Browsing by Subject "SIGNAL"

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  • Stotani, Silvia; Gatta, Viviana; Medda, Federico; Padmanaban, Mohan; Karawajzyk, Anna; Tammela, Päivi Sirpa Marjaana; Giordanetto, Fabrizio; Tzalis, Dimitrios; Collina, Simona (2018)
    Resistance to antibiotics is an increasingly serious threat to global public health and its management translates to significant health care costs. The validation of new Gram-negative antibacterial targets as sources for potential new antibiotics remains a challenge for all the scientists working in this field. The interference with bacterial Quorum Sensing (QS) mechanisms represents a potentially interesting approach to control bacterial growth and pursue the next generation of antimicrobials. In this context, our research is focused on the discovery of novel compounds structurally related to (S)-4,5-dihydroxy-2,3-pentanedione, commonly known as (S)-DPD, a small signaling molecule able to modulate bacterial QS in both Gram-negative and Gram-positive bacteria. In this study, a practical and versatile synthesis of racemic DPD is presented. Compared to previously reported syntheses, the proposed strategy is short and robust: it requires only one purification step and avoids the use of expensive or hazardous starting materials as well as the use of specific equipment. It is therefore well suited to the synthesis of derivatives for pharmaceutical research, as demonstrated by four series of novel DPD-related compounds described herein.
  • Laaksonen, Kristina; Helle, Liisa; Parkkonen, Lauri; Kirveskari, Erika; Mäkelä, Jyrki; Mustanoja, Satu; Tatlisumak, Turgut; Kaste, Markku; Forss, Nina (2013)
  • Rönkä, Katja; Valkonen, Janne K.; Nokelainen, Ossi; Rojas, Bibiana; Gordon, Swanne; Burdfield-Steel, Emily; Mappes, Johanna (2020)
    Warning signals are predicted to develop signal monomorphism via positive frequency-dependent selection (+FDS) albeit many aposematic systems exhibit signal polymorphism. To understand this mismatch, we conducted a large-scale predation experiment in four countries, among which the frequencies of hindwing warning coloration of the aposematic moth,Arctia plantaginis,differ. Here we show that selection by avian predators on warning colour is predicted by local morph frequency and predator community composition. We found +FDS to be the strongest in monomorphic Scotland and lowest in polymorphic Finland, where the attack risk of moth morphs depended on the local avian community. +FDS was also found where the predator community was the least diverse (Georgia), whereas in the most diverse avian community (Estonia), hardly any models were attacked. Our results support the idea that spatial variation in predator communities alters the strength or direction of selection on warning signals, thus facilitating a geographic mosaic of selection.
  • Sairanen, Viljami; Ocampo-Pineda, Mario; Granziera, Cristina; Schiavi, Simona; Daducci, Alessandro (2022)
    A B S T R A C T The white matter structures of the human brain can be represented using diffusion-weighted MRI tractography. Unfortunately, tractography is prone to find false-positive streamlines causing a severe decline in its specificity and limiting its feasibility in accurate structural brain connectivity analyses. Filtering algorithms have been pro-posed to reduce the number of invalid streamlines but the currently available filtering algorithms are not suitable to process data that contains motion artefacts which are typical in clinical research. We augmented the Con-vex Optimization Modelling for Microstructure Informed Tractography (COMMIT) algorithm to adjust for these signals drop-out motion artefacts. We demonstrate with comprehensive Monte-Carlo whole brain simulations and in vivo infant data that our robust algorithm is capable of properly filtering tractography reconstructions despite these artefacts. We evaluated the results using parametric and non-parametric statistics and our results demonstrate that if not accounted for, motion artefacts can have severe adverse effects in human brain structural connectivity analyses as well as in microstructural property mappings. In conclusion, the usage of robust filtering methods to mitigate motion related errors in tractogram filtering is highly beneficial, especially in clinical stud-ies with uncooperative patient groups such as infants. With our presented robust augmentation and open-source implementation, robust tractogram filtering is readily available.
  • Heikkilä, Jenni; Fagerlund, Petra; Tiippana, Kaisa (2018)
    In the course of normal aging, memory functions show signs of impairment. Studies of memory in the elderly have previously focused on a single sensory modality, although multisensory encoding has been shown to improve memory performance in children and young adults. In this study, we investigated how audiovisual encoding affects auditory recognition memory in older (mean age 71 years) and younger (mean age 23 years) adults. Participants memorized auditory stimuli (sounds, spoken words) presented either alone or with semantically congruent visual stimuli (pictures, text) during encoding. Subsequent recognition memory performance of auditory stimuli was better for stimuli initially presented together with visual stimuli than for auditory stimuli presented alone during encoding. This facilitation was observed both in older and younger participants, while the overall memory performance was poorer in older participants. However, the pattern of facilitation was influenced by age. When encoding spoken words, the gain was greater for older adults. When encoding sounds, the gain was greater for younger adults. These findings show that semantically congruent audiovisual encoding improves memory performance in late adulthood, particularly for auditory verbal material.
  • Peret, Benjamin; Middleton, Alistair M.; French, Andrew P.; Larrieu, Antoine; Bishopp, Anthony; Njo, Maria; Wells, Darren M.; Porco, Silvana; Mellor, Nathan; Band, Leah R.; Casimiro, Ilda; Kleine-Vehn, Juergen; Vanneste, Steffen; Sairanen, Ilkka; Mallet, Romain; Sandberg, Goran; Ljung, Karin; Beeckman, Tom; Benkova, Eva; Friml, Jiri; Kramer, Eric; King, John R.; De Smet, Ive; Pridmore, Tony; Owen, Markus; Bennett, Malcolm J. (2013)
  • Zhang, Linli; Huang, Gang; Liu, Anping; Fan, Ruili (2015)
    We introduce the fractional-order derivatives into an HIV infection model with nonlinear incidence and show that the established model in this paper possesses nonnegative solution, as desired in any population dynamics. We also deal with the stability of the infection-free equilibrium, the immune-absence equilibrium, and the immune-presence equilibrium. Numerical simulations are carried out to illustrate the results.
  • Aly, Ashraf A.; Hassan, Alaa A.; Mohamed, Nasr K.; Abd El-Haleem, Lamiaa E.; Bräse, Stefan; Polamo, Mika; Nieger, Martin; Brown, Alan B. (2019)
    Herein, we report the synthesis of 5,12-dihydropyrazino[2,3-c:5,6-c ' ]difuro[2,3-c:4,5-c ']-diquinoline-6,14(5H,12H)diones, 2-(4-hydroxy-2-oxo-1,2-dihydroquinolin-3-yl)-1,4-diphenyl- butane-1,4-diones and 4-(benzo-[d]oxazol-2-yl)-3-hydroxy-1H-[4,5]oxazolo[3,2-a]pyridine-1-one. The new candidates were synthesized and identified by different spectroscopic techniques, and X-ray crystallography.
  • Kurki, Ilmari; Hyvärinen, Aapo; Saarinen, Jussi (2016)
    We studied how learning changes the processing of a low-level Gabor stimulus, using a classification-image method (psychophysical reverse correlation) and a task where observers discriminated between slight differences in the phase (relative alignment) of a target Gabor in visual noise. The method estimates the internal "template" that describes how the visual system weights the input information for decisions. One popular idea has been that learning makes the template more like an ideal Bayesian weighting; however, the evidence has been indirect. We used a new regression technique to directly estimate the template weight change and to test whether the direction of reweighting is significantly different from an optimal learning strategy. The subjects trained the task for six daily sessions, and we tested the transfer of training to a target in an orthogonal orientation. Strong learning and partial transfer were observed. We tested whether task precision (difficulty) had an effect on template change and transfer: Observers trained in either a high-precision (small, 608 phase difference) or a low-precision task (1808). Task precision did not have an effect on the amount of template change or transfer, suggesting that task precision per se does not determine whether learning generalizes. Classification images show that trainingmade observers use more task-relevant features and unlearn some irrelevant features. The transfer templates resembled partially optimized versions of templates in training sessions. The template change direction resembles ideal learning significantly but not completely. The amount of template change was highly correlated with the amount of learning.
  • Kaltiainen, Hanna; Helle, Liisa; Liljeström, Mia; Renvall, Hanna; Forss, Nina (2018)
    Mild traumatic brain injury (mTBI) patients continue to pose a diagnostic challenge due to their diverse symptoms without trauma-specific changes in structural imaging. We addressed here the possible early changes in spontaneous oscillatory brain activity after mTBI, and their feasibility as an indicator of injury in clinical evaluation. We recorded resting-state magnetoencephalography (MEG) data in both eyes-open and eyes-closed conditions from 26 patients (11 females and 15 males, aged 20-59) with mTBI 6days-6months after the injury, and compared their spontaneous oscillatory activity to corresponding data from 139 healthy controls. Twelve of the patients underwent a follow-up measurement at 6months. Ten of all patients were without structural lesions in MRI. At single-subject level, aberrant 4-7Hz (theta) band activity exceeding the +2 SD limit of the healthy subjects was visible in 7 out of 26 patients; three out of the seven patients with abnormal theta activity were without any detectable lesions in MRI. Of the patients that participated in the follow-up measurements, five showed abnormal theta activity in the first recording, but only two in the second measurement. Our results suggest that aberrant theta-band oscillatory activity can provide an early objective sign of brain dysfunction after mTBI. In 3/7 patients, the slow-wave activity was transient and visible only in the first recording, urging prompt timing for the measurements in clinical settings.
  • Dunn, Cory D.; Paavilainen, Ville O. (2019)
    Many functions of eukaryotic cells are compartmentalized within membrane-bound organelles. One or more cis-encoded signals within a polypeptide sequence typically govern protein targeting to and within destination organelles. Perhaps unexpectedly, organelle targeting does not occur with high specificity, but instead is characterized by considerable degeneracy and inefficiency. Indeed, the same peptide signals can target proteins to more than one location, randomized sequences can easily direct proteins to organelles, and many enzymes appear to traverse different subcellular settings across eukaryotic phylogeny. We discuss the potential benefits provided by flexibility in organelle targeting, with a special emphasis on horizontally transferred and de novo proteins. Moreover, we consider how these new organelle residents can be protected and maintained before they contribute to the needs of the cell and promote fitness.