led to the extraction of about 6% w/w of recyclables with respect to the RMSW weight. Maximum selection efficiency was achieved for metals, about 98% w/w, whereas it was lower for Waste Electrical and Electronic Equipment (WEEE), about 2% w/w. After a simulated lab scale soil washing treatment it was possible to extract about 2% w/w of inert exploitable substances recoverable as construction materials, with respect to the amount of RMSW. The passing curve showed that inert materials were mainly sand with a particle size ranging from 0.063 to 2mm. Leaching tests showed quite low heavy metal concentrations with the exception of the particles retained by the 0.5mm sieve. A minimum pollutant concentration was in the leachate from the 10 and 20mm particle size fractions.

Enhancement of Taihu blue algae anaerobic digestion efficiency by natural storage

Taihu blue algae after different storage time from 0 to 60 d were anaerobic fermented to evaluate their digestibility and process stability. Results showed that anaerobic digestion (AD) of blue algae under 15 d natural storage led to the highest CH4 production of 287.6 mL g(-1) VS at inoculum substrate ratio 2.0, demonstrating 36.69% improvement comparing with that from fresh algae. Storage of blue algae led to cell death, microcystins (MCs) release and VS reduction by spontaneous fermentation. However, it also played an important role in removing algal cell wall barrier, pre-hydrolysis and pre-acidification, leading to the improvement in CH4 yield. Closer examination of volatile fatty acids (VFA) variation, VS removal rates and key enzymes change during AD proved short storage time (≤ 15 d) of blue algae had higher efficiencies in biodegradation and methanation. Furthermore, AD presented significant biodegradation potential for MCs released from Taihu blue algae.

Biogas production from co-digestion of corn stover and chicken manure under anaerobic wet, hemi-solid, and solid state conditions

Corn stover (CS) and chicken manure (CM) are ubiquitous agricultural wastes at low cost and have the potential to achieve a nutrient-balance when mixed together to produce biomethane via anaerobic digestion (AD). The main objective of this work was to investigate methane production at different CS to CM ratios and to evaluate the process stability under wet (W-AD), hemi-solid state (HSS-AD) and solid state (SS-AD) conditions. Results showed that synergistic effects were found when mixing two substrates at CS:CM ratios of 3:1 and 1:1 (on volatile solid basis). The highest methane yield of 218.8 mL/g VS added was achieved in W-AD at CS:CM ratio of 3:1. In SS-AD, the highest volumetric methane productivity of 14.2L methane/L reactor volume was found at CS:CM of 1:1. The results of this work provide useful information to improve the efficiency and stability of co-digestion of CS and CM under different AD conditions.

Factors modulating neural reactivity to drug cues in addiction: a survey of human neuroimaging studies

Human neuroimaging studies suggest that neural cue reactivity is strongly associated with indices of drug use, including addiction severity and treatment success. However, little is known about factors that modulate cue reactivity. The goal of this review, in which we survey published fMRI and PET studies on drug cue reactivity in cocaine, alcohol, and tobacco cigarette users, is to highlight major factors that modulate brain reactivity to drug cues. First, we describe cue reactivity paradigms used in neuroimaging research and outline the brain circuits that underlie cue reactivity. We then discuss major factors that have been shown to modulate cue reactivity and review specific evidence as well as outstanding questions related to each factor. Building on previous model-building reviews on the topic, we then outline a simplified model that includes the key modulatory factors and a tentative ranking of their relative impact. We conclude with a discussion of outstanding challenges and future research directions, which can inform future neuroimaging studies as well as the design of treatment and prevention programs.

Generalised modelling approach for anaerobic co-digestion of fermentable substrates

A general methodology to implement fermentable soluble substrates in the IWA Anaerobic Digestion Model No. 1 (ADM1) that extends its application to anaerobic co-digestion of multiple substrates is presented. The approach considers the fermentation of new soluble substrates, not originally described in ADM1, as channelled through mass- and electron-balanced sugar fermentation equivalent reactions, and that fermentable substrates are degraded by a generic group of fermenters instead of the original ADM1 sugar fermenters. Therefore, no additional microbial group state is required. An additional term that modifies the ADM1 sugar fermentation kinetics equation was included to account for the competition among multiple substrates to be degraded by a particular biomass group. The model was validated at pilot scale treating a blend of pig manure (soluble fraction), wine and gelatine at mesophilic conditions. Only the ADM1 acetoclastic ammonia inhibition parameter was calibrated to obtain consistent model prediction of gas and liquid composition.

Establishment and assessment of a novel cleaner production process of corn grain fuel ethanol

An integrated corn ethanol-methane fermentation system was proposed to solve the problem of stillage handling, where thin stillage was treated by anaerobic digestion and then reused to make mash for the following ethanol fermentation. This system was evaluated at laboratory and pilot scale. Anaerobic digestion of thin stillage ran steadily with total chemical oxygen demand removal efficiency of 98% at laboratory scale and 97% at pilot scale. Ethanol production was not influenced by recycling anaerobic digestion effluent at laboratory and pilot scale. Compared with dried distillers' grains with solubles produced in conventional process, dried distillers' grains in the proposed system exhibited higher quality because of increased protein concentration and decreased salts concentration. Energetic assessment indicated that application of this novel process enhanced the net energy balance ratio from 1.26 (conventional process) to 1.76. In conclusion, the proposed system possessed technical advantage over the conventional process for corn fuel ethanol production.

Modelling the interactions between C and N farm balances and GHG emissions from confinement dairy farms in northern Spain

There is world-wide concern for the contribution of dairy farming to global warming. However, there is still a need to improve the quantification of the C-footprint of dairy farming systems under different production systems and locations since most of the studies (e.g. at farm-scale or using LCA) have been carried out using too simplistic and generalised approaches. A modelling approach integrating existing and new sub-models has been developed and used to simulate the C and N flows and to predict the GHG burden of milk production (from the cradle to the farm gate) from 17 commercial confinement dairy farms in the Basque Country (northern Spain). We studied the relationship between their GHG emissions, and their management and economic performance. Additionally, we explored some of the effects on the GHG results of the modelling methodology choice. The GHG burden values resulting from this study (0.84-2.07 kg CO2-eq kg(-l) milk ECM), although variable, were within the range of values of existing studies. It was evidenced, however, that the methodology choice used for prediction had a large effect on the results. Methane from the rumen and manures, and N2O emissions from soils comprised most of the GHG emissions for milk production. Diet was the strongest factor explaining differences in GHG emissions from milk production. Moreover, the proportion of feed from the total cattle diet that could have directly been used to feed humans (e.g. cereals) was a good indicator to predict the C-footprint of milk. Not only were some other indicators, such as those in relation with farm N use efficiency, good proxies to estimate GHG emissions per ha or per kg milk ECM (C-footprint of milk) but they were also positively linked with farm economic performance.

Effects of hydrothermal pre-treatments on Giant reed (Arundo donax) methane yield

Twelve hydrothermal pre-treatment combinations of temperature (150 and 180 °C), time (10 and 20 min) and acid catalyst (no catalyst; H2SO4 at 2% w/w immediately before steam cooking or in 24-h pre-soaking) were tested to assess their effects on methane yield of Giant reed biomass vs. untreated control. A batch anaerobic digestion was conducted with 4 g VS l(-1) at 53 °C for 39 days. Untreated biomass exhibited a potential CH4 yield of 273 ml g(-1) VS; the four pre-treatments without acid catalyst achieved a 10%, 7%, 23% and 4% yield gain in the respective temperature/time combinations 150 °C/10 min, 150 °C/20 min, 180 °C/10 min and 180 °C/20 min. Conversely, the eight pre-treatments with H2SO4 catalyst incurred a methanogenic inhibition in association with high SO4(2-) concentration in the hydrolysate, known to enhance sulphate reducing bacteria. Furfurals were also detected in the hydrolysate of five strong pre-treatments with H2SO4 catalyst.

Impact of co-digestion on existing salt and nutrient mass balances for a full-scale dairy energy project

Anaerobic digestion of manure and other agricultural waste streams with subsequent energy production can result in more sustainable dairy operations; however, importation of digester feedstocks onto dairy farms alters previously established carbon, nutrient, and salinity mass balances. Salt and nutrient mass balance must be maintained to avoid groundwater contamination and salination. To better understand salt and nutrient contributions of imported methane-producing substrates, a mass balance for a full-scale dairy biomass energy project was developed for solids, carbon, nitrogen, sulfur, phosphorus, chloride, and potassium. Digester feedstocks, consisting of thickened manure flush-water slurry, screened manure solids, sudan grass silage, and feed-waste, were tracked separately in the mass balance. The error in mass balance closure for most elements was less than 5%. Manure contributed 69.2% of influent dry matter while contributing 77.7% of nitrogen, 90.9% of sulfur, and 73.4% of phosphorus. Sudan grass silage contributed high quantities of chloride and potassium, 33.3% and 43.4%, respectively, relative to the dry matter contribution of 22.3%. Five potential off-site co-digestates (egg waste, grape pomace, milk waste, pasta waste, whey wastewater) were evaluated for anaerobic digestion based on salt and nutrient content in addition to bio-methane potential. Egg waste and wine grape pomace appeared the most promising co-digestates due to their high methane potentials relative to bulk volume. Increasing power production from the current rate of 369 kW to the design value of 710 kW would require co-digestion with either 26800 L d(-1) egg waste or 60900 kg d(-1) grape pomace. However, importation of egg waste would more than double nitrogen loading, resulting in an increase of 172% above the baseline while co-digestion with grape pomace would increase potassium by 279%. Careful selection of imported co-digestates and management of digester effluent is required to manage salt and nutrient mass loadings and reduce groundwater impacts.

Comparison of methanogenic community structure and anaerobic process performance treating swine wastewater between pilot and optimized lab scale bioreactors

To investigate methanogenic community structure and process performance of anaerobic digestion treating swine wastewater at different scale, a pilot plant with 20 m(3) of effective working volume and lab scale methanogenic digester with 6L working volume were operated for 71 days and 6 turnover periods, respectively. During the steady state of anaerobic digestion, COD and VS removal efficiency in pilot plant were 65.3±3.2, 51.6±4.3%, respectively, which was similar to those in lab scale. However, calculated VFAs removal efficiency and methane yield were lower in pilot plant than in lab scale digester. Also, organics removal efficiencies, which consist of total carbohydrates, proteins, and lipids, were different between pilot and lab scale. These results were thought to be due to the ratio of carbohydrates to proteins in the raw swine wastewater. As a result of qualitative microbial analysis, Methanoculleus receptaculii, and Methanoculleus bourgensis, were commonly concerned with methane production.

Effect of microwave hydrolysis on transformation of steroidal hormones during anaerobic digestion of municipal sludge cake

Fate and removal of 16 steroidal (estrogenic, androgenic and progestogenic) hormones were studied during advanced anaerobic digestion of sludge cake using microwave (MW) pretreatment. Effect of pretreatment temperature (80, 120, 160 °C), operating temperature (mesophilic at 35 ± 2 °C, thermophilic at 55 ± 2 °C) and sludge retention time (SRT: 20, 10, 5 days) were studied employing eight lab-scale semi-continuously fed digesters. To determine the potential effect of MW hydrolysis, hormones were quantified in total (sorbed + soluble) and supernatant (soluble) phases of the digester influent and effluent streams. Seven of 16 hormones were above the method reporting limit (RL) in one or more of the samples. Hormone concentrations in total phase of un-pretreated (control) and pretreated digester feeds ranged in <157-2491 ng/L and <157-749 ng/L, respectively. The three studied factors were found to be statistically significant (95% confidence level) in removal of one or more hormones from soluble and/or total phase. MW hydrolysis of the influent resulted in both release (from sludge matrix) and attenuation of hormones in the soluble phase. Accumulation of estrone (E1) as well as progesterone (Pr) and androstenedione (Ad) in most of the digesters indicated possible microbial transformations among the hormones. Compared to controls, all pretreated digesters had lower total hormone concentrations in their influent streams. At 20 days SRT, highest total removal (E1+E2+Ad +Pr) was observed for the thermophilic control digester (56%), followed by pretreated mesophilic digesters at 120 °C and 160 °C with around 48% efficiency. In terms of conventional performance parameters, relative (to control) improvements of MW pretreated digesters at a 5-d SRT ranged in 98-163% and 57-121%, for volatile solids removal and methane production, respectively.

Parathyroid hormone reverses radiation induced hypovascularity in a murine model of distraction osteogenesis

BACKGROUND

Radiation treatment results in a severe diminution of osseous vascularity. Intermittent parathyroid hormone (PTH) has been shown to have an anabolic effect on osteogenesis, though its impact on angiogenesis remains unknown. In this murine model of distraction osteogenesis, we hypothesize that radiation treatment will result in a diminution of vascularity in the distracted regenerate and that delivery of intermittent systemic PTH will promote angiogenesis and reverse radiation induced hypovascularity.

MATERIALS AND METHODS

Nineteen Lewis rats were divided into three groups. All groups underwent distraction of the left mandible. Two groups received radiation treatment to the left mandible prior to distraction, and one of these groups was treated with intermittent subcutaneous PTH (60 μg/kg, once daily) beginning on the first day of distraction for a total duration of 21 days. One group underwent mandibular distraction alone, without radiation. After consolidation, the rats were perfused and imaged with micro-CT angiography and quantitative vascular analysis was performed.

RESULTS

Radiation treatment resulted in a severe diminution of osseous vascularity in the distracted regenerate. In irradiated mandibles undergoing distraction osteogenesis, treatment with intermittent PTH resulted in significant increases in vessel volume fraction, vessel thickness, vessel number, degree of anisotropy, and a significant decrease in vessel separation (p < 0.05). No significant difference in quantitative vascularity existed between the group that was irradiated, distracted and treated with PTH and the group that underwent distraction osteogenesis without radiation treatment.

CONCLUSIONS

We quantitatively demonstrate that radiation treatment results in a significant depletion of osseous vascularity, and that intermittent administration of PTH reverses radiation induced hypovascularity in the murine mandible undergoing distraction osteogenesis. While the precise mechanism of PTH-induced angiogenesis remains to be elucidated, this report adds a key component to the pleotropic effect of intermittent PTH on bone formation and further supports the potential use of PTH to enhance osseous regeneration in the irradiated mandible.

Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery

Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease etiology with over half of all human PTP genes implicated in at least one disease. Small molecule inhibitors targeting individual PTPs are important biological tools, and are needed to fully characterize the function of these enzymes. Moreover, potent and selective PTP inhibitors hold the promise to transform the treatment of many diseases. While numerous methods exist to develop PTP-directed small molecules, we have found that complimentary use of both virtual (in silico) and biochemical (in vitro) screening approaches expedite compound identification and drug development. Here, we summarize methods pertinent to our work and others. Focusing on specific challenges and successes we have experienced, we discuss the considerable caution that must be taken to avoid enrichment of inhibitors that function by non-selective oxidation. We also discuss the utility of using "open" PTP structures to identify active-site directed compounds, a rather unconventional choice for virtual screening. When integrated closely, virtual and biochemical screening can be used in a productive workflow to identify small molecules targeting PTPs.

New scaffolds of natural origin as Integrase-LEDGF/p75 interaction inhibitors: virtual screening and activity assays

The disruption of crucial interactions between HIV-1 Integrase and cellular cofactor LEDGF/p75 represents an emerging approach for the design and development of new antiretroviral agents. In this study we report the successful application of a structure-based virtual screening strategy for the discovery of natural hit structures able to inhibit Integrase-LEDGF/p75 interaction. The application of sequential filters (drug-likeness, 3D-pharmacophore mapping, docking, molecular dynamics simulations) yielded a hit list of compounds, out of which 9 were tested in the in vitro AlphaScreen assays and 8 exhibited a detectable inhibition of the interaction between the two proteins. The best inhibitors belong to different chemical classes and could be represent a good starting point for further optimization and structure-activity relationship studies.

Altered resting state effective connectivity in long-standing vegetative state patients: an EEG study

OBJECTIVE

Recent evidence mainly based on hemodynamic measures suggests that the impairment of functional connections between different brain areas may help to clarify the neuronal dysfunction occurring in patients with disorders of consciousness (DOC). The aim of this study was to evaluate effective EEG connectivity in a cohort of 18 patients in a chronic vegetative state (VS) observed years after the occurrence of hypoxic (eight) and traumatic or hemorrhagic brain insult.

METHODS

we analysed the EEG signals recorded under resting conditions using a frequency domain linear index of connectivity (partial directed coherence: PDC) estimated from a multivariate autoregressive model. The results were compared with those obtained in ten healthy controls.

RESULTS

Our findings indicated significant connectivity changes in EEG activities in delta and alpha bands. The VS patients showed a significant and widespread decrease in delta band connectivity, whereas the alpha activity was hyper-connected in the central and posterior cortical regions.

CONCLUSION

These changes suggest the occurrence of severe circuitry derangements probably due to the loose control of the subcortical connections. The alpha hyper-synchronisation may be due to simplified networks mainly involving the short-range connections between intrinsically oscillatory cortical neurons that generate aberrant EEG alpha sources. This increased connectivity may be interpreted as a reduction in information capacity, implying an increasing prevalence of stereotypic activity patterns.

SIGNIFICANCE

Our observations suggest a remarkable rearrangement of connectivity in patients with long-standing VS. We hypothesize that in persistent VS, after a first period characterized by a breakdown of cortical connectivity, neurodegenerative processes, largely independent from the type of initial insult, lead to cortex de-afferentation and to a severe reduction of possible cortical activity patterns and states.

Do rehospitalization rates differ among injury severity levels in the NIDRR Traumatic Brain Injury Model Systems program?

OBJECTIVE

To compare the rate and nature of rehospitalization in a cohort of patients enrolled in the National Institute on Disability and Rehabilitation Research Traumatic Brain Injury Model Systems (TBIMS) who have disorders of consciousness (DOC) at the time of rehabilitation admission with those in persons with moderate or severe traumatic brain injury (TBI) but without DOC at rehabilitation admission.

DESIGN

Prospective observational study.

SETTING

Inpatient rehabilitation within TBIMS with annual follow-up.

PARTICIPANTS

Of 9028 persons enrolled from 1988 to 2009 (N=9028), 366 from 20 centers met criteria for DOC at rehabilitation admission and follow-up data, and another 5132 individuals met criteria for moderate (n=769) or severe TBI (n=4363).

INTERVENTIONS

Not applicable.

MAIN OUTCOME MEASURES

Participants and/or their family members completed follow-up data collection including questions about frequency and nature of rehospitalizations at 1 year postinjury. For the subset of participants with DOC, additional follow-up was conducted at 2 and 5 years postinjury.

RESULTS

The DOC group demonstrated an overall 2-fold increase in rehospitalization in the first year postinjury relative to those with moderate or severe TBI without DOC. Persons with DOC at rehabilitation admission have a higher rate of rehospitalization across several categories than persons with moderate or severe TBI.

CONCLUSIONS

Although the specific details of rehospitalization are unknown, greater injury severity resulting in DOC status on rehabilitation admission has long-term implications. Data highlight the need for a longitudinal approach to patient management.

Disorders of consciousness and disordered care: families, caregivers, and narratives of necessity

By their nature, care decisions for patients with severe disorders of consciousness must involve surrogates. Patients, so impaired, have lost their decision-making capacity and the ability to direct their own care. Surrogates-family members, friends, or other intimates-must step in and make decisions about ongoing care or its withdrawal. This article shares the narrative experiences of these surrogate decision makers as they encounter the American health care system and accompany patients from injury through rehabilitation. Through their perspectives, the article considers challenges to ongoing care and rehabilitation that are a function of a prevailing medical infrastructure and reimbursement framework better suited to patients with acute care needs. Specific attention is paid to the ethical challenges posed by reimbursement strategies such as "medical necessity" as well as those proposed for the Affordable Care Act. The argument concludes that when it comes to care for a disorder related to consciousness, its provision is not discretionary, and its receipt is not an entitlement but a civil right.

Medical complications during inpatient rehabilitation among patients with traumatic disorders of consciousness

OBJECTIVE

To assess the incidence of medical complications in patients with recent traumatic disorders of consciousness (DOCs).

DESIGN

Data on adverse events in a placebo controlled trial of amantadine hydrochloride revealed no group difference, which allowed these events to be reanalyzed descriptively as medical complications experienced by the 2 groups collectively.

SETTING

Eleven clinical facilities in the United States, Denmark, and Germany with specialty rehabilitation programs for patients with DOCs.

PARTICIPANTS

Patients (N=184) with nonpenetrating traumatic brain injury enrolled from acute inpatient rehabilitation programs between 4 and 16 weeks postinjury.

INTERVENTIONS

Participants were randomized to receive 200 to 400mg of amantadine hydrochloride or placebo daily for 4 weeks, and followed for an additional 2 weeks. Adverse events were recorded and categorized with respect to their nature, timing, and severity.

MAIN OUTCOME MEASURE

Number, type, and severity of medical complications occurring during the 6-week study interval.

RESULTS

A total of 468 medical complications were documented among the patients (.40 events per week per patient). More than 80% of patients experienced at least 1 medical complication, and 41 of these were defined as serious adverse events. New medical complications declined over time in rehabilitation and were not dependent on time since injury. Hypertonia, agitation/aggression, urinary tract infection, and sleep disturbance were the most commonly reported problems. Hydrocephalus, pneumonia, gastrointestinal problems, and paroxysmal sympathetic hyperactivity were the most likely to be severe.

CONCLUSIONS

Patients with DOCs have a high rate of medical complications early after injury. Many of these complications require brain injury expertise for optimal management. Active medical management appears to contribute to the reduction in new complications. An optimal system of care for DOC patients must provide expert medical management in the early weeks after injury.

Specialized early treatment for persons with disorders of consciousness: program components and outcomes

OBJECTIVES

To describe a specialized early treatment program for persons with disorders of consciousness (DOC) that includes family education; to identify rates of secondary conditions, imaging used, and selected interventions; and to evaluate outcomes.

DESIGN

A single-center, retrospective, pre-post design using electronic medical record data.

SETTING

A Commission on Accreditation of Rehabilitation Facilities-accredited, long-term acute care hospital that provides acute medical and inpatient rehabilitation levels of care for people with catastrophic injuries.

PARTICIPANTS

Persons (N=210) aged 14 to 69 years with DOC of primarily traumatic etiology admitted at a mean ± SD of 41.0 ± 27.2 days postinjury; 2% were in coma, 41% were in the vegetative state, and 57% were in the minimally conscious state.

INTERVENTIONS

An acute medical level of care with ≥90 minutes of daily interdisciplinary rehabilitation and didactic and hands-on caretaking education for families.

MAIN OUTCOME MEASURES

Coma Recovery Scale-Revised, Modified Ashworth Scale, and discharge disposition.

RESULTS

Program admission medical acuity included dysautonomia (15%), airway modifications (79%), infections (eg, pneumonia, 16%; urinary tract infection, 14%; blood, 11%), deep vein thrombosis (17%), pressure ulcers (14%), and marked hypertonia (30% in each limb). There were 168 program interruptions (ie, 139 surgeries, 29 nonsurgical intensive care unit transfers). Mean length of stay ± SD was 39.1 ± 29.4 days (range, 6-204d). Patients showed improved consciousness and respiratory function and reduced presence or severity of pressure ulcers and upper extremity hypertonia. At discharge, 54% showed sufficient emergence from a minimally conscious state to transition to mainstream inpatient rehabilitation, and 29% did not emerge but were discharged home to family with ongoing programmatic support; only 13% did not emerge and were institutionalized.

CONCLUSIONS

Persons with DOC resulting primarily from a traumatic etiology who receive specialized early treatment that includes acute medical care and ≥90 minutes of daily rehabilitation are likely to show improved consciousness and body function; more than half may transition to mainstream inpatient rehabilitation. Families who receive comprehensive education and hands-on training with ongoing follow-up support may be twice as likely to provide care for medically stable persons with DOC in their homes versus nursing facility placement.

Functional outcomes in traumatic disorders of consciousness: 5-year outcomes from the National Institute on Disability and Rehabilitation Research Traumatic Brain Injury Model Systems

OBJECTIVE

To characterize the 5-year outcomes of patients with traumatic brain injury (TBI) not following commands when admitted to acute inpatient rehabilitation.

DESIGN

Secondary analysis of prospectively collected data from the National Institute on Disability and Rehabilitation Research-funded Traumatic Brain Injury Model Systems (TBIMS).

SETTING

Inpatient rehabilitation hospitals participating in the TBIMS program.

PARTICIPANTS

Patients (N=108) with TBI not following commands at admission to acute inpatient rehabilitation were divided into 2 groups (early recovery: followed commands before discharge [n=72]; late recovery: did not follow commands before discharge [n=36]).

INTERVENTIONS

Not applicable.

MAIN OUTCOME MEASURES

FIM items.

RESULTS

For the early recovery group, depending on the FIM item, 8% to 21% of patients were functioning independently at discharge, increasing to 56% to 85% by 5 years postinjury. The proportion functioning independently increased from discharge to 1 year, 1 to 2 years, and 2 to 5 years. In the late recovery group, depending on the FIM item, 19% to 36% of patients were functioning independently by 5 years postinjury. The proportion of independent patients increased significantly from discharge to 1 year and from 1 to 2 years, but not from 2 to 5 years.

CONCLUSIONS

Substantial proportions of patients admitted to acute inpatient rehabilitation before following commands recover independent functioning over as long as 5 years, particularly if they begin to follow commands before hospital discharge.

Rationale and design of the prospective German registry of outcome in patients with severe disorders of consciousness after acute brain injury

OBJECTIVE

To describe the rationale and design of a new patient registry (Koma Outcome von Patienten der Frührehabilitation-Register [KOPF-R; Registry for Coma Outcome in Patients Undergoing Acute Rehabilitation]) that has the scope to examine determinants of long-term outcome and functioning of patients with severe disorders of consciousness (DOC).

DESIGN

Prospective multicenter neurologic rehabilitation registry.

SETTING

Five specialized neurologic rehabilitation facilities.

PARTICIPANTS

Patients (N=42) with DOC in vegetative state or minimally conscious state (MCS) as defined by the Coma Recovery Scale-Revised (CRS-R) after brain injury. Patients are being continuously enrolled. The data presented here cover the enrollment period from August 2011 to January 2012.

INTERVENTIONS

Not applicable.

MAIN OUTCOME MEASURES

CRS-R, FIM, and emergence from MCS.

RESULTS

The registry was set up in 5 facilities across the state of Bavaria/Germany with a special expertise in the rehabilitation of acquired brain injury. Inclusion of patients started in August 2011. Measures include sociodemographic and clinical characteristics, course of acute therapy, electrophysiologic measures (evoked potentials, electroencephalogram), neuron-specific enolase, current medication, functioning, cognition, participation, quality of life, quantity and characteristics of rehabilitation therapy, caregiver burden, and attitudes toward end-of-life decisions. Main diagnoses were traumatic brain injury (24%), intracerebral or subarachnoid hemorrhage (31%), and anoxic-ischemic encephalopathy (45%). Mean CRS-R score ± SD at admission to rehabilitation was 5.9 ± 3.3, and mean FIM score ± SD at admission was 18 ± 0.4.

CONCLUSIONS

The KOPF-R aspires to contribute prospective data on prognosis in severe DOC.

Corticomotor facilitation in vegetative state: results of a pilot study

OBJECTIVE

To investigate whether corticomotor facilitation induced by transcranial magnetic stimulation (TMS-CF) could evoke a simple purposeful motor behavior in patients with a diagnosis of vegetative state.

DESIGN

Cross-sectional survey.

SETTING

Post-coma and rehabilitation care unit.

PARTICIPANTS

Patients (N=6) with a diagnosis of vegetative state.

INTERVENTIONS

A cascade of consecutive motor-evoked potentials (MEPs) was elicited under 3 different conditions: in the first condition, patients were at rest (Rest); in the second, they were asked to open and close the right hand (Execution); in the third, the examiner modeled a movement of abduction of the thumb in front of the patient who was encouraged in advance to imitate the action (Observation to Imitate).

MAIN OUTCOME MEASURES

Changes in MEP values from the abductor pollicis brevis muscle and improvement in scores on the Coma Recovery Scale-Revised.

RESULTS

TMS-CF alone or combined with verbal instructions did not yield any change; only the combination with imitation caused changes in MEPs (shorter latency and increased amplitude) associated with behavioral improvement in 4 patients.

CONCLUSIONS

Encouraging observation to imitate may favor the transformation of some perceived actions into motor images and performances, probably depending on the activation of mirror motor neurons. In our opinion, combining visual input with TMS-CF might have reinforced the coupling between movement planning and execution, promoting the recovery of elementary motor activities in some patients. The proposed protocol may contribute to unmasking signs of preserved consciousness in patients with latent capacities for recovery.

Deep brain stimulation for treatment-resistant depression

BACKGROUND

Major depressive disorder is a common and disabling illness and is the leading cause of disability worldwide. Despite aggressive medical, behavioral, and electroconvulsive therapies, a significant number of patients remain refractory to treatment. Deep brain stimulation (DBS) has proven efficacy in neurobehavioral disorders and, in a general sense, works by modulation of corticostriatopallidothalamocortical circuits implicated in these disorders.

METHODS

Current data, treatment rationales, and future directions are presented.

RESULTS

The two targets most commonly used for DBS in treatment-resistant depression are the subgenual cingulate gyrus and the ventral capsule/ventral striatum. Data on DBS of these regions are preliminary, with promise shown in early studies.

CONCLUSIONS

Early work suggests DBS may become a therapeutic option in treatment-resistant depression. Further study is justified given the immense burden of disease.

Deep brain stimulation surgery for alcohol addiction. World Neurosurg. 2012;80:S28.e21-S28.e31. [PMID: 22824557 DOI: 10.1016/j.wneu.2012.07.011]

BACKGROUND

The consequences of chronic alcohol dependence cause important health and economic burdens worldwide. Relapse rates after standard treatment (medication and psychotherapy) are high. There is evidence from in vivo investigations and from studies in patients that the brain's reward system is critically involved in the development and maintenance of addictive behavior, suggesting that modification of this system could significantly improve the prognosis of addictive patients. Motivated by an accidental observation, we used the nucleus accumbens (NAc), which has a central position in the dopaminergic reward system for deep brain stimulation (DBS) of alcohol addiction.

METHODS

We report our first experiences with NAc DBS for alcohol dependence and review the literature addressing the mechanisms leading to addiction.

RESULTS

Five patients were treated off-label with bilateral NAc DBS for severe alcohol addiction (average follow-up 38 months). All patients experienced significant and ongoing improvement of craving. Two patients remained completely abstinent for more than 4 years. NAc stimulation was tolerated without permanent side effects. Simultaneous recording of local field potentials from the target area and surface electroencephalography while patients performed neuropsychological tasks gave a hint on the pivotal role of the NAc in processing alcohol-related cues.

CONCLUSIONS

To our knowledge, the data presented here reflect the first attempt to treat alcohol-addicted patients with NAc DBS. Electrical NAc stimulation probably counterbalances the effect of drug-related stimuli triggering involuntarily drug-seeking behavior. Meanwhile, two prospective clinical studies using randomized, double-blind, and crossover stimulation protocols for DBS are underway to corroborate these preliminary results.

Deep brain stimulation and spinal cord stimulation for vegetative state and minimally conscious state

OBJECTIVE

On the basis of the findings of the electrophysiological evaluation of vegetative state (VS) and minimally conscious state (MCS), the effect of deep brain stimulation (DBS) was examined according to long-term follow-up results. The results of spinal cord stimulation (SCS) on MCS was also examined and compared with that of DBS.

METHODS

One hundred seven patients in VS and 21 patients in MCS were evaluated neurologically and electrophysiologically over 3 months after the onset of brain injury. Among the 107 VS patients, 21 were treated by DBS. Among the 21 MCS patients, 5 were treated by DBS and 10 by SCS.

RESULTS

Eight of the 21 patients recovered from VS and were able to follow verbal instructions. These eight patients showed desynchronization on continuous electroencephalographic frequency analysis. The Vth wave of the auditory brainstem response and N20 of somatosensory evoked potential were recorded even with a prolonged latency, and pain-related P250 was recorded with an amplitude of more than 7 μV. In addition, DBS and SCS induced a marked functional recovery in MCS patients who satisfied the electrophysiological inclusion criteria.

CONCLUSION

DBS for VS and MCS patients and SCS for MCS patients may be useful, when the candidates are selected on the basis of the electrophysiological inclusion criteria. Only 16 (14.9%) of the 107 VS patients and 15 (71.4%) of the 21 MCS patients satisfied the electrophysiological inclusion criteria.