A Variable Neighbourhood Descent Heuristic for Conformational Search Using a Quantum Annealer.

Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in in silico materials design and drug discovery. In this paper, we propose a variable neighbourhood search heuristic for the conformational search problem. Using the structure of a molecule, neighbourhoods are chosen to allow for the efficient use of a binary quadratic optimizer for conformational search. The method is flexible with respect to the choice of molecular force field and the number of discretization levels in the search space, and can be further generalized to take advantage of higher-order binary polynomial optimizers. It is well-suited for the use of devices such as quantum annealers. After carefully defining neighbourhoods, the method easily adapts to the size and topology of these devices, allowing for seamless scaling alongside their future improvements.

HBeAg levels at week 24 predict response to 8 years of tenofovir in HBeAg-positive chronic hepatitis B patients.

BACKGROUND: Hepatitis B e antigen (HBeAg) seroconversion is a treatment endpoint for HBeAg-positive CHB, and a necessary precursor to HBsAg loss. Biomarkers that predict serological outcomes would be useful. AIM: To evaluate the utility of measuring HBeAg levels for predicting HBeAg seroconversion and HBsAg loss under long-term tenofovir (TDF) therapy. METHODS: A total of 266 patients were enrolled into a phase III study of TDF vs adefovir (ADV) for 48 weeks in HBeAg-positive patients, followed by open-label TDF up to 384 weeks. Serum HBeAg levels were measured for subjects with samples available at both baseline and week 24 of treatment (n = 200). Analysis compared subjects who achieved HBeAg seroconversion by week 384 vs no HBeAg seroconversion. RESULTS: HBeAg seroconversion rate was 52% by week 384. Time to HBeAg seroconversion was 80 weeks (IQR: 36-162). HBeAg decline at week 24 was associated with HBeAg seroconversion (1.63 vs 0.90 log10 PEIU/mL, P = .002). The optimal threshold for identifying HBeAg seroconversion was HBeAg decline ≥2.2 log10 PEIU/mL at week 24, with HBeAg seroconversion achieved by 76% of patients, compared to 44% if HBeAg decline <2.2 log10 (P < .0001). HBeAg decline ≥2.2 log10 PEIU/mL at week 24 was associated with HBsAg loss in genotype A or D patients (38% vs 15%, P = .03). Precore/basal core promotor variants were associated with lower baseline HBeAg levels, but not HBeAg seroconversion. CONCLUSION: Decline in HBeAg levels by week 24 was associated with HBeAg seroconversion and HBsAg loss in HBeAg-positive chronic hepatitis B patients treated with long-term TDF.

Biochemical markers in vascular cognitive impairment associated with subcortical small vessel disease - A consensus report.

BACKGROUND: Vascular cognitive impairment (VCI) is a heterogeneous entity with multiple aetiologies, all linked to underlying vascular disease. Among these, VCI related to subcortical small vessel disease (SSVD) is emerging as a major homogeneous subtype. Its progressive course raises the need for biomarker identification and/or development for adequate therapeutic interventions to be tested. In order to shed light in the current status on biochemical markers for VCI-SSVD, experts in field reviewed the recent evidence and literature data. METHOD: The group conducted a comprehensive search on Medline, PubMed and Embase databases for studies published until 15.01.2017. The proposal on current status of biochemical markers in VCI-SSVD was reviewed by all co-authors and the draft was repeatedly circulated and discussed before it was finalized. RESULTS: This review identifies a large number of biochemical markers derived from CSF and blood. There is a considerable overlap of VCI-SSVD clinical symptoms with those of Alzheimer's disease (AD). Although most of the published studies are small and their findings remain to be replicated in larger cohorts, several biomarkers have shown promise in separating VCI-SSVD from AD. These promising biomarkers are closely linked to underlying SSVD pathophysiology, namely disruption of blood-CSF and blood-brain barriers (BCB-BBB) and breakdown of white matter myelinated fibres and extracellular matrix, as well as blood and brain inflammation. The leading biomarker candidates are: elevated CSF/blood albumin ratio, which reflects BCB/BBB disruption; altered CSF matrix metalloproteinases, reflecting extracellular matrix breakdown; CSF neurofilment as a marker of axonal damage, and possibly blood inflammatory cytokines and adhesion molecules. The suggested SSVD biomarker deviations contrasts the characteristic CSF profile in AD, i.e. depletion of amyloid beta peptide and increased phosphorylated and total tau. CONCLUSIONS: Combining SSVD and AD biomarkers may provide a powerful tool to identify with greater precision appropriate patients for clinical trials of more homogeneous dementia populations. Thereby, biomarkers might promote therapeutic progress not only in VCI-SSVD, but also in AD.

Intranuclear matrix metalloproteinases promote DNA damage and apoptosis induced by oxygen-glucose deprivation in neurons.

Degradation of the extracellular matrix by elevated matrix metalloproteinase (MMP) activity following ischemia/reperfusion is implicated in blood-brain barrier disruption and neuronal death. In contrast to their characterized extracellular roles, we previously reported that elevated intranuclear MMP-2 and -9 (gelatinase) activity degrades nuclear DNA repair proteins and promotes accumulation of oxidative DNA damage in neurons in rat brain at 3-h reperfusion after ischemic stroke. Here, we report that treatment with a broad-spectrum MMP inhibitor significantly reduced neuronal apoptosis in rat ischemic hemispheres at 48-h reperfusion after a 90-min middle cerebral artery occlusion (MCAO). Since extracellular gelatinases in brain tissue are known to be neurotoxic during acute stroke, the contribution of intranuclear MMP-2 and -9 activities in neurons to neuronal apoptosis has been unclear. To confirm and extend our in vivo observations, oxygen-glucose deprivation (OGD), an in vitro model of ischemia/reperfusion, was employed. Primary cortical neurons were subjected to 2-h OGD with reoxygenation. Increased intranuclear gelatinase activity was detected immediately after reoxygenation onset and was maximal at 24h, while extracellular gelatinase levels remained unchanged. We detected elevated levels of both MMP-2 and -9 in neuronal nuclear extracts and gelatinase activity in neurons co-localized primarily with MMP-2. We found a marked decrease in PARP1, XRCC1, and OGG1, and decreased PARP1 activity. Pretreatment of neurons with selective MMP-2/9 inhibitor II significantly decreased gelatinase activity and downregulation of DNA repair enzymes, decreased accumulation of oxidative DNA damage, and promoted neuronal survival after OGD. Our results confirm the nuclear localization of gelatinases and their nuclear substrates observed in an animal stroke model, further supporting a novel role for intranuclear gelatinase activity in an intrinsic apoptotic pathway in neurons during acute stroke injury.

[Is bovine leishmaniasis spreading in Switzerland?]. / Breitet sich die bovine kutane Leishmaniose in der Schweiz aus?

The purpose of the present study was based upon the first diagnosed bovine cutaneous leishmaniasis in a cow in Switzerland in April 2009. We continued descriptively the search for other bovine cases in Switzerland. We carried out similar investigations in the original farm where the case had occurred, and in parallel also in the neighboring farm. Additionally, veterinary practitioners sent us an overall of 12 suspected cases of bovine leishmaniasis. Following diagnostic investigations, all cases were negative for Leishmania. The occurrence of this infection appears therefore to be a very rare event. Finally some differential diagnoses are discussed.

[A survey on intestinal parasites of livestock guardian dogs and herding dogs in Switzerland]. / Überblick über intestinale Parasiten bei Herdenschutzhunden und Hütehunden in der Schweiz.

The present study describes the occurrence of intestinal parasite infections in livestock guardian dogs and herding dogs. A total of 71 guardian dogs (more than half of the total number of guardian dogs in Switzerland) and 21 herding dogs were coprologically examined, using a combined sedimentation-flotation method. In 21 (23 %) of the dogs intestinal parasites were detected, and 8 (8.7 %) of these dogs shed either sporocysts of Sarcocystis sp. (n = 6) or taeniid eggs (n = 2). The evaluation of questionnaires providing data on age, origin and deworming schemes of the dogs completed the study.

Transient immunosuppression: a bridge between infection and the atypical autoimmunity of Guillain-Barré syndrome?

Guillain-Barré syndrome (GBS) is an acute, usually monophasic, disorder of the peripheral nervous system that is assumed to be of immune-mediated pathogenesis. However, several clinical features and experimental findings of GBS are uncharacteristic for an immune-mediated disorder and set this condition apart from other disorders with a putative immune-mediated pathogenesis. These features include, among others, the monophasic nature of GBS, the lack of response to immunosuppressive (unlike immunomodulatory) therapy, the absence of a typical association with immunogenetic background and the inability to establish a valid and relevant animal model. We suggest a comprehensive hypothesis for the pathogenesis of GBS that is based on the assumption that the condition is due to a transient (or occasionally chronic) immune deficiency, as in most cases GBS follows an infection with pathogens known to induce immunosuppression. Such infections may be followed by breakdown of immune tolerance and induction of an immune attack on peripheral nerves. Mounting of the immune-mediated assault might be triggered either by the same infective pathogen or by secondary infection. Clearance of the infection and resumption of a normal immune response and tolerance eventually terminate the immune-mediated damage to the peripheral nerves and enable recovery. This hypothesis assumes that the entire sequence of events that culminates in GBS is due to transient exogenous factors and excludes a significant role for inherent host susceptibility, which explains the monophasic nature of the disorder.

Topological Anderson insulator in three dimensions.

We show that disorder, when sufficiently strong, can transform an ordinary metal with strong spin-orbit coupling into a strong topological "Anderson" insulator, a new topological phase of quantum matter in three dimensions characterized by disordered insulating bulk and topologically protected conducting surface states.

A study to demonstrate freedom from Trichinella spp. in domestic pigs in Switzerland.

Trichinellosis is a food-borne zoonotic disease caused by the nematode Trichinella spp. Many omnivorous and carnivorous animal species can act as host for this parasite, including domestic pigs. To protect public health, it should be ensured that pork should not contain infective Trichinella larvae. Surveillance for Trichinella spp. can be done using direct (larval detection) and indirect (antibody detection) diagnostic techniques. The aim of this study was to demonstrate the absence of infection in Swiss domestic pigs. An ELISA was used as the initial screening test, and sera reacting in ELISA were further investigated using both a Western blot for serology and an artificial digestion test with 20 g of diaphragm tissue for larval detection. A total of 7412 adult pigs, 9973 finishing pigs and 2779 free-ranging pigs were tested. Samples from 17 (0.23%) adult pigs, 16 (0.16%) finishing pigs and nine (0.32%) free-ranging pigs were ELISA-positive, but all of these sera were subsequently negative by Western blot and by the artificial digestion method. Based on these findings, an absence of Trichinella infections in adult pigs (target prevalence 0.04%) and finishing pigs (target prevalence 0.03%) can be concluded. The results also demonstrated that the prevalence of Trichinella infections does not exceed 0.11% in free-ranging pigs, the group with the highest risk of exposure.

Finite element analysis of stresses developed in the blood sac of a left ventricular assist device.

The goal of this research is to develop a 3D finite element (FE) model of a left ventricular assist device (LVAD) to predict stresses in the blood sac. The hyperelastic stress-strain curves for the segmented poly(ether polyurethane urea) (SPEUU) blood sac were determined in both tension and compression using a servo-hydraulic testing system at various strain rates. Over the range of strain rates studied, the sac was not strain rate sensitive, however the material response was different for tension versus compression. The experimental tension and compression properties were used in a FE model that consisted of the pusher plate, blood sac and pump case. A quasi-static analysis was used to allow for nonlinearities due to contact and material deformation. The 3D FE model showed that blood sac stresses are not adversely affected by the location of the inlet and outlet ports of the device and that over the systolic ejection phase of the simulation the prediction of blood sac stresses from the full 3D model and an axisymmetric model are the same. Minimizing stresses in the blood sac will increase the longevity of the blood sac in vivo.

Diverse roles of matrix metalloproteinases and tissue inhibitors of metalloproteinases in neuroinflammation and cerebral ischemia.

Regulation of the extracellular matrix by proteases and protease inhibitors is a fundamental biological process for normal growth, development and repair in the CNS. Matrix metalloproteinases (MMPs) and the tissue inhibitors of metalloproteinases (TIMPs) are the major extracellular-degrading enzymes. Two other enzyme families, a disintegrin and metalloproteinase (ADAM), and the serine proteases, plasminogen/plasminogen activator (P/PA) system, are also involved in extracellular matrix degradation. Normally, the highly integrated action of these enzyme families remodels all of the components of the matrix and performs essential functions at the cell surface involved in signaling, cell survival, and cell death. During the inflammatory response induced in infection, autoimmune reactions and hypoxia/ischemia, abnormal expression and activation of these proteases lead to breakdown of the extracellular matrix, resulting in the opening of the blood-brain barrier (BBB), preventing normal cell signaling, and eventually leading to cell death. There are several key MMPs and ADAMs that have been implicated in neuroinflammation: gelatinases A and B (MMP-2 and -9), stromelysin-1 (MMP-3), membrane-type MMP (MT1-MMP or MMP-14), and tumor necrosis factor-alpha converting enzyme (TACE). In addition, TIMP-3, which is bound to the cell surface, promotes cell death and impedes angiogenesis. Inhibitors of metalloproteinases are available, but balancing the beneficial and detrimental effects of these agents remains a challenge.

Tissue inhibitor of matrix metalloproteinases-3 (TIMP-3) lacks involvement in bacterial collagenase-induced intracerebral hemorrhage in mouse.

Intracerebral hemorrhage (ICH) leads to delayed cell death in the regions around the hemorrhagic mass. Apoptosis has been identified in the dying cells, but the mechanism involved is unclear. Others and us have shown that matrix metalloproteinases (MMPs) are increased in ICH and could directly contribute to cell death. Tissue inhibitor to metalloproteinases-3 (TIMP-3) facilitates apoptosis in cancer cells and neurons by inhibiting the shedding of tumor necrosis factor-alpha (TNF-alpha) death receptors, Fas and p55TNF receptor 1, by MMP-3 and TNF-alpha converting enzyme (TACE), respectively. Therefore, TIMP-3 may contribute to cell death in ICH. We adapted the bacterial collagenase-induced hemorrhage (CIH) model to the mouse. Adult C57Bl/6 and Timp-3 knockout mice had CIH. Expression of mRNA for TIMP-3 was determined by real-time PCR. Hemorrhage volume and numbers of apoptotic cells were measured by unbiased stereology. Timp-3 mRNA was similar in the knockout and wild-type mice prior to injury and induction of CIH failed to cause an increase in Timp-3 mRNA in the wild-type. Furthermore, there were no differences found in the hemorrhage size or in the numbers of apoptotic cells between the Timp-3 knockout or wild-type. We were unable to prove the hypothesis that TIMP-3 is involved cell death in CIH in the mouse.

Analysis of transcripts from intracellular stages of Eimeria acervulina using expressed sequence tags.

Coccidiosis in chickens is caused by 7 species of Eimeria. Even though coccidiosis is a complex disease that can be caused by any combination of these species, most of the molecular research concerning chicken coccidiosis has been limited to Eimeria tenella. The present study describes the first large-scale analysis of expressed sequence tags (ESTs) generated primarily from second-stage merozoites (and schizonts) of E. acervulina. In total, 1,847 ESTs were sequenced; these represent 1,026 unique sequences. Approximately half of the ESTs encode proteins of unknown function, or hypothetical proteins. Twenty-nine percent of the E. acervulina ESTs share significant sequence identity with sequences in the E. tenella genome. Additionally, EST hits seem to be much different compared with those of E. tenella. One of the differences is the very low number of ESTs that encode putative microneme proteins. This study underlines the potential differences in the molecular aspects of 2 Eimeria species that in the past were thought to be highly similar in nature.

Tissue inhibitor of metalloproteinases-3 facilitates Fas-mediated neuronal cell death following mild ischemia.

Tissue inhibitor of metalloproteinase-3 (TIMP-3) is a natural inhibitor of metalloproteinases involved in matrix degradation and ectodomain shedding of many cell-surface proteins, including death receptors and/or their ligands. In the present study, we examined the role of TIMP-3 in Fas-mediated neuronal cell death following cerebral ischemia, using both gene deletion and pharmacological approaches. In culture, exposure of primary cortical neurons to 2 h of oxygen-glucose deprivation (OGD) resulted in delayed neuronal cell death that was dependent on activation of the death receptor, Fas. Cortical cultures derived from timp-3(-/-) mice displayed partial resistance against OGD-induced neuronal cell death and also displayed increased shedding of Fas ligand (FasL) into the culture media, compared to wild-type control cultures. Both the increased neuroprotection and increased FasL shedding in timp-3(-/-) cultures were reversed by addition of exogenous metalloproteinase inhibitors, recombinant TIMP-3 or GM6001. In vivo, timp-3(-/-) mice showed marked resistance to a brief (30 min) middle cerebral artery occlusion (MCAO), but were not protected against more severe lesions induced by 90 min of MCAO. These studies demonstrate that TIMP-3 facilitates Fas-mediated neuronal cell death following OGD and plays a pro-apoptotic role in mild cerebral ischemia.

The mechanisms of action of valproate in neuropsychiatric disorders: can we see the forest for the trees?

After more than 40 years of clinical use, the mechanisms of action of valproate in epilepsy, bipolar disorder and migraine are still not fully understood. However, recent findings reviewed here shed new light on the cellular effects of valproate. Beyond the enhancement of gamma-aminobutyric acid-mediated neurotransmission, valproate has been found to affect signalling systems like the Wnt/beta-catenin and ERK pathways and to interfere with inositol and arachidonate metabolism. Nevertheless, the clinical relevance of these effects is not always clear. Valproate treatment also produces marked alterations in the expression of multiple genes, many of which are involved in transcription regulation, cell survival, ion homeostasis, cytoskeletal modifications and signal transduction. These alterations may well be relevant to the therapeutic effects of valproate, and result from its enhancement of activator protein-1 DNA binding and direct inhibition of histone deacetylases, and possibly additional, yet unknown, mechanism(s). Most likely, both immediate biochemical and longer-term genomic influences underlie the effects of valproate in all three indications.

A novel phospholipid derivative of indomethacin, DP-155 [mixture of 1-steroyl and 1-palmitoyl-2-{6-[1-(p-chlorobenzoyl)-5-methoxy-2-methyl-3-indolyl acetamido]hexanoyl}-sn-glycero-3-phosophatidyl [corrected] choline], shows superior safety and similar efficacy in reducing brain amyloid beta in an Alzheimer's disease model.

Indomethacin has been suggested for the treatment of Alzheimer's disease (AD), but its use is limited by gastrointestinal and renal toxicity. To overcome this limitation, D-Pharm Ltd. (Rehovot, Israel) developed DP-155 (mixture of 1-steroyl and 1-palmitoyl-2-{6-[1-(p-chlorobenzoyl)-5-methoxy-2-methyl-3-indolyl acetamido] hexanoyl}-Sn-glycero-3-phosophatidyl [corrected] choline), a lecithin derivative of indomethacin. Safety was tested by daily oral administration of DP-155 or indomethacin to rats in a dose range of 0.007 to 0.28 mmol/kg. The prevalence of gastrointestinal ulceration was significantly lower (10-fold) for DP-155 than for indomethacin, and the ulcerations were delayed. Signs of renal toxicity, namely reduced urine output and increased urine N-acetyl glycosaminidase to creatinine ratio, were 5-fold lower for DP-155. Indomethacin, but not an equimolar dose of DP-155, reduced urine bicyclo-prostaglandin E(2). An equimolar oral dose of DP-155 or indomethacin, administered every 4 h for 3 days, was equally efficacious in reducing the levels of Abeta42 in the brains of Tg2576 mice. Indomethacin was the principal metabolite of DP-155 in the serum. After DP-155 oral administration, indomethacin's half-life in the serum and the brain was 22 and 93 h, respectively, compared with 10 and 24 h following indomethacin oral administration. The brain to serum ratio was 3.5 times higher for DP-155 than indomethacin. This finding explains the efficacy of DP-155 in reducing Abeta42 brain levels, despite the low systemic blood concentrations of indomethacin derived from DP-155. In conclusion, compared with indomethacin, DP-155 has significantly lower toxicity in the gut and kidney while maintaining similar efficacy to indomethacin in lowering Abeta42 in the brains of Tg2576 mice. This superior safety profile highlights DP-155's potential as an improved indomethacin-based therapy for AD.

[Long-term outcome of type V lupus membranous glomerulonephritis]. / Curso clínico de la nefropatía membranosa lúpica pura.

BACKGROUND: The long-term outcome of the pure form of WHO type V lupus membranous glomerulonephritis is apparently more benign than that of other forms of lupus glomerulonephritis. However 12% of such patients progress to terminal renal failure. The presence of proteinuria may be an indication of cytotoxic agents. AIM: To study the clinical long-term outcome of WHO type V lupus membranous glomerulonephritis. MATERIAL AND METHODS: A retrospective analysis of all kidney biopsies of a University Pathology Department, with the diagnosis of WHO type V lupus membranous glomerulonephritis. Review of medical records of patients with the disease and one clinical assessment of all living patients. RESULTS: Between 1973 and 2000, 703 kidney biopsies were done to patients with systemic lupus erythematosus. Of these, 40 were membranous glomerulonephritis and in 33 patients (28 women, age range 6-71 years), data on the evolution and survival was obtained. Nineteen had type Va and the rest type Vb nephritis. Two presented with renal failure and 11 with proteinuria over 3.5 g/24 h. The median follow-up since the renal biopsy was 63 months (range 1-316). At the end of follow-up, four had a creatinine clearance of less then 15 ml/h and four a clearance between 15 and 29 ml/h (one of these received a renal allograft). Eleven (33%) patients had died, mostly due to infections. Life expectancy at five years with a creatinine clearance over 15 ml/h was 75%. Bad prognostic factors were an elevated creatinine clearance over 15 ml/h was 75%. Bad prognostic factors were an elevated creatinine and high blood pressure at the moment of the biopsy. CONCLUSIONS: The clinical outcome of these patients was bad. Twelve percent reached a stage of terminal renal failure. This is in contrast with the 3% progression to a similar stage of proliferative glomerulonephritis treated with i.v. cyclophosphamide. New therapies for this condition must be sought.