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In a previous paper [Ghysels et al., J. Chem. Phys. 126, 224102 (2007)] the mobile block Hessian (MBH) approach was presented. The method was designed to accurately compute vibrational modes of partially optimized molecular structures. The key concept was the introduction of several blocks of atoms, which can move as rigid bodies with respect to a local, fully optimized subsystem. The choice of the blocks was restricted in the sense that none of them could be connected, and also linear blocks were not taken into consideration. In this paper an extended version of the MBH method is presented that is generally applicable and allows blocks to be adjoined by one or two common atoms. This extension to all possible block partitions of the molecule provides a structural flexibility varying from very rigid to extremely relaxed. The general MBH method is very well suited to study selected normal modes of large macromolecules (such as proteins and polymers) because the number of degrees of freedom can be greatly reduced while still keeping the essential motions of the molecular system. The reduction in the number of degrees of freedom due to the block linkages is imposed here directly using a constraint method, in contrast to restraint methods where stiff harmonic couplings are introduced to restrain the relative motion of the blocks. The computational cost of this constraint method is less than that of an implementation using a restraint method. This is illustrated for the α-helix conformation of an alanine-20-polypeptide. [ABSTRACT FROM AUTHOR]

Vibrational force fields for the ground states of 1,3-butadiene, 1,3,5-hexatriene, and 1,3,5,7-octatetraene are calculated from extended Pariser–Parr–Pople CI theory. For the ground state of butadiene, the principal π-system force constants are compared to those determined by empirical, other semiempirical, and ab initio methods. The calculated vibrational frequency shifts for a series of deuterium substituted butadienes are found to be in good agreement with experiment. Trends in the principal π-system force constants of the polyenes for the ground states of ethylene through octatetraene are described, including the effects of introducing cis linkages in the polyene chain and of using single- vs single-plus-double-excitation CI. Correlations between the force constants and the calculated vibrational frequencies are discussed, and current assignments of the vibrational spectra of the polyenes are examined in view of the theoretical results. [ABSTRACT FROM AUTHOR]

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009. [ABSTRACT FROM AUTHOR]

Motor fatigue, during 30 seconds of maximum voluntary isometric contraction (MVIC) was simultaneously evaluated by the decline in mechanical force output, and from the compression in the power spectrum obtained from surface electromyogram (sEMG). Measurements were performed in patients diagnosed with amyotrophic lateral sclerosis (ALS) and normal control (NC) in two muscle groups, elbow flexors (EF) and ankle dorsiflexors (DF). The decline in force output, as a manifestation of mechanical fatigue, was digitally calculated online by partitioning the force versus time curve to determine the percent of MVIC reduction over a 30 sec period and was expressed as force fatigue index (FFI). The compression in the sEMG power spectrum, as a manifestation of myoelectrical fatigue, was tracked by calculating the median frequency shift (MFS) from the first 5 sec to the last 5 sec of the 30 sec MVIC using digital Fast Fourier Transformation. In ALS patients, the significantly higher reduction in mechanical force output during the 30 sec MVIC (higher FFI) was accompanied with significantly less compression in the sEMG power spectrum (less MFS) as compared to NC ( P ≤0.005) in the two muscle groups. This dissociation between the mechanical and myoelectrical manifestation of muscle fatigue in ALS indicates that a reduction in muscle fiber conduction velocity (MFCV) may be a contributing peripheral factor in the pathogenesis of muscle fatigue in ALS. Alterations in motor unit functionality, especially in type II fast motor unit muscle fibers, and structural damage in denervated muscle fibers may contribute to the lower MFCV during motor fatigue in ALS patients. [ABSTRACT FROM AUTHOR]

Explores strategies to develop mosaic chemotherapeutic approaches for amyotrophic lateral sclerosis/motor neurone disease (ALS/MND). Inclusion of beta-2 adrenergic agonists for ALS/MND treatment; Pathogenesis-based and symptom-directed therapies in ALS/MND; Effect of beta-2 adrenergic agonists in the central nervous system and muscular system; Side-effects of beta-2 adrenergic agonists.

The bifunctional aldehydes glyoxal and malondialdehyde, known to be toxic products of the radiolysis of sugar and other food constituents, interact with DNA in vitro and in vivo as demonstrated by thermal denaturation profiles, chromatographic behavior, and incomplete degradation of the reaction product by deoxyribonuclease. After irradiation of DNA in diluted radioactive glucose solution followed by incubation at slightly acid pH, the radioactivity is found in the core of the enzymic digest only. Attempts to locate the binding site proved that the radiolytic compound is associated preferentially with the guanine and cytidine moiety of the DNA core. [ABSTRACT FROM AUTHOR]

In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [ J. Chem. Phys. 2007 , 126 ( 22 ), 224102. ]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.

The aim of this study was to assess the long-term safety and efficacy of glatiramer acetate (GA) for patients with multiple sclerosis (MS) who received active treatment versus those on placebo for approximately 30 months (24-35 months) before receiving GA during a six-year organized, prospective open label study. Entry required two relapses in the previous two years and an Expanded Disability Status Scale (EDSS) score of 0-5. Patients (251) were equally randomized to daily subcutaneous GA, 20 mg, or to placebo. After approximately 30 months, 208 patients continued in an open label study: 101 continued on GA and 107 switched from placebo to active drug. Groups were well matched at randomization and entry to the open label study. Patients always on GA showed a steady decline in relapses: a mean of 1.5 per year at entry, a mean of 0.42 over the entire six years (95% CI = 0.34-0.51), a 72% reduction (P = 0.0001). They averaged a relapse every four + years (yearly rate 0.23 in year six) and 26/101 remain relapse free. Patients did less well if on placebo for 30 months, but relapses then declined, and by year six the rates were similar. Of patients always on GA, 69% showed neurological improvement of > or = 1 EDSS steps or remained stable compared with 57% if GA treatment was delayed. Of relapse-free patients always on GA over six years, only three of 26 (11%) were worse by > or = 1 EDSS steps, whereas nine of 21 (43%) in the placebo/active group were worse (P < 0.03). Disability, measured every six months, showed that the group of patients always on GA was relatively stable over the six years, while the group who received placebo for the first two-and-a-half years did significantly less well. Daily injections of GA were well tolerated. This longest ever organized MS treatment trial shows that delaying therapy with GA increases the risk of neurologic disability, reinforcing the rationale for using GA as a first-line treatment early in the course of relapsing-remitting MS.

This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure.

Motor fatigue is a common complaint in patients with amyotrophic lateral sclerosis (ALS), but is often excluded, unlike weakness, from the clinical assessment of these patients. This could be due to the complexity and often painful assessment techniques of this motor deficit. This study examines the feasibility of quantitative assessment of motor fatigue by modifying presently available force measurements. The relationship between weakness and fatigue in ALS patients was also examined. Fifty-four ALS patients and 39 normal control subjects performed 30 s of sustained maximal voluntary isometric contraction (MVIC) of elbow flexors (EF), knee extensors (NE), and ankle dorsiflexors (DF), using a computerized force measurement system and standardized testing procedures. Fatigue index (FI) was digitally calculated, from the force-time curve, as the percentage of MVIC unable to be sustained over the 30-s period. Fatigue was greater in ALS patients than in normal control (mean=23% vs. 15%) in all muscles including muscles that were not clearly weak. Weakness and fatigue were poorly correlated in ALS patients and may be independent measures of the pathogeneses of ALS.

Functional imaging studies of the cerebellum have mostly investigated motor performance or have been limited to the anterior lobe and therefore the somatosensory representations in the human cerebellum have not been fully demonstrated. We used fMRI of the entire cerebellum during tactile stimulation of the hand and foot in six normal subjects. Our results demonstrate that the tactile projections to the cerebellum in humans are represented in both the anterior and posterior lobes. in agreement with previous functional imaging studies, our results show a large-scale, between-limb somatotopy comparable to that shown in early animal studies.

The human rhinovirus 14 (HRV14) protomer, with or without the antiviral compound WIN 52084s, was simulated using molecular dynamics and rotational symmetry boundary conditions to model the effect of the entire icosahedral capsid. The protein asymmetrical unit, comprising four capsid proteins (VP1, VP2, VP3, and VP4) and two calcium ions, was solvated both on the exterior and the interior to fill the inside of the capsid. The stability of the simulations of this large system (~800 residues and 6,650 water molecules) is comparable to more conventional globular protein simulations. The influence of the antiviral compound on compressibility and positional fluctuations is reported. The compressibility, estimated from the density fluctuations in the region of the binding pocket, was found to be greater with WIN 52084s bound than without the drug, substantiating previous computations on reduced viral systems. An increase in compressibility correlates with an entropically more favorable system. In contrast to the increase in density fluctuations and compressibility, the positional fluctuations decreased dramatically for the external loops of VP1 and the N-terminus of VP3 when WIN 52084s is bound. Most of these VP1 and VP3 loops are found near the fivefold axis, a region whose mobility was not considered in reduced systems, but can be observed with this simulation of the full viral protomer. Altered loop flexibility is consistent with changes in proteolytic sensitivity observed experimentally. Moreover, decreased flexibility in these intraprotomeric loops is noteworthy since the externalization of VP4, part of VP1, and RNA during the uncoating process is thought to involve areas near the fivefold axis. Both the decrease in positional fluctuations at the fivefold axis and the increase in compressibility near the WIN pocket are discussed in relationship to the antiviral activity of stabilizing the virus against uncoating.

In a randomized, placebo-controlled, double-blind study, glatiramer acetate (Copaxone) reduced the relapse rate and slowed accumulation of disability for patients with relapsing - remitting multiple sclerosis. Of the original 251 patients randomized to receive glatiramer acetate or placebo, 208 chose to continue in an open-label study with all patients receiving active drug. The majority of the original double-blind cohort continues to receive glatiramer acetate by daily subcutaneous injection and are evaluated at 6-month intervals and during suspected relapse. The data reported here are from approximately 6 years of organized evaluation, including the double-blind phase of up to 35 months and the open-label phase of over 36 months. Daily subcutaneous injections of 20 mg glatiramer acetate were well tolerated. The mean annual relapse rate of the patients who received glatiramer acetate since randomization and continued into the open-label study was 0.42 (95% confidence interval (CI), CI=0.34 - 0.51). The rate per year has continued to drop and for the sixth year is 0.23. Of the group who have received glatiramer acetate without interruption for 5 or more years, 69.3% were neurologically unchanged or have improved from baseline by at least one step on the Expanded Disability Status Scale (EDSS). Patients who left the open-label phase were surveyed by questionnaire. The majority responded, providing information about their current status and reasons for dropping out. This study demonstrates the sustained efficacy of glatiramer acetate in reducing the relapse rate and in slowing the accumulation of disability in patients with relapsing forms of multiple sclerosis. Multiple Sclerosis (2000) 6 255 - 266

Premature termination products of reverse transcription that consist physically of viral minus-sense single-stranded DNA that is shorter than one long terminal repeat and partial DNA duplexes are dramatically increased in the central nervous system (CNS) of FVB/N mice that are infected by ts1, a temperature-sensitive mutant of Moloney murine leukemia virus. Due to their migration in agarose gels, these incomplete physical forms of DNA have been designated high-mobility (HM) DNA. In non-CNS tissues, the level of HM DNA is either low or not detectable. In order to determine the conditions that are necessary for the synthesis of HM DNA in vivo, we have characterized the physical forms of HM DNA that were synthesized in vitro in chronically infected SC-1 cells after temperature upshift. At the permissive temperature of 34 degrees C, the chronically infected SC-1 cells did not synthesize HM DNA. After temperature upshift of the cultured cells from 34 to 37 degrees C, the chronically infected SC-1 cells developed extremely high levels of HM DNA. Following temperature downshift of the cultured cells from 37 to 34 degrees C, a decrease in the level of HM DNA and an increase in the level of unintegrated linear proviral DNA occurred simultaneously. These results suggested that the accumulation of HM DNA both in vitro and in vivo may be the result of superinfection.

Functional magnetic resonance imaging (fMRI) provides high-resolution, non-invasive estimates of neural activity detected by a blood oxygen level dependent signal by assessing the increase in blood flow to the local vasculature that accompanies neural activity in the brain. fMRI studies with standard hand motor test (index-thumb opposition, ITO, or pinch) in ALS patients show good test-retest reliability and similar amplitude of signals in ALS patients compared with control subjects. Isometric force can be performed with careful control for the force exerted, recruitment of other muscles and motion artefact. The volume (number of voxels above threshold) of sensorimotor and cerebellar cortex activated by ITO is reproducibly larger in ALS patients compared with control subjects. Imagined movements in ALS have been studied, as in amputees, and larger volumes are activated in ALS patients with imagined movements as well, compared with control subjects. fMRI studies in ALS patients evaluating cortical activation during pure somatosensory stimulation cutaneous stimulation of the hand to elicit the palmomental response and cutaneous stimulation of the sole to elicit the plantar response - indicate that ALS patients activate a significantly smaller volume of the contralateral sensorimotor cortex compared to control subjects. No statistically significant difference was seen in other areas, including the ipsilateral cerebellum and the contralateral thalamus. An anterior shift in the volume of cortex activated by these paradigms occurs in ALS patients, with a volume of activation, anteriorly, not activated in control subjects. fMRI studies will complement other clinical neurophysiological and neuroimaging techniques in our future attempts to solve the riddle of ALS and other motor neuron diseases.

The 2nd Consensus Conference (Versailles) recommended that an ALS knowledge-base for initial healthcare providers, diagnosing neurologists and confirming neurologists should be defined to include a simplified version of diagnostic criteria less formal than the World Federation of Neurology El Escorial Revisted Criteria ('ALS diagnosis - An algorithm'), a set of rules concerning red flags which should increase the suspicion of ALS as the diagnosis and minimize the time between suspicion and referral for confirmation of diagnosis ('ALS axioms of referral'), as well as a site of symptom onset-specific checklist of minimal clinical examination, neuroimaging, electrodiagnostic, pulmonary function and laboratory test information required to confirm the diagnosis of ALS ('Versailles minimal dataset'). Although introductory discussions addressed the advantages and disadvantages of earlier diagnosis, false-positive or false-negative diagnosis, the frequency of follow-up and what potential biological markers to be followed, these issues will have to be further evaluated at future consensus conferences.

The 2nd Consensus Conference (Versailles) on the early diagnosis of amyotrophic lateral sclerosis (ALS) developed themes identified at the 1st Consensus Conference (Chicago) on defining optimal management in ALS. These themes included describing the problems and limitations in current diagnostic practices, identifying consequences of early diagnosis on patient management, establishing recommendations to help healthcare personnel achieve the early diagnosis and proposing solutions to facilitate early diagnosis of ALS. Lessons from the ISIS Survey and the 1st Consensus Conference focused on the variability of the first-contact physician, supply factors for specialists and variability of application of medical techniques. The recently introduced concept of 'ALS health states or stages' was reviewed in terms of ongoing and potential prospective studies. The relative contribution of neuroimaging or clinical neurophysiological investigations to accelerating the diagnosis of ALS in clinical practice was debated. The role of a common ALS knowledge-base among patients, initial healthcare providers, diagnosing neurologists and confirming neurologists was critically appraised with regard to simplified 'ALS diagnostic algorithm', 'ten aphorisms in the diagnosis of ALS' and 'ALS axioms of referral'. Refining this ALS knowledge-base is required to identify a minimum dataset required for the evaluation and diagnosis of ALS.

Patient-specific (endogenous) and population-specific (exogenous) risk factor analysis is identifying novel physical and chemical exposures which might be time-linked to the development of amyotrophic lateral sclerosis (ALS) and other motor neuron diseases. Electric injury in a number of case-control studies as well as prolonged exposure at work and home to agricultural chemicals in pesticides and herbicides have been identified as significant risk factors. Heavy exercise, trauma with or without bone fractures and heavy metal exposure at work have not been confirmed as risk factors. Surprisingly, occupation as a pilot or navigator has recently been identified as a potential risk factor, which will need to be confirmed. The introduction of international patient registries in North America (ALS CARE) and in Europe (ALS HPS) will facilitate future studies on the prognosis of ALS, adherence to standards of practice, quality of life and patient outcome studies. An initial survey of the ALS Patient Care Database in January 1999, when nearly 1800 patients had been entered across North America, indicated the median time from ALS onset to diagnosis is 14 months when no second opinion is requested, 12 months if the patient requests a second opinion and 10 months when the neurologist requests an additional opinion. No significant difference was found in the median time to diagnose sporadic ALS patients compared with familial ALS patients.