Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidation of the Small RNA Component of the Transcriptome

Small RNAs play important regulatory roles in most eukaryotes, but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new microRNAs (miRNAs) were among the most abundant of the nonredundant set of more than 75,000 sequences, whereas more than half represented lower abundance small interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs.
Retinoids regulate stem cell differentiation

Retinoids are ubiquitous signaling molecules that influence nearly every cell type, exert profound effects on development, and complement cancer chemotherapeutic regimens. All‐trans retinoic acid (RA) and other active retinoids are generated from vitamin A (retinol), but key aspects of the signaling pathways required to produce active retinoids remain unclear. Retinoids generated by one cell type can affect nearby cells, so retinoids also function in intercellular communication. RA induces differentiation primarily by binding to RARs, transcription factors that associate with RXRs and bind RAREs in the nucleus. Binding of RA: (1) initiates changes in interactions of RAR/RXRs with co‐repressor and co‐activator proteins, activating transcription of primary target genes; (2) alters interactions with proteins that induce epigenetic changes; (3) induces transcription of genes encoding transcription factors and signaling proteins that further modify gene expression (e.g., FOX03A, Hoxa1, Sox9, TRAIL, UBE2D3); and (4) results in alterations in estrogen receptor α signaling. Proteins that bind at or near RAREs include Sin3a, N‐CoR1, PRAME, Trim24, NRIP1, Ajuba, Zfp423, and MN1/TEL. Interactions among retinoids, RARs/RXRs, and these proteins explain in part the powerful effects of retinoids on stem cell differentiation. Studies of this retinol signaling cascade enhance our ability to understand and regulate stem cell differentiation for therapeutic and scientific purposes. In cancer chemotherapeutic regimens retinoids can promote tumor cell differentiation and/or induce proteins that sensitize tumors to drug combinations. Mechanistic studies of retinoid signaling continue to suggest novel drug targets and will improve therapeutic strategies for cancer and other diseases, such as immune‐mediated inflammatory diseases. J. Cell. Physiol. 226: 322–330, 2011. © 2010 Wiley‐Liss, Inc.
Block and Permeation of CaV 3 . 1 ( 1 G ) T-Type Calcium Channels : Candidate Mechanism for Non – Transferrin-Mediated Fe 2 Influx

Iron is a biologically essential metal, but excess iron can cause damage to the cardiovascular and nervous systems. We examined the effects of extracellular Fe on permeation and gating of CaV3.1 channels stably transfected in HEK293 cells, by using whole-cell recording. Precautions were taken to maintain iron in the Fe state (e.g., use of extracellular ascorbate). With the use of instantaneous I-V currents (measured after strong depolarization) to isolate the effects on permeation, extracellular Fe rapidly blocked currents with 2 mM extracellular Ca in a voltage-dependent manner, as described by a Woodhull model with KD 2.5 mM at 0 mV and apparent electrical distance 0.17. Extracellular Fe also shifted activation to more-depolarized voltages (by 10 mV with 1.8 mM extracellular Fe ) somewhat more strongly than did extracellular Ca or Mg , which is consistent with a Gouy-Chapman-Stern model with surface charge density 1 e /98 Å and KFe 4.5 M 1 for extracellular Fe . In the absence of extracellular Ca (and with extracellular Na replaced by TEA), Fe carried detectable, whole-cell, inward currents at millimolar concentrations (73 7 pA at 60 mV with 10 mM extracellular Fe ). With a two-site/three-barrier Eyring model for permeation of CaV3.1 channels, we estimated a transport rate for Fe of 20 ions/s for each open channel at 60 mV and pH 7.2, with 1 M extracellular Fe (with 2 mM extracellular Ca ). Because CaV3.1 channels exhibit a significant “window current” at that voltage (open probability, 1%), CaV3.1 channels represent a likely pathway for Fe entry into cells with clinically relevant concentrations of extracellular Fe .
Some comments on the swelling of polymeric networks in relation to their structure

Abstract We report measurements of the equilibrium concentration and of the elastic modulus for polystyrene networks containing controlled amounts of pendent chains that have been swollen in benzene and cyclohexane. The results are compared with the predictions of the classical theory of rubber elasticity and of a new approach based on an analogy with semidilute solutions.
Transient global amnesia: a study with Tc-99m ECD SPECT shortly after symptom onset and after recovery.

PURPOSE Transient global amnesia (TGA) is characterized by sudden loss of memory of recent events, transient inability to retain new information, and retrograde amnesia. We investigated the changes of regional cerebral blood flow in patients with TGA shortly after symptom onset and after recovery using Tc-99m-ethyl cysteinate dimer single-photon emission computed tomography (Tc-99m ECD SPECT) and statistical parametric mapping (SPM) analysis. METHODS Six right-handed patients with TGA were studied using Tc-99m ECD SPECT shortly after symptom onset and after recovery. As a control group, six healthy individuals were also studied. Images were analyzed using SPM8 using voxel-based analysis to estimate the differences between TGA patients and controls. RESULTS There was significant hypoperfusion in the left hippocampus, left thalamus, and bilateral cerebellum. In the follow-up SPECT scan, hypoperfusion in hippocampus and thalamus were restored, while hypoperfusion was noted in the temporoparietal region. CONCLUSION Our results suggest that the underlying mechanism of TGA may be temporary ischemia in the hippocampus and thalamus. There was significant restoration of perfusion in the hippocampus and thalamus after recovery from TGA.
Source-level execution time estimation of C programs

In this paper a comprehensive methodology for software execution time estimation is presented. The methodology is supported by rigorous mathematical models of C statements in terms of elementary operations. The deterministic contribution is combined with a statistical term accounting for all those aspects that cannot be quantified exactly. The methodology has been validated by realizing a complete prototype toolset, used to carry out the experiments.
Recurrent and founder mutations in the PMS2 gene

Germline mutations in PMS2 are associated with Lynch syndrome (LS), the most common known cause of hereditary colorectal cancer. Mutation detection in PMS2 has been difficult due to the presence of several pseudogenes, but a custom‐designed long‐range PCR strategy now allows adequate mutation detection. Many mutations are unique. However, some mutations are observed repeatedly across individuals not known to be related due to the mutation being either recurrent, arising multiple times de novo at hot spots for mutations, or of founder origin, having occurred once in an ancestor. Previously, we observed 36 distinct mutations in a sample of 61 independently ascertained Caucasian probands of mixed European background with PMS2 mutations. Eleven of these mutations were detected in more than one individual not known to be related and of these, six were detected more than twice. These six mutations accounted for 31 (51%) ostensibly unrelated probands. Here, we performed genotyping and haplotype analysis in four mutations observed in multiple probands and found two (c.137G>T and exon 10 deletion) to be founder mutations and one (c.903G>T) a probable founder. One (c.1A>G) could not be evaluated for founder mutation status. We discuss possible explanations for the frequent occurrence of founder mutations in PMS2.
Stories about life narrated by people with Alzheimer's disease.

AIM To explore how people with Alzheimer's disease present their life story. BACKGROUND Life story work is a key concept in a person-centred care. An important aspect in understanding the subjective experience and supporting the identity of people with dementia is to listen to their life stories. DESIGN A narrative design with interviews was used. METHOD Nine participants with Alzheimer's disease were encouraged to tell about their lives from childhood, adult life, to present life and about their thoughts on the future. The interviews were conducted between September 2010-March 2011 in the participants' homes, with their spouses present and were analysed with a method for analysis of narratives. FINDINGS Contentment, Connectedness, Self-reliance and Personal growth were identified as core dimensions in the participants' life stories and shown like threads throughout life, from childhood, adult life to present life. All participants expressed an overall contentment with life, and connectedness was related to their relation with significant persons and to be included in the local community. Self-reliance was expressed as a strong confidence in the own ability and an overall curiosity throughout life as a sustained quest for personal growth. CONCLUSIONS It is important for healthcare professionals, who work with people with dementia, to understand that people with Alzheimer's disease can maintain an overall trusting and hopeful approach to life. It is also important to use life story work to enhance feelings of being connected to the world and thereby support their identity and sense of self.
Prepositions in Context

Prepositions are highly polysemous, and their variegated senses encode significant semantic information. In this paper we match each preposition's complement and attachment and their interplay crucially to the geometry of the word vectors to the left and right of the preposition. Extracting such features from the vast number of instances of each preposition and clustering them makes for an efficient preposition sense disambigution (PSD) algorithm, which is comparable to and better than state-of-the-art on two benchmark datasets. Our reliance on no external linguistic resource allows us to scale the PSD algorithm to a large WikiCorpus and learn sense-specific preposition representations -- which we show to encode semantic relations and paraphrasing of verb particle compounds, via simple vector operations.
Interhemispheric balance of overt attention: a theta burst stimulation study

Interhemispheric imbalance is discussed as a pathophysiological mechanism in visuospatial neglect. It is suggested that after a lesion of the right hemisphere the mutual transcallosal inhibition is impaired, resulting in an increased activity of the left hemisphere. We investigated the interhemispheric balance of attention in healthy subjects by using a free visual exploration task and by interfering with the neural activity of the posterior parietal cortex (PPC) of either hemisphere using an inhibitory transcranial magnetic stimulation routine with theta burst stimulation (TBS). Subjects explored colour photographs of real‐life scenes presented on a computer screen under four conditions: (i) without TBS; (ii) after TBS over the right PPC; (iii) after TBS over the left PPC; and (iv) after TBS over the right PPC and, after the first half of the task, over the left PPC. Eye movements were measured, and distribution of mean cumulative fixation duration over screen halves was analyzed. TBS over the right PPC resulted in a significant rightward shift of mean cumulative fixation duration of ∼30 min. The shift could be reversed when a subsequent train of TBS was applied over the left PPC. However, left PPC stimulation alone had no significant effect on visual exploration behaviour. The present study shows that the effect of TBS on the PPC depends on which hemisphere is stimulated and on the state of the contralateral homologue area. These findings are in accordance with the predictions of the interhemispheric rivalry model in neglect.
3D facial expression recognition via multiple kernel learning of Multi-Scale Local Normal Patterns

In this paper, we propose a fully automatic approach for person-independent 3D facial expression recognition. In order to extract discriminative expression features, each aligned 3D facial surface is compactly represented as multiple global histograms of local normal patterns from multiple normal components and multiple binary encoding scales, namely Multi-Scale Local Normal Patterns (MS-LNPs). 3D facial expression recognition is finally carried out by modeling multiple kernel learning (MKL) to efficiently embed and combine these histogram based features. By using the SimpleMKL algorithm with the chi-square kernel, we achieved an average recognition rate of 80.14% based on a fair experimental setup. To the best of our knowledge, our method outperforms most of the state-of-the-art ones.
Fast vocabulary-independent audio search using path-based graph indexing

Classical audio retrieval techniques consist in transcribing audio documents using a large vocabulary speech recognition system and indexing the resulting transcripts. However, queries that are not part of the recognizer’s vocabulary or have a large probability of getting misrecognized can significantly impair the performance of the retrieval system. Instead, we propose a fast vocabulary independent audio search approach that operates on phonetic lattices and is suitable for any query. However, indexing phonetic lattices so that any arbitrary phone sequence query can be processed efficiently is a challenge, as the choice of the indexing unit is unclear. We propose an inverted index structure on lattices that uses paths as indexing features. The approach is inspired by a general graph indexing method that defines an automatic procedure to select a small number of paths as indexing features, keeping the index size small while allowing fast retrieval of the lattices matching a given query. The effectiveness of the proposed approach is illustrated on broadcast news and Switchboard databases.
AC-Framework for Privacy-Preserving Collaboration

The secure mlllti-party compnt.ation (ShIC) illode1 provitles ineails for l~alailciilg the use and confidentiality of distribut.ed data. Iilcreasiilg security coilcerils 11al.e led to a surge in work oil practical secure 1nult.i-party coinputatioil protocols. However. inost are only proveil secure under the semi-hoilest model, and security under this adversary illode1 is iils~~fici~iit for illost applications. I11 this paper: we propose a no\rel frame~vork: accoui~tal~le coinputi~ig (XC) framework. ~17llicll is sufficient or practical for man! applic.ations \vitlioiit the coinplesit,y and cost of a ShIC-protocol under the malicious model. F~lrtherinore. to s h o ~ tlie a~)plical~ilit~of t.1le AC-framework. we present an applicatioil under this framework regarding PI-i\-acy-preser\. iilg illillillg frequent it,emset,s.
Selective quality rendering by exploiting human inattentional blindness: looking but not seeing

There are two major influences on human visual attention: bottom-up and top-down processing. Bottom-up processing is the automatic direction of gaze to lively or colourful objects as determined by low-level vision. In contrast, top-down processing is consciously directed attention in the pursuit of predetermined goals or tasks. Previous work in perception-based rendering has exploited bottom-up visual attention to control detail (and therefore time) spent on rendering parts of a scene. In this paper, we demonstrate the principle of Inattentional Blindness, a major side effect of top-down processing, where portions of the scene unrelated to the specific task go unnoticed. In our experiment, we showed a pair of animations rendered at different quality levels to 160 subjects, and then asked if they noticed a change. We instructed half the subjects to simply watch our animation, while the other half performed a specific task during the animation.When parts of the scene, outside the focus of this task, were rendered at lower quality, almost none of the task-directed subjects noticed, whereas the difference was clearly visible to the control group. Our results clearly show that top-down visual processing can be exploited to reduce rendering times substantially without compromising perceived visual quality in interactive tasks.
Response of broiler chickens to different dietary crude protein and feeding regimens

Five isocaloric (3200kcal/kg) diets were used in an experiment designed to investigate the effects of dietary crude protein (CP) and feeding regimens on broiler performance. Day-old broilers were randomly distributed into four groups using a completely randomized design. Each group was replicated three times with ten broiler chicks per replicate. The experiment lasted for eight weeks. Broilers in group 1 received 23% CP from 0 to 3 weeks, 20% CP from 3 to 6 weeks and 18% CP from 6 to 8 weeks, while broilers in group 2 received 23% CP between 0 and 6 weeks and 18% CP between 6 and 8 weeks. Besides, broilers in group 3 were fed 23% CP from 0 to 4 weeks and 16% CP from 4 to 8 weeks, whereas group 4 was given 18% CP from 0 to weeks. Water was supplied ad libitum for broilers in the different dietary groups. A metabolic trial was carried out on the third week of the experiment using a total collection method. Proximate analyses of diets and faecal samples were performed according to the methods outlined by the Association Of the Official Analytical Chemists. Results at market age showed that broiler performance with respect to feed intake, weight gain, feed to gain ratio and water intake were not significantly influenced by CP regimens (p>0.05). Furthermore, CP regimens did not significantly influence broilers liveability (p>0.05). Protein retention, fat utilization and available fiber were not significantly influenced among treatments (p> 0.05). Economic data showed that cost to benefit ratio of producing broilers was comparable among broilers for all CP regimens used in this trial (p>0.05). It was concluded that a single diet of 18% CP and 3200kcal/kg metabolizable energy would be most suitable and convenient for farmers who are engaged in on-farm feed production for broilers as compared with the standard feeding regimens of broiler starter and broiler finisher diets.
Segmentation of retinal blood vessels using normalized Gabor filters and automatic thresholding

Although computerized retinal image blood vessel segmentation has been extensively researched, there is still room for improvement in the quality of the segmented images. Since retinal image analysis is still widely used in the diagnosis of diabetic retinopathy, efficient and accurate image characterization techniques are required. Previous work has mainly focused on improving segmentation accuracy rates with little regard to the false positives that are produced by illumination variation. This research work presents a hybrid approach towards the segmentation of retinal blood vessels. New approaches towards the reduction of background illumination variation are proposed using normalized Gabor filtering. These are the base-offset encoding and a modified version of an existing zero-integral kernel technique. The valley emphasis automatic thresholding scheme is used to segment the Gabor response images. Experiments are conducted on the DRIVE and STARE retinal image data sets. Accuracy rates of up to 94% are achieved through the zero-integral and base offset methods. This is comparable with results from literature, where the same data sets are segmented using other classification techniques. The median-offset method is found to most effectively reduce background illumination variation.
Strength Training Improves Upper-Limb Function in Individuals With Stroke: A Meta-Analysis

Background and Purpose— After stroke, maximal voluntary force is reduced in the arm and hand muscles, and upper-limb strength training is 1 intervention with the potential to improve function. Methods— We performed a meta-analysis of randomized controlled trials. Electronic databases were searched from 1950 through April 2009. Strength training articles were assessed according to outcomes: strength, upper-limb function, and activities of daily living. The standardized mean difference (SMD) was calculated to estimate the pooled effect size with random-effect models. Results— From the 650 trials identified, 13 were included in this review, totaling 517 individuals. A positive outcome for strength training was found for grip strength (SMD=0.95, P=0.04) and upper-limb function (SMD=0.21, P=0.03). No treatment effect was found for strength training on measures of activities of daily living. A significant effect for strength training on upper-limb function was found for studies including subjects with moderate (SMD=0.45, P=0.03) and mild (SMD=0.26, P=0.01) upper-limb motor impairment. No trials reported adverse effects. Conclusions— There is evidence that strength training can improve upper-limb strength and function without increasing tone or pain in individuals with stroke.
Touch-based user interface for elderly users

This paper reports the results of a field experiment where a Near Field Communication (NFC) enabled mobile phone was used as a user interface element so as to enable home-dwelling elderly people to choose their meals to be delivered by means of a home care service. The primary research focus was on examining the suitability of a touch-based user interface in the everyday life activities of elderly users. The eight-week experiment took place in the autumn of 2006. The results show that the touch-based user interface was easy to learn and adopt and the users were able to successfully use it regardless of their physical or cognitive weaknesses.
Hepatocyte senescence in vivo following preconditioning for liver repopulation

In the retrorsine (RS)‐based model of massive liver repopulation, preexposure to this naturally occurring alkaloid is sufficient to prime normal host parenchymal cells to be slowly replaced by transplanted normal hepatocytes. The basis for this striking effect is yet to be fully elucidated. In the present studies the possible involvement of cell senescence was investigated. Fischer 344 rats were treated according to the RS‐based protocol for hepatocyte transplantation, i.e., two doses of RS, 2 weeks apart, and were killed at 4 or 8 weeks after treatment. Control groups were given saline. Expression of senescence‐associated beta‐galactosidase was greatly induced in hepatocytes exposed to RS. In addition, several other changes that have been related to cell senescence were observed: these included markers of persistent activation of a DNA damage response, an increased expression of mammalian target of rapamycin, and positive regulators of the cell cycle, together with the induction of p21 and p27 cyclin‐dependent kinase inhibitors. Furthermore, RS treatment increased levels of interleukin‐6 in the liver, consistent with the activation of a senescence‐associated secretory phenotype. Conclusion: These findings indicate that RS induces hepatocyte senescence in vivo. We propose that cell senescence and the associated secretory phenotype can contribute to the selective growth of transplanted hepatocytes in this system. (HEPATOLOGY 2012)