Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA: From rigid base-pairs to semiflexible polymers

The sequence–dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base–pair model, whose strains are the relative position and orientation of adjacent base– pairs. Corresponding elastic potentials have been obtained from all–atom MD simulation and from high–resolution structural data. On the scale of a hundred nm, DNA is successfully described by a continuous worm–like chain model with homogeneous elastic properties characterized by a set of four elastic constants, which have been directly measured in single–molecule experiments. We present here a theory that links these experiments on different scales, by systematically coarse–graining the rigid base–pair model for random sequence DNA to an effective worm–like chain description. The average helical geometry of the molecule is exactly taken into account in our approach. We find that the available microscopic parameters sets predict qualitatively similar mesoscopic parameters. The thermal bending and twisting persistence lengths computed from MD data are 42 and 48 nm, respectively. The static persistence lengths are generally much higher, in agreement with cyclization experiments. All microscopic parameter sets predict negative twist–stretch coupling. The variability and anisotropy of bending stiffness in short random chains lead to non–Gaussian bend angle distributions, but become unimportant after two helical turns.
Less-Affected Hand Function in Children With Hemiparetic Unilateral Cerebral Palsy: A Comparison Study With Typically Developing Peers

Background. Neurorehabilitation interventions in children with unilateral cerebral palsy (UCP) target motor abilities in daily life yet deficits in hand skills persist. Limitations in the less-affected hand may affect overall bimanual hand skills. Objective. To compare hand function, by timed motor performance on the Jebsen-Taylor Test of Hand Function (JTTHF) and grip strength of children with UCP to children with typical development (CTD), aged 8 to 18 years old. Exploratory analyses compared hand function measures with regard to neurophysiological outcomes measured by transcranial magnetic stimulation and between group comparisons of hemispheric motor threshold. Methods. Baseline hand skills were evaluated in 47 children (21 UCP; 26 CTD). Single-pulse transcranial magnetic stimulation testing assessed corticospinal tract and motor threshold. Results. The mean difference of the less-affected hand of children with UCP to the dominant hand of CTD on the JTTHF was 21.4 seconds (95% CI = 9.32-33.46, P = .001). The mean difference in grip strength was −30.8 N (95% CI = −61.9 to 0.31, P = .052). Resting motor thresholds between groups were not significant, but age was significantly associated with resting motor threshold (P < .001; P = .001). Children with UCP ipsilateral pattern of motor representation demonstrated greater mean differences between hands than children with contralateral pattern of motor representation (P < .001). All results were adjusted for age and sex. Conclusions. The less-affected hand in children with UCP underperformed the dominant hand of CTD. Limitations were greater in children with UCP ipsilateral motor pattern. Rehabilitation in the less-affected hand may be warranted. Bilateral hand function in future studies may help identify the optimal rehabilitation and neuromodulatory intervention.
A noise robust method for segmentation of moving objects in video sequences

An algorithm for automatic, noise robust segmentation of moving objects in image sequences is presented. Such algorithms are required for object-based coding techniques like the upcoming ISO/MPEG-4 standard. In a first step, a mask of changed image areas is estimated by a local thresholding relaxation technique. Then, areas of uncovered background are removed from this mask, taking into account an estimated displacement vector field. The resulting object mask is finally improved by applying a grey-level edge adaptation and an object mask memory. The algorithm is compared to a global thresholding technique which is known from the literature. Experimental results show the improvement of the estimated object masks.
The use of the defence style questionnaire in major depressive and panic disorders: a comprehensive meta-analysis.

PURPOSE The issue of defence mechanisms is of great importance in clinical practice. The aim of this meta-analysis is to compare different defence styles (Mature, Neurotic, and Immature), assessed using the three-factor defence style questionnaire (DSQ), in major depressive disorder (MDD), and panic disorder (PD) in order to evaluate potential differences in defence profiles among these disorders. METHODS We assessed all publications listed in PubMed, PsycINFO, ISI, and Lilacs databases focusing on DSQ defence styles in MDD and PD. To be included studies had to be published in English, to include psychiatric patients, to provide defence style mean scores, and to employ the three-factor DSQ versions. Data were entered into the Cochrane Collaboration Review Manager Software and analysed by RevMan version 4.2. RESULTS MDD patients reported significantly lower scores in Mature style and both MDD and PD patients reported significantly higher scores in Neurotic and Immature styles. CONCLUSIONS A dissimilarity between depressive and anxious profiles emerged, since the former profile was characterized by low Mature and high Neurotic and Immature scores while the latter by high Neurotic and Immature scores only. These results could indicate the use of specific strategies in clinical and psychotherapeutic management of patients with these diagnoses. Nevertheless, present results should be considered with caution because of the high heterogeneity of the studies and some weaknesses in the psychometric properties of the DSQ.
The Neural Language Systems That Support Healthy Aging: Integrating Function, Structure, and Behavior

Although healthy aging is generally characterized by declines in both brain structure and function, there is variability in the extent to which these changes result in observable cognitive decline. Specific to language, age-related differences in language production are observed more frequently than in language comprehension, although both are associated with increased right prefrontal cortex activation in older adults. The current paper explores these differences in the language system, integrating them with theories of behavioral and neural cognitive aging. Overall, data indicate that frontal reorganization of the dorsal language stream in older adults benefits task performance during comprehension, but not always during production. We interpret these results in the CRUNCH framework (compensation-related utilization of neural circuits hypothesis), which suggests that differences in task and process difficulty may underlie older adults' ability to successfully adapt. That is, older adults may be able to neurally adapt to less difficult tasks (i.e., comprehension), but fail to do so successfully as difficulty increases (i.e., production). We hypothesize greater age-related differences in aspects of language that rely more heavily on the dorsal language stream (e.g., syntax and production) and that recruit general cognitive resources that rely on frontal regions (e.g., executive function, working memory, inhibition). Moreover, there should be a relative sparing of tasks that rely predominantly on ventral stream regions. These results are both consistent with patterns of age-related structural decline and retention and with varying levels of difficulty across comprehension and production. This neurocognitive framework for understanding age-related differences in the language system centers on the interaction between prefrontal cortex activation, structural integrity, and task difficulty.
Limited engraftment capacity of bone marrow-derived mesenchymal cells following T-cell-depleted hematopoietic stem cell transplantation.

The engraftment capacity of bone marrow-derived mesenchymal cells was investigated in 41 patients who had received a sex-mismatched, T-cell-depleted allograft from human leukocyte antigen (HLA)-matched or -mismatched family donors. Polymerase chain reaction (PCR) analysis of the human androgen receptor (HUMARA) or the amelogenin genes was used to detect donor-derived mesenchymal cells. Only 14 marrow samples (34%) from 41 consenting patients generated a marrow stromal layer adequate for PCR analysis. Monocyte-macrophage contamination of marrow stromal layers was reduced below the levels of sensitivity of HUMARA and amelogenin assays (5% and 3%, respectively) by repeated trypsinizations and treatment with the leucyl-leucine (leu-leu) methyl ester. Patients who received allografts from 12 female donors were analyzed by means of the HUMARA assay, and in 5 of 12 cases a partial female origin of stromal cells was demonstrated. Two patients who received allografts from male donors were analyzed by amplifying the amelogenin gene, and in both cases a partial male origin of stromal cells was shown. Fluorescent in situ hybridization analysis using a Y probe confirmed the results of PCR analysis and demonstrated in 2 cases the existence of a mixed chimerism at the stromal cell level. There was no statistical difference detected between the dose of fibroblast progenitors (colony-forming unit-F [CFU-F]) infused to patients with donor- or host-derived stromal cells (1.18 +/- 0.13 x 10(4)/kg vs 1. 19 +/- 0.19 x 10(4)/kg; P >/=. 97). In conclusion, marrow stromal progenitors reinfused in patients receiving a T-cell-depleted allograft have a limited capacity of reconstituting marrow mesenchymal cells.
Adherence and dosing interval of subcutaneous antitumour necrosis factor biologics among patients with inflammatory arthritis: analysis from a Canadian administrative database

Objectives Subcutaneous tumour necrosis factor alpha TNFαinhibitors (SC-TNFis) such as golimumab (GLM), adalimumab (ADA), etanercept (ETA) and certolizumab pegol (CZP) have been used for many years for the treatment of inflammatory arthritis. Non-adherence to therapy is an important modifiable factor that may compromise patient outcomes. The aim of this analysis was to compare adherence and dosing interval of SC-TNFis in the treatment of people with inflammatory arthritis. Design We used the IMS Brogan database combining both Canadian private and public drug plan databases of Ontario and Quebec. Target drugs included SC-TNFis for inflammatory arthritis. The index period was from 1 January 2010 to 30 June 2012 and patients were followed for 24 months through 30 June 2014. Inclusion criteria were adult patients newly prescribed a SC-TNFis with at least three prescriptions and retained on therapy at 24 months. Dosing regimens as per the product monographs were used to compare actual versus expected drug utilisation. The mean possession ratio was used as a marker for adherence. Patients who scored >80% were considered adherent. The average days between units was estimated by taking the total days on therapy and divided by the number of units the patient received. Results 4035 patients were included: 683 (16.9%), 1400 (34.7%), 1765 (43.7%) and 187 (4.6%) were treated with GLM, ADA, ETA and CZP, respectively. The proportion of adherent patients in the GLM cohort (n=595/683, 87%, p<0.0001) was greater compared with ADA (n=1044/1400, 75%), ETA (n=1285/1765, 73%) and CZP-treated patients (132/187, 71%). In addition, the number of patients receiving biological drug at a shorter dosing interval was similar between cohorts, and was 5%, 6%, 12% and 4% in GLM (≤26 days), ADA (≤12 days), ETA (≤6 days) and CZP-treated patients (≤12 days), respectively. Conclusions In this real-life administrative database, GLM had better adherence compared with other SC-TNFis.
Trace optimization and eigenproblems in dimension reduction methods

This paper gives an overview of the eigenvalue problems encountered in areas of data mining that are related to dimension reduction. Given some input high‐dimensional data, the goal of dimension reduction is to map them to a low‐dimensional space such that certain properties of the original data are preserved. Optimizing these properties among the reduced data can be typically posed as a trace optimization problem that leads to an eigenvalue problem. There is a rich variety of such problems and the goal of this paper is to unravel relationships between them as well as to discuss effective solution techniques. First, we make a distinction between projective methods that determine an explicit linear mapping from the high‐dimensional space to the low‐dimensional space, and nonlinear methods where the mapping between the two is nonlinear and implicit. Then, we show that all the eigenvalue problems solved in the context of explicit linear projections can be viewed as the projected analogues of the nonlinear or implicit projections. We also discuss kernels as a means of unifying linear and nonlinear methods and revisit some of the equivalences between methods established in this way. Finally, we provide some illustrative examples to showcase the behavior and the particular characteristics of the various dimension reduction techniques on real‐world data sets. Copyright © 2010 John Wiley & Sons, Ltd.
Evaluation Metrics For End-to-End Coreference Resolution Systems

Commonly used coreference resolution evaluation metrics can only be applied to key mentions, i.e. already annotated mentions. We here propose two variants of the B3 and CEAF coreference resolution evaluation algorithms which can be applied to coreference resolution systems dealing with system mentions, i.e. automatically determined mentions. Our experiments show that our variants lead to intuitive and reliable results.
Fatty acid profile , color and lipid oxidation of organic fermented sausage during

Organic fermented sausages typically spoil during long-term storage due to oxidative rancidity. The application of natural antioxidants to meat stuffing is a major practice intended to inhibit the oxidation process and color changes. This study aimed to assess the effect of two unusual starter cultures: three probiotic strains (Lactobacillus casei LOCK 0900, Lactobacillus casei LOCK 0908 and Lactobacillus paracasei LOCK 0919) and lactic acid bacteria from acid whey on model fermented sausage type products focusing on oxidative stability by measuring instrumental color (L*, a*, b* values), conjugated dienes (CD), TBARS immediately after 21 days of ripening (0) and after 90 and 180 days of refrigerated storage (4 oC). Determination of fatty acid composition, in meat product was performed after ripening and after 180 days of storage. At the end of the storage period, the salted sausages were characterized by the same content of polyunsaturated fatty acids (PUFA) compared to cured samples. The addition of acid whey and a mixture of probiotic strains to nitrite-free sausage formulation was barely able to protect lipids against oxidation in comparison to nitrite during vacuum storage. Surprisingly, the use of acid whey has an influence on the desired red-pinkish color of organic fermented sausage after ripening and after 180 days of storage period.
Manipulation of the endocytic pathway and phagocyte functions by Mycobacterium tuberculosis lipoarabinomannan

Lipoarabinomannan is a major immunomodulatory lipoglycan found in the cell envelope of Mycobacterium tuberculosis and related human pathogens. It reproduces several salient properties of M. tuberculosis in phagocytic cells, including inhibition of pro-inflammatory cytokine production, inhibition of phagolysosome biogenesis, and inhibition of apoptosis as well as autophagy. In this review, we present our current knowledge on lipoarabinomannan structure and ability to manipulate the endocytic pathway as well as phagocyte functions. A special focus is put on the molecular mechanisms employed and the signaling pathways hijacked. Available information is discussed in the context of M. tuberculosis pathogenesis.
Experimental Infection of Plants with an Herbivore-Associated Bacterial Endosymbiont Influences Herbivore Host Selection Behavior

Although bacterial endosymbioses are common among phloeophagous herbivores, little is known regarding the effects of symbionts on herbivore host selection and population dynamics. We tested the hypothesis that plant selection and reproductive performance by a phloem-feeding herbivore (potato psyllid, Bactericera cockerelli) is mediated by infection of plants with a bacterial endosymbiont. We controlled for the effects of herbivory and endosymbiont infection by exposing potato plants (Solanum tuberosum) to psyllids infected with “Candidatus Liberibacter solanacearum” or to uninfected psyllids. We used these treatments as a basis to experimentally test plant volatile emissions, herbivore settling and oviposition preferences, and herbivore population growth. Three important findings emerged: (1) plant volatile profiles differed with respect to both herbivory and herbivory plus endosymbiont infection when compared to undamaged control plants; (2) herbivores initially settled on plants exposed to endosymbiont-infected psyllids but later defected and oviposited primarily on plants exposed only to uninfected psyllids; and (3) plant infection status had little effect on herbivore reproduction, though plant flowering was associated with a 39% reduction in herbivore density on average. Our experiments support the hypothesis that plant infection with endosymbionts alters plant volatile profiles, and infected plants initially recruited herbivores but later repelled them. Also, our findings suggest that the endosymbiont may not place negative selection pressure on its host herbivore in this system, but plant flowering phenology appears correlated with psyllid population performance.
Efficient Algorithms for Scheduling Single and Multiple Channel Data Broadcast

With the increasing popularity of portable wireless computers, mechanisms to efficiently transmit information to such clients, are of significant interest. The environment under consideration is asymmetric, in that the information server has much more bandwidth available, as compared to the clients. It has been proposed that in such systems the server should broadcast the information periodically. A broadcast schedule, determines what is broadcast by the server and when. In this report, we present an algorithm for scheduling broadcast in such environments. This algorithm is based on a fair queueing, algorithm, and can be executed in O(log M) time, where M is the number of information items. The algorithm significantly improves the time-complexity over previously proposed broadcast scheduling algorithms. We evaluate performance of the algorithm and find it to be close to optimal. We also present an algorithm to coordinate broadcasts over multiple channels, and evaluate its performance for two channels.
Preparation of Size Controlled Nanometric Spheres of Colloidal Silica for Synthetic Opal Manufacture

In this work, we present a modification of the sol-gel based, Stöber, Fink and Bohn’s (SBF) procedure for the preparation of nanometric spheres of silica with a monomodal distribution of size and controlled diameter. In the SBF method, tetraethyl orthosilicate (TEOS) is used as a precursor molecule and hydrolysis and condensation reactions to form chains and branches of Si-O bonds are carried out. The novelty of this work consists in the use of an aqueous ammonium hydroxide solution as ammonia source. Graphics of particle size as a function of reagent contents are presented (reaction yield control) and differences to the results from the original SBF method are discussed. This procedure is the very first step for the development of a sol-gel synthetic opals preparation process. As a result, the best route to prepare monodisperse spheres in the whole range of 250 to 850 nm is that of keeping constant the TEOS and NH3 contents at 0.28:1M varying water contents in the range of 8 – 12.5 M.
Phosphorylation-dependent Activation of Peroxisome Proliferator Protein PEX11 Controls Peroxisome Abundance*

Peroxisomes are dynamic organelles that divide continuously in growing cell cultures and expand extensively in lipid-rich medium. Peroxisome population control is achieved in part by Pex11p-dependent regulation of peroxisome size and number. Although the production of Pex11p in yeast is tightly linked to peroxisome biogenesis by transcriptional regulation of the PEX11 gene, it remains unclear if and how Pex11p activity could be modulated by rapid signaling. We report the reversible phosphorylation of Saccharomyces cerevisiae Pex11p in response to nutritional cues and delineate a mechanism for phosphorylation-dependent activation of Pex11p through the analysis of phosphomimicking mutants. Peroxisomal phenotypes in the PEX11-A and PEX11-D strains expressing constitutively dephosphorylated and phosphorylated forms of Pex11p resemble those of PEX11 gene knock-out and overexpression mutants, although PEX11 transcript and Pex11 protein levels remain unchanged. We demonstrate functional inequality and differences in subcellular localization of the Pex11p forms. Pex11Dp promotes peroxisome fragmentation when reexpressed in cells containing induced peroxisomes. Pex11p translocates between endoplasmic reticulum and peroxisomes in a phosphorylation-dependent manner, whereas Pex11Ap and Pex11Dp are impaired in trafficking and constitutively associated with mature and proliferating peroxisomes, respectively. Overexpression of cyclin-dependent kinase Pho85p results in hyperphosphorylation of Pex11p and peroxisome proliferation. This study provides the first evidence for control of peroxisome dynamics by phosphorylation-dependent regulation of a peroxin.
Emerging therapies for herpes viral infections (types 1 – 8)

There are eight members of the herpesviridae family: herpes simplex virus-1 (HSV-1), HSV-2, varicella-zoster virus, Epstein–Barr virus, cytomegalovirus, human herpes virus-6, human herpes virus-7 and human herpes virus-8. The diseases caused by viruses of the herpesviridae family are treated with and managed by systemic and topical antiviral therapies and immunomodulating drugs. Because these viruses establish a latent state in hosts, antiherpetic agents, such as nucleoside analogues, only control symptoms of disease or prevent outbreaks, and cannot cure the infections. There is a need for treatments that require less frequent dosing, can be taken even when lesions are more advanced than the first signs or symptoms, and can treat resistant strains of the viruses without the toxicities of existing therapies. Immunomodulating agents, such as resiquimod, can act on the viruses indirectly by inducing host production of cytokines, and can thereby reduce recurrences of herpes. The new helicase primase inhibitors, which are the first non-nucleoside antiviral compounds, are being investigated for treatment of HSV disease, including infections resistant to existing therapy.