Advanced capabilities for materials modelling with Quantum ESPRESSO

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Polymorphisms in the promoter regions of the CXCL1 and CXCL2 genes contribute to increased risk of alopecia areata in the Korean population

Alopecia areata (AA) is a common disease, which causes hair loss in humans. AA has a genetically complex inheritance. This study investigated the possible correlations between single nucleotide polymorphisms (SNPs) in the promoter regions of the chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) (CXCL1) and chemokine (C-X-C motif) ligand 2 (CXCL2) genes and the development of AA in the Korean population. Two hundred and thirty-five AA patients and 240 control subjects were recruited. The specific SNPs occurring in the promoter regions of the CXCL1 and CXCL2 genes (rs3117604, -429C/T and rs3806792, -264T/C, respectively) were genotyped. All data obtained was evaluated using the SNPStats, SPSS 18.0, and the Haploview v.4.2 software platforms. The Odd's ratios (OR), 95% confidence intervals (CI), and P values were calculated using multiple logistic regression models. Analyses of the genetic sequences obtained revealed a significant correlation between the two SNPs and the development of AA (rs3117604, P = 0.0009 in co-dominant model 1, P = 0.01 in co-dominant model 2, P = 0.004 in the dominant model, P = 0.005 in the log-additive model, P = 0.012 in allele distribution; rs3806792, P = 0.036 in co-dominant model 2, P = 0.0046 in the log-additive model). The TT and CC haplotypes were also observed to show a significant association with increased risk of AA (TT haplotype, P = 0.0018; CC haplotype, P = 0.0349). Our data suggests that the CXCL1 and CXCL2 genes may be associated with AA susceptibility.

The novel miR-9500 regulates the proliferation and migration of human lung cancer cells by targeting Akt1

MicroRNAs have crucial roles in lung cancer cell development. They regulate cell growth, proliferation and migration by mediating the expression of tumor suppressor genes and oncogenes. We identified and characterized the novel miR-9500 in human lung cancer cells. The miR-9500 forms a stem-loop structure and is conserved in other mammals. The expression levels of miR-9500 were reduced in lung cancer cells and lung cancer tissues compared with normal tissues, as verified by TaqMan miRNA assays. It was confirmed that the putative target gene, Akt1, was directly suppressed by miR-9500, as demonstrated by a luciferase reporter assay. The miR-9500 significantly repressed the protein expression levels of Akt1, as demonstrated via western blot, but did not affect the corresponding mRNA levels. Akt1 has an important role in lung carcinogenesis, and depletion of Akt1 has been shown to have antiproliferative and anti-migratory effects in previous studies. In the current study, the overexpression of miR-9500 inhibited cell proliferation and the expression of cell cycle-related proteins. Likewise, the overexpression of miR-9500 impeded cell migration in human lung cancer cells. In an in vivo assay, miR-9500 significantly suppressed Fluc expression compared with NC and ASO-miR-9500, suggesting that cell proliferation was inhibited in nude mice. Likewise, miR-9500 repressed tumorigenesis and metastasis by targeting Akt1. These data indicate that miR-9500 might be applicable for lung cancer therapy.

Factors associated with early onset post-traumatic syringomyelia

STUDY DESIGN

Retrospective study.

OBJECTIVES

To identify factors associated with the development of early onset post-traumatic syringomyelia within 5 years of spinal cord injury.

SETTING

Department of Rehabilitation Medicine, Pusan National University School of Medicine, Korea.

METHODS

We retrospectively examined the records of 502 patients with traumatic cervical or thoracic spinal cord injury who underwent follow-up magnetic resonance imaging (MRI) examinations more than once a year for at least 5 years. Patients were assessed in terms of the neurological level of injury, the severity of initial spinal cord injury, the use of surgery and the extent of spinal canal involvement. The latter was evaluated by calculating the shortest antero-posterior diameter of the injured vertebral canal and the spinal reserve capacity as shown on MRI at the time of trauma onset and at the time of diagnosis of syringomyelia.

RESULTS

Syringomyelia developed within 5 years in 37 (7.3%) of the 502 patients. The mean age of these 37 patients was 44.6 years (range, 17-67 years) and the mean interval from spinal cord injury to onset of syringomyelia was 38.8 months (range, 2-54 months). The development of post-traumatic syringomyelia within 5 years was not significantly related to the severity or level of injury, the use of spinal surgery or the extent of spinal canal encroachment (P≥0.05 for each comparison).

CONCLUSION

Early onset syringomyelia occurring within 5 years after spinal cord injury was not associated with neurological injury level, severity of injury, the use of spinal surgery or canal encroachment.

Gross quantitative measurements of spinal cord segments in human

STUDY DESIGN

Anatomical measurement.

OBJECTIVE

To obtain quantitative anatomical data on each spinal cord segment in human, and determine the presence of correlations between the measures.

SETTING

Department of Rehabilitation Medicine, Pusan National University Hospital, Pusan, Korea.

METHODS

A total of 15 embalmed Korean adult human cadavers (13 males, two females; mean age 57.3 years) were used. The length of each cord segment was defined as the root attachment length plus the upper inter-root length. After performing a total vertebrectomy, a transverse cut was made at the approximate proximal and distal point of each segment from segment C3 to S5. Sagittal and transverse diameters at the proximal end of each segment, and cross-sectional area, height, and volume of the segment were measured.

RESULTS

The transverse diameter was largest at segment C5, and decreased progressively to segment T8. However, the sagittal diameter of each segment did not change distinctly with the segment. The cervical and lumbar enlargements were determined by the transverse diameters of the segments. Segment C5 had the largest cross-sectional area, at 75.0 mm(2). Segment T6 was the longest, averaging 22.4 mm in length. The longest segment in the cervical spinal cord was segment C5, at 15.5 mm, and segment L1 in the lumbar spinal cord. The volume was largest at segment C5, with a value of 1173.9 mm(3).

CONCLUSIONS

We found characteristic quantitative differences in the values of the parameters measured in the thoracic spinal cord compared to those measured in the cervical and lumbar or lumbosacral spinal cords. These measurements of spinal cord segments appear to provide valuable and practical standard quantitative features and may provide basic data for understanding the morphometric characteristics relevant to pathophysiologic conditions of the spinal cord.

Walking index for spinal cord injury (WISCI): an international multicenter validity and reliability study

STUDY DESIGN

Construction of an international walking scale by a modified Delphi technique.

OBJECTIVE

The purpose of the study was to develop a more precise walking scale for use in clinical trials of subjects with spinal cord injury (SCI) and to determine its validity and reliability.

SETTING

Eight SCI centers in Australia, Brazil, Canada (2), Korea, Italy, the UK and the US.

METHODS

Original items were constructed by experts at two SCI centers (Italy and the US) and blindly ranked in an hierarchical order (pilot data). These items were compared to the Functional Independence Measure (FIM) for concurrent validity. Subsequent independent blind rank ordering of items was completed at all eight centers (24 individuals and eight teams). Final consensus on rank ordering was reached during an international meeting (face validation). A videotape comprised of 40 clips of patients walking was forwarded to all eight centers and inter-rater reliability data collected.

RESULTS

Kendall coefficient of concordance for the pilot data was significant (W=0. 843, P<0.001) indicating agreement among the experts in rank ordering of original items. FIM comparison (Spearman's rank correlation coefficient=0.765, P<0.001) showed a theoretical relationship, however a practical difference in what is measured by each scale. Kendall coefficient of concordance for the international blind hierarchical ranking showed significance (W=0.860, P<0.001) indicating agreement in rank ordering across all eight centers. Group consensus meeting resulted in a 19 item hierarchical rank ordered 'Walking Index for Spinal Cord Injury (WISCI)'. Inter-rater reliability scoring of the 40 video clips showed 100% agreement.

CONCLUSIONS

This is the first time a walking scale for SCI of this complexity has been developed and judged by an international group of experts. The WISCI showed good validity and reliability, but needs to be assessed in clinical settings for responsiveness.

Electrophysiologic recovery after vitamin E-deficient neuropathy

A case report is presented of an electrophysiologic recovery from vitamin E-deficient neuropathy after treatment with water-soluble vitamin E in a patient with chronic hepatobiliary disease. The patient was a 64-year-old man who had experienced progressive difficulty in ambulation, with ataxia, over the previous 3 years. The symptoms were associated with pain, tingling sensation in the extremities, and reduced fine motor activity. The patient had chronic hepatobiliary disease, with recurrent cholangitis and external drainage of bile acid through a T-tube for more than 20 years. Vitamin E level was barely detectable (<0.5 mg/L). Sensory conduction was absent in both sural nerves. Other sensory and motor conduction studies in the upper and lower extremities showed decreased amplitude. The patient was treated with water-soluble vitamin E. After 4 months of therapy, his ambulation function improved, but pain and tingling sensation in both hands remained. Sensory nerve action potentials appeared in both sural nerves, and amplitudes of other sensory nerves were increased. In a second follow-up study after 9 months, all of the evaluated parameters in the nerve conduction studies, as well as the vitamin E level, were normal. The authors conclude that vitamin E-deficient neuropathy is reversible and electrophysiologic recovery can occur with water-soluble vitamin E therapy.

The pattern of reflex recovery during spinal shock

STUDY DESIGN

A prospective descriptive study of the course of recovery of reflexes following acute spinal cord injury (SCI).

OBJECTIVES

The purpose of the study was to observe the pattern of reflex recovery following acute SCI in order to determine the prognostic significance of reflexes for ambulation and their relationship to spinal shock.

SETTING

A regional spinal cord injury center in Philadelphia, Pennsylvania, USA.

METHODS

Fifty subjects admitted consecutively over a 9 month period and on the day of injury were observed for the following reflexes; bulbo-cavernosis (BC), delayed plantar response (DPR), cremasteric (CRM), ankle jerk (AJ), knee jerk (KJ), and normal plantar response for 5 7 days a week and 6-8 weeks duration. The 50 subjects were assessed for ambulation of 200 feet at time of discharge. MRI studies were reviewed on 13/28 complete (ASIA A) injuries.

RESULTS

Thirty-five subjects (28 ASIA A, 4 ASIA B, 3 ASIA C) had a DPR of 2 days or longer duration and these subjects were not ambulatory. The fourteen subjects (12 ASIA D and 2 ASIA C), who were ambulatory, either had no DPR (11/14) or had a DPR of only 1 days duration (3/14). One subject (ASIA B) was not ambulatory and had a DRP of 1 days duration. The DPR was the first reflex to recover most often, followed by the BC, CRM in the first few days and later followed by the deep tendon reflexes (AJ & KJ) by 1-2 weeks respectively. Less than 8% of subjects had no reflexes on the day of injury and the reflexes did not follow a caudal-rostral pattern of recovery.

CONCLUSIONS

Prognosis for ambulation based on reflexes early after SCI should not be linked to current descriptions of spinal shock. In fact, the view of spinal shock, based on the absence of reflexes and the recovery of reflexes in a caudal to rostral sequence, is of limited clinical utility and should be discarded. The evolution of reflexes over several days following injury may be more relevant to prognosis than the use of the term spinal shock and the presence or absence of reflexes on the day of injury.

Spinal cord injury secondary to cervical disc herniation in ambulatory patients with cerebral palsy

Early onset of degeneration of the cervical spine and instability due to sustained abnormal tonicity or abnormal movement of the neck are found in patients with cerebral palsy. An unexplained change or deterioration of neurological function in patients with cerebral palsy should merit the consideration of the possibility of cervical myelopathy due to early degeneration or instability of the cervical spine. We describe two patients who had a spinal cord injury due to a cervical disc herniation, one patient was athetoid and the second had spastic diplegia, they both had cerebral palsy. It is not easy to determine whether new neurological symptoms are as a result of the cervical spinal cord disorder. These cases suggest that consideration of a cervical spine disorder with myelopathy is required in the evaluation of patients with cerebral palsy who develop deterioration of neurological function or activities over a short period of time.

Facet tropism in lumbar motion segments and its significance in disc herniation

OBJECTIVE AND DESIGN

To define facet tropism (FT) for each motion segment of the lower lumbar spine for subjects without disc herniation, and to evaluate the significance of facet tropism in disc herniation.

METHODS

Sixty subjects were evaluated by measuring the facet angle (FA) of three lower lumbar motion segments with the use of computed tomography (CT) and a computer program. The subjects were divided into two groups: 33 without disc herniation and 27 with disc herniation at one or more levels of lower lumbar motion segments. The FA was defined as the angle of the facet and midsagittal lines. The difference between the right and left FAs at each motion segment was calculated. FT was defined as an angle difference larger than the mean and one standard deviation of the angle differences between the right and left FAs at each motion segment in the group without disc herniation.

OUTCOME MEASUREMENTS

Statistical significance of the bilateral angle difference of each lower lumbar motion segment between the two groups was analyzed by the two-sample t test. Using the defined angle difference for FT, the incidence of FT in the two groups at each motion segment was analyzed by the Fisher's exact test.

RESULTS

FT was defined for the 33 subjects without disc herniation on CT scans as an angle difference larger than 12 degrees at L3-L4, 15 degrees at L4-L5, and 12 degrees at L5-S1, approximately. There was no statistical significance in the bilateral FA difference (p > .05) and incidence of FT (p > .05) at each segment between the two groups.

CONCLUSION

This study did not show that facet joint tropism plays a significant role in disc herniation in the lower lumbar spine.

Treatment of external urethral sphincter hypertonicity by pudendal nerve block using phenol solution in patients with spinal cord injury

We report our experience utilizing the technique of phenol block of the pudendal nerve in the treatment of voiding dysfunction due to hypertonicity of the external urethral sphincter. We have performed 13 pudendal nerve blocks using a 7% phenol solution in seven patients with spinal cord injury who could not obtain relaxation of the external urethral sphincter with a large postvoid urine residual (150 ml to 600 ml) despite large doses of antispasticity drugs and intermittent catheterisations over three weeks. These drugs were discontinued at least 48 hours before this procedure. The efficacy of the pudendal nerve block could also be tested by the ease of facilitating micturition during or just after the block and measuring the amount of postvoid residual urine and intravesical leak pressure. A pudendal nerve block was produced by injecting a 7% phenol solution medial to the ischial tuberosity having specifically localized the nerve by electrical stimulation. This procedure improved the voiding pattern dramatically, leading to a full stream of urine and a remarkable decrease of postvoid residual volume and intravesical leak pressure. The mean difference of the postvoid residual volume and the intravesical leak pressure before and after pudendal nerve block was 255.7 ml and 57.5 cmH2O, respectively. We conclude that pudendal nerve block with a phenol solution as a treatment of external urethral sphincter hypertonicity was effective, easy to perform, and had no complication. This treatment should be considered as a possible alternative to more invasive surgical procedures.

Prognostic significance of the delayed plantar reflex following spinal cord injury

The delayed plantar reflex (DPR) is a pathologic flexor variant which requires unusually strong stimulation of the sole of the foot and is characterized by a prolonged interval between the stimulus and the response, slow and protracted plantarflexion of the great toe and/or other toes and slow return to the neutral position. The purpose of this study was to evaluate prospectively the functional outcome of spinal cord injury (SCI) patients based on the presence or absence of a DPR immediately following injury. Thirty-six subjects were evaluated within one week of injury. A complete neurological evaluation following American Spinal Injury Association (ASIA) standards was performed and the presence or absence of a DPR was noted on admission. Ambulation status and ASIA Impairment Scales were recorded at discharge from the rehabilitation unit and the data were analyzed by the Chi-square method with Yates' correction for continuity. The data demonstrated a high correlation of the DPR with motor complete injuries (p < 0.01) and a poor prognosis for recovery of ambulation (p < 0.01). Clinicians should recognize this abnormal reflex, which may be used in conjunction with a complete neurological examination, to help prognosticate future function in the acute SCI patient.

Surveyor v: lunar surface mechanical properties

The mechanical properties of the lunar soil at the Surveyor V landing site seem to be generally consistent with values determined for soils at the landing sites of Surveyor I and III. These three maria sites are hundreds of kilometers apart. However, the static bearing capability may be somewhat lower than that at the previous landing sites (2 x 10(5) to 6 x 10(5) dynes per square centimeter or 3 to 8 pounds per square inch). The results of the erosion experiment, the spacecraft landing effects, and other observations indicate that the soil has significant amounts of fine-grained material and a measurable cohesion.