Miracle-dz/UniFAR-FTUs huggingface dataset:
From high-content to super-resolution investigation of cell behaviour on nanostructured surfaces

The environment in which cells find themselves is a complex, three dimensional one which provides a variety of inputs and cues capable of controlling and guiding cell behaviour. These environmental signals take a fertilised egg through development to become an adult human being made up of trillions of cells. As such, the power of environmental cues to provide context and guidance to cell behaviour cannot be understated. Without attempting to directly mimic the in vivo environment, it has been shown that micro- and nanostructured surfaces can influence cell behaviour when we try and engineer biology in vitro. Identification and optimisation of powerful topographies is, however, tedious, and so this thesis provides techniques to expedite the discovery of new and potent surfaces to drive cell behaviour. A new fabrication technique has been developed which allows for the fabrication of gradients of feature height at both the micro- and nanoscale. This involves the use of plasma polymer gradients as novel etch masks alongside existing lithographic techniques. After fabrication and mass replication by injection moulding, use of these surfaces as platforms for the high-content screening of cell response is demonstrated. These can be considered high-content due to both the range of surface structures on a single sample, and also the microscopy techniques used to investigate cell response. Distinct cell types were found to respond differently to topographical cues, exhibiting varying degrees of alignment, proliferation, and organisation in both mono- and co-culture systems. A new cell culture device has also been developed and patented which ensures that screening experiments begin with an accurate and repeatable distribution of cells across the high content array. The impact of uneven cell seeding on studies involving stem cell differentiation was also investigated – showing the importance of improved control. Finally, the interaction of cells with such nanostructured surfaces is investigated using new super-resolution microscopy techniques. New methods are presented for the correlation of multiple nanoscale imaging techniques to view cell-nanostructure interactions with unprecedented resolution. This reveals insights into the way in which the cellular substructure is being modulated by underlying nanotopography. Indeed, it paints a picture which is remarkably different to the structure observed under a standard widefield microscope over the past 10 years.
Response of patients with Alzheimer disease to rivastigmine treatment is predicted by the rate of disease progression.

BACKGROUND Evidence suggests that disease severity predicts the response of patients with Alzheimer disease (AD) to cholinesterase inhibitor treatment, raising the question of whether disease progression also predicts response to this treatment. OBJECTIVE To evaluate retrospectively whether rate of disease progression during placebo treatment affects response to subsequent rivastigmine tartrate therapy for patients with mild to moderately severe AD. DESIGN A 26-week, open-label extension study following a 26-week, double-blind, randomized, placebo-controlled trial. SETTING Outpatient research centers at 22 sites in the United States. PATIENTS We studied 187 of 235 patients originally randomized to receive placebo treatment in the double-blind phase of the trial who continued with open-label (rivastigmine) extension therapy. INTERVENTION Placebo treatment for 26 weeks followed by rivastigmine treatment, 2 to 12 mg/d, for 26 weeks. MAIN OUTCOME MEASURES Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-Cog), Progressive Deterioration Scale, Mini-Mental State Examination, and Global Deterioration Scale scores. RESULTS Rivastigmine administration during open-label extension therapy benefited patients who had progressed slowly and those who had progressed rapidly during initial double-blind placebo treatment. Slowly progressive patients responded with a mean 1.03-point improvement in the week 26 (ie, start of open-label rivastigmine treatment) ADAS-Cog score at 12 weeks of rivastigmine treatment (week 38 of treatment; P =.02 vs week 26). However, more rapidly progressive patients had a significantly larger mean 4.97-point improvement from the week 26 ADAS-Cog score at 12 weeks (with respect to week 26 of treatment and slowly progressive patient scores, P<.001 for both). Thus, a more rapid disease progression rate while receiving placebo treatment was predictive of a significantly stronger patient response to rivastigmine therapy. This relation also was observed with the other 3 outcome measures and was still apparent when accounting for disease severity. CONCLUSIONS Rate of disease progression for patients with mild to moderate AD seems to predict response to rivastigmine treatment. Patients with more rapidly progressive disease might be particularly likely to benefit from rivastigmine therapy.
Nonseparable, Stationary Covariance Functions for Space–Time Data

Geostatistical approaches to spatiotemporal prediction in environmental science, climatology, meteorology, and related fields rely on appropriate covariance models. This article proposes general classes of nonseparable, stationary covariance functions for spatiotemporal random processes. The constructions are directly in the space–time domain and do not depend on closed-form Fourier inversions. The model parameters can be associated with the data's spatial and temporal structures, respectively; and a covariance model with a readily interpretable space–time interaction parameter is fitted to wind data from Ireland.
Rumen simulation technique study on the interactions of dietary lauric and myristic acid supplementation in suppressing ruminal methanogenesis

The interactions of lauric (C12) and myristic acid (C14) in suppressing ruminal methanogenesis and methanogens were investigated with the rumen simulation technique (Rusitec) using bovine ruminal fluid. The fatty acids were added to basal substrates (grass hay:concentrate, 1:1.5) at a level of 48 g/kg DM, provided in C12:C14 ratios of 5:0, 4:1, 3:2, 2·5:2.5, 2:3, 1:4 and 0:5. Additionally, an unsupplemented control consisting of the basal substrates only was employed. Incubation periods lasted for 15 (n 4) and 25 (n 2) d. CH4 formation was depressed by any fatty acid mixture containing at least 40 % C12, and effects persisted over the complete incubation periods. The greatest depression (70 % relative to control) occurred with a C12:C14 ratio of 4:1, whereas the second most effective treatment in suppressing CH4 production (60 % relative to control) was found with a ratio of 3:2. Total methanogenic counts were decreased by those mixtures of C12 and C14 also successful in suppressing methanogenesis, the 4:1 treatment being most efficient (60 % decline). With this treatment in particular, the composition of the methanogenic population was altered in such a way that the proportion of Methanococcales increased and Methanobacteriales decreased. Initially, CH4 suppression was associated with a decreased fibre degradation, which, however, was reversed after 10 d of incubation. The present study demonstrated a clear synergistic effect of mixtures of C12 and C14 in suppressing methanogenesis, mediated probably by direct inhibitory effects of the fatty acids on the methanogens.
Iterative equalization in non-linear satellite channels

The nonlinear distortion in efficiently operated wide bandwidth and high power amplifiers often limits the throughput and performance of satellite communications. Volterra series decomposition provides an efficient and analytically tractable way to represent the nonlinear satellite communication channel. Realizing that only a few dominant terms in the Volterra series are needed to accurately describe the channel, this paper proposes a computationally efficient nonlinear soft interference cancellation (SIC) minimum mean square error (MMSE) equalizer. Simulation demonstrates that the nonlinear SIC MMSE equalizer outperforms its linear counter part in performance while achieving an 80% computational complexity reduction.
Smoking behaviour and toxin exposure during six weeks use of a potential reduced exposure product: Omni

Objective: To determine smoking behaviour, acceptability, and toxin exposure when smokers switch to the potential reduced exposure product—Omni cigarette. Design: 12 week randomised, crossover study of Omni versus own cigarettes. Participants: 19 light/ultralight and 15 regular smokers. Outcomes: Cigarettes/day, smoking topography, craving, withdrawal symptoms, urinary cotinine plus its glucuronide (total cotinine), nicotine plus its glucuronide (total nicotine), and carcinogen metabolites (4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol plus its glucuronides and 1-hydroxypyrene). Results: When switched to Omni, smokers smoked the same number of cigarettes/day, smoked Omni cigarettes less intensely (total puff volume = −11%) and had slightly lower total cotinine (−18%) levels than their own cigarettes, but had a slightly greater carbon monoxide boost/cig (+21%). Craving and withdrawal ratings were similar with Omni and own cigarettes. Carcinogen metabolite levels were somewhat but not significantly lower with Omni. About half of smokers rated Omni as better for their health and about two thirds stated it was weaker and worse tasting than their own cigarettes. Conclusions: Although Omni may be an adequate behavioural and pharmacological substitute for traditional cigarettes, it may not decrease carcinogen exposure and may increase carbon monoxide. Replications with larger sample sizes and longer follow up are needed. These results indicate the need for regulation of reduced exposure and reduced risk claims.
Increase in sexually transmitted infections among homosexual men in Amsterdam in relation to HAART

Objectives: We investigated if a rise in rectal gonorrhoea and early syphilis among men who have sex with men (MSM) in Amsterdam coincided with the introduction of highly active antiretroviral therapies (HAART) in July 1996 and determined risk factors for these sexually transmitted infections (STI). Methods: Subjects were patients of the STI clinic of the municipal health service in Amsterdam. Surveillance data (1994–9) represented consultations (n=11 240) of MSM (n=6103). For analyses we used logistic regression. Results: Comparing the periods before and after the introduction of HAART, the infection rate for rectal gonorrhoea increased from 4% to 5.4% (p=.001) and for syphilis, from 0.5% to 0.8% (p = 0.050). Independent risk factors for rectal gonorrhoea (younger age, western nationality, and concurrent infection with another STI) and for early syphilis (non-western nationality and concurrent infection with rectal gonorrhoea) did not change after HAART became available. For rectal gonorrhoea, however, the infection rate increased only among men who had exclusively homosexual contacts (OR 1.38, p<0.01), compared with bisexual men. For early syphilis, the infection rate increased only among men of western nationality (OR 3.38, p<0.01) compared to men of non-western nationality. Conclusions: Infection rates of rectal gonorrhoea and early syphilis increased, indicating a change in sexual behaviour, possibly as a result of the introduction of HAART. For now, it is important to find out how sexual behaviour is changing and to keep monitoring trends in STIs (including HIV) among MSM in Amsterdam.
Effects of dietary fish oil and flax seed on cholesterol and fatty acid composition of egg yolk and blood parameters of laying hens

This study was conducted to determine the effects of the supplementation of different levels of fish oil (FO) and flax seed (FS) in the diets of layers on the content of egg yolk fatty acid, cholesterol, blood parameters, egg production and egg quality criteria. In the experiment, a total of 120 Isa-White laying hens of 34 weeks of age were used. Hens were divided randomly into five groups and fed different diets containing no FO and FS; 1.5% FO; 4.32% FS; 1.5% FO+4.32% FS and 8.64% FS for eight weeks. A significant decrease in yolk cholesterol content (mg/g yolk) was found in the eggs from hens fed the diets containing 1.5 % FO and 8.64% FS as compared with the control. Adding FO and FS to diets significantly increased the total omega-3 fatty acids in eggs at 28 (phase 1) and 56 (phase 2) days of the trial. By contrast, the addition of both FO and FS to diets had no effect on total omega-6 fatty acids in eggs in phase 1. But dietary 1.5% FO, 4.32% FS and 1.5% FO+4.32% FS supplementation decreased significantly the total omega-6 fatty acids compared to the controls in phase 2. The linolenic acid content of eggs was the highest in eggs from hens fed the diet with added FS, while docosahexaenoic acid content was the highest in eggs from hens fed diets with added FO. Dietary supplementation of FO and FS did not significantly affect the concentrations of serum trigliceride and high density lipoprotein. The serum cholesterol level of hens fed diets containing 1.5% FO+4.32% FS and 8.64% FS was lower than the control group. The addition of FO and FS to diets did not cause any negative effect on some egg quality criteria such as egg weight, yolk weight, yolk ratio, albumen weight, albumen ratio, shell weight, shell ratio, shell strength and shell thickness. The egg production of hens fed a diet containing 4.32% FS was significantly higher than the controls. Feed intake and feed conversion were not affected by all treatments.
Sarcoma Immunotherapy

Much of our knowledge regarding cancer immunotherapy has been derived from sarcoma models. However, translation of preclinical findings to bedside success has been limited in this disease, though several intriguing clinical studies hint at the potential efficacy of this treatment modality. The rarity and heterogeneity of tumors of mesenchymal origin continues to be a challenge from a therapeutic standpoint. Nonetheless, sarcomas remain attractive targets for immunotherapy, as they can be characterized by specific epitopes, either from their mesenchymal origins or specific alterations in gene products. To date, standard vaccine trials have proven disappointing, likely due to mechanisms by which tumors equilibrate with and ultimately escape immune surveillance. More sophisticated approaches will likely require multimodal techniques, both by enhancing immunity, but also geared towards overcoming innate mechanisms of immunosuppression that favor tumorigenesis.
IL-2 Stimulated but Not Unstimulated NK Cells Induce Selective Disappearance of Peripheral Blood Cells: Concomitant Results to a Phase I/II Study

In an ongoing clinical phase I/II study, 16 pediatric patients suffering from high risk leukemia/tumors received highly purified donor natural killer (NK) cell immunotherapy (NK-DLI) at day (+3) +40 and +100 post haploidentical stem cell transplantation. However, literature about the influence of NK-DLI on recipient's immune system is scarce. Here we present concomitant results of a noninvasive in vivo monitoring approach of recipient's peripheral blood (PB) cells after transfer of either unstimulated (NK-DLI(unstim)) or IL-2 (1000 U/ml, 9–14 days) activated NK cells (NK-DLI(IL-2 stim)) along with their ex vivo secreted cytokine/chemokines. We performed phenotypical and functional characterizations of the NK-DLIs, detailed flow cytometric analyses of various PB cells and comprehensive cytokine/chemokine arrays before and after NK-DLI. Patients of both groups were comparable with regard to remission status, immune reconstitution, donor chimerism, KIR mismatching, stem cell and NK-DLI dose. Only after NK-DLI(IL-2 stim) was a rapid, almost complete loss of CD56(bright)CD16(dim/−) immune regulatory and CD56(dim)CD16(+) cytotoxic NK cells, monocytes, dendritic cells and eosinophils from PB circulation seen 10 min after infusion, while neutrophils significantly increased. The reduction of NK cells was due to both, a decrease in patients' own CD69(−) NCR(low)CD62L(+) NK cells as well as to a diminishing of the transferred cells from the NK-DLI(IL-2 stim) with the CD56(bright)CD16(+/−)CD69(+)NCR(high)CD62L(−) phenotype. All cell counts recovered within the next 24 h. Transfer of NK-DLI(IL-2 stim) translated into significantly increased levels of various cytokines/chemokines (i.e. IFN-γ, IL-6, MIP-1β) in patients' PB. Those remained stable for at least 1 h, presumably leading to endothelial activation, leukocyte adhesion and/or extravasation. In contrast, NK-DLI(unstim) did not cause any of the observed effects. In conclusion, we assume that the adoptive transfer of NK-DLI(IL-2 stim) under the influence of ex vivo and in vivo secreted cytokines/chemokines may promote NK cell trafficking and therefore might enhance efficacy of immunotherapy.
The dynamics of cortical and hippocampal atrophy in Alzheimer disease.

OBJECTIVE To characterize rates of regional Alzheimer disease (AD)-specific brain atrophy across the presymptomatic, mild cognitive impairment, and dementia stages. DESIGN Multicenter case-control study of neuroimaging, cerebrospinal fluid, and cognitive test score data from the Alzheimer's Disease Neuroimaging Initiative. SETTING Research centers across the United States and Canada. PATIENTS We examined a total of 317 participants with baseline cerebrospinal fluid biomarker measurements and 3 T1-weighted magnetic resonance images obtained within 1 year. MAIN OUTCOME MEASURES We used automated tools to compute annual longitudinal atrophy in the hippocampus and cortical regions targeted in AD. We used Mini-Mental State Examination scores as a measure of cognitive performance. We performed a cross-subject analysis of atrophy rates and acceleration on individuals with an AD-like cerebrospinal fluid molecular profile. RESULTS In presymptomatic individuals harboring indicators of AD, baseline thickness in AD-vulnerable cortical regions was significantly reduced compared with that of healthy control individuals, but baseline hippocampal volume was not. Across the clinical spectrum, rates of AD-specific cortical thinning increased with decreasing cognitive performance before peaking at approximately the Mini-Mental State Examination score of 21, beyond which rates of thinning started to decline. Annual rates of hippocampal volume loss showed a continuously increasing pattern with decreasing cognitive performance as low as the Mini-Mental State Examination score of 15. Analysis of the second derivative of imaging measurements revealed that AD-specific cortical thinning exhibited early acceleration followed by deceleration. Conversely, hippocampal volume loss exhibited positive acceleration across all study participants. CONCLUSIONS Alzheimer disease-specific cortical thinning and hippocampal volume loss are consistent with a sigmoidal pattern, with an acceleration phase during the early stages of the disease. Clinical trials should carefully consider the nonlinear behavior of these AD biomarkers.
Prediction of Selective Serotonin Reuptake Inhibitor Response Using Diffusion-Weighted MRI

Pre-treatment differences in serotonergic binding between those who remit to antidepressant treatment and those who do not have been found using Positron Emission Tomography (PET). To investigate these differences, an exploratory study was performed using a second imaging modality, diffusion-weighted MRI (DW-MRI). Eighteen antidepressant-free subjects with Major Depressive Disorder received a 25-direction DW-MRI scan prior to 8 weeks of selective serotonin reuptake inhibitor treatment. Probabilistic tractography was performed between the midbrain/raphe and two target regions implicated in depression pathophysiology (amygdala and hippocampus). Average fractional anisotropy (FA) within the derived tracts was compared between SSRI remitters and non-remitters, and correlation between pre-treatment FA values and SSRI treatment outcome was assessed. Results indicate that average FA in DW-MRI-derived tracts to the right amygdala was significantly lower in non-remitters (0.55 ± 0.04) than remitters (0.61 ± 0.04, p < 0.01). In addition, there was a significant correlation between average FA in tracts to the right amygdala and SSRI treatment response. These relationships were found at a trend level when using the left amygdala as a tractography target. No significant differences were observed when using the hippocampus as target. These regional differences, consistent with previous PET findings, suggest that the integrity and/or number of white matter fibers terminating in the right amygdala may be compromised in SSRI non-remitters. Further, this study points to the benefits of multimodal imaging and suggests that DW-MRI may provide a pre-treatment signature of SSRI depression remission at 8 weeks.
Rational Design of a Carrier Protein for the Production of Recombinant Toxic Peptides in Escherichia coli

Commercial uses of bioactive peptides require low cost, effective methods for their production. We developed a new carrier protein for high yield production of recombinant peptides in Escherichia coli very well suited for the production of toxic peptides like antimicrobial peptides. GKY20, a short antimicrobial peptide derived from the C-terminus of human thrombin, was fused to the C-terminus of Onconase, a small ribonuclease (104 amino acids), which efficiently drove the peptide into inclusion bodies with very high expression levels (about 200–250 mg/L). After purification of the fusion protein by immobilized metal ion affinity chromatography, peptide was obtained by chemical cleavage in diluted acetic acid of an acid labile Asp-Pro sequence with more than 95% efficiency. To improve peptide purification, Onconase was mutated to eliminate all acid labile sequences thus reducing the release of unwanted peptides during the acid cleavage. Mutations were chosen to preserve the differential solubility of Onconase as function of pH, which allows its selective precipitation at neutral pH after the cleavage. The improved carrier allowed the production of 15–18 mg of recombinant peptide per liter of culture with 96–98% purity without the need of further chromatographic steps after the acid cleavage. The antimicrobial activity of the recombinant peptide, with an additional proline at the N-terminus, was tested on Gram-negative and Gram-positive strains and was found to be identical to that measured for synthetic GKY20. This finding suggests that N-terminal proline residue does not change the antimicrobial properties of recombinant (P)GKY20. The improved carrier, which does not contain cysteine and methionine residues, Asp-Pro and Asn-Gly sequences, is well suited for the production of peptides using any of the most popular chemical cleavage methods.
The Role of Reflexes Versus Central Pattern Generators in Dynamical Legged Locomotion

Animals execute locomotor behaviors and more with ease. They have evolved these breath-taking abilities over millions of years. Cheetahs can run, dolphins can swim and flies can fly like no artificial technology can. It is often argued that if human technology could mimic nature, then biological-like performance would follow. Unfortunately, the blind copying or mimicking of a part of nature [Ritzmann et al., 2000] does not often lead to the best design for a variety of reasons [Vogel, 1998]. Evolution works on the "just good enough" principle. Optimal designs are not the necessary end product of evolution. Multiple satisfactory solutions can result in similar performances. Animals do bring to our attention amazing designs, but these designs carry with them the baggage of their history. Moreover, natural design is constrained by factors that may have no relationship to human engineered designs. Animals must be able to grow over time, but still function along the way. Finally, animals are complex and their parts serve multiple functions, not simply the one we happen to examine. In short, in their daunting complexity and integrated function, understanding animal behaviors remains as intractable as their capabilities are tantalizing.