Miracle-dz/UniFAR-FTUs huggingface dataset:
A Bone Sample Containing a Bone Graft Substitute Analyzed by Correlating Density Information Obtained by X-ray Micro Tomography with Compositional Information Obtained by Raman Microscopy

The ability of bone graft substitutes to promote new bone formation has been increasingly used in the medical field to repair skeletal defects or to replace missing bone in a broad range of applications in dentistry and orthopedics. A common way to assess such materials is via micro computed tomography (µ-CT), through the density information content provided by the absorption of X-rays. Information on the chemical composition of a material can be obtained via Raman spectroscopy. By investigating a bone sample from miniature pigs containing the bone graft substitute Bio Oss®, we pursued the target of assessing to what extent the density information gained by µ-CT imaging matches the chemical information content provided by Raman spectroscopic imaging. Raman images and Raman correlation maps of the investigated sample were used in order to generate a Raman based segmented image by means of an agglomerative, hierarchical cluster analysis. The resulting segments, showing chemically related areas, were subsequently compared with the µ-CT image by means of a one-way ANOVA. We found out that to a certain extent typical gray-level values (and the related histograms) in the µ-CT image can be reliably related to specific segments within the image resulting from the cluster analysis.
Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

A major problem in genome annotation is whether it is valid to transfer the function from a characterised protein to a homologue of unknown activity. Here, we show that one can employ a strategy that uses a structure-based prediction of protein functional sites to assess the reliability of functional inheritance. We have automated and benchmarked a method based on the evolutionary trace approach. Using a multiple sequence alignment, we identified invariant polar residues, which were then mapped onto the protein structure. Spatial clusters of these invariant residues formed the predicted functional site. For 68 of 86 proteins examined, the method yielded information about the observed functional site. This algorithm for functional site prediction was then used to assess the validity of transferring the function between homologues. This procedure was tested on 18 pairs of homologous proteins with unrelated function and 70 pairs of proteins with related function, and was shown to be 94 % accurate. This automated method could be linked to schemes for genome annotation. Finally, we examined the use of functional site prediction in protein-protein and protein-DNA docking. The use of predicted functional sites was shown to filter putative docked complexes with a discrimination similar to that obtained by manually including biological information about active sites or DNA-binding residues.
Role of goal-orientated attention and expectations in visual processing and perception

Visual processing is not fixed, but changes dynamically depending on the spatiotemporal context of the presented stimulus, and the behavioural task being performed. In this thesis, I describe theoretical and experimental work that was conducted to investigate how and why visual perception and neural responses are altered by the behavioural and statistical context of presented stimuli. The process by which stimulus expectations are acquired and then shape our sensory experiences is not well understood. To investigate this, I conducted a psychophysics experiment where participants were asked to estimate the direction of motion of presented stimuli, with some directions presented more frequently than others. I found that participants quickly developed expectations for the most frequently presented directions and that this altered their perception of new stimuli, inducing biases in the perceived motion direction as well as visual hallucinations in the absence of a stimulus. These biases were well explained by a model that accounted for their behaviour using a Bayesian strategy, combining a learned prior of the stimulus statistics with their sensory evidence using Bayes’ rule. Altering the behavioural context of presented stimuli results in diverse changes to visual neuron responses, including alterations in receptive field structure and firing rates. While these changes are often thought to reflect optimization towards the behavioural task, what exactly is being optimized and why different tasks produce such varying effects is unknown. To account for the effects of a behavioural task on visual neuron responses, I extend previous Bayesian models of visual processing, hypothesizing that the brain learns an internal model that predicts how both the sensory input and the reward received for performing different actions are determined by a common set of explanatory causes. Short-term changes in visual neural responses would thus reflect optimization of this internal model to deal with changes in the sensory environment (stimulus statistics) and behavioural demands (reward statistics), respectively. This framework is used to predict a range of experimentally observed effects of goal-orientated attention on visual neuron responses. Together, these studies provide new insight into how and why sensory processing adapts in response to changes in the environment. The experimental results support the idea of a very plastic visual system, in which prior knowledge is rapidly acquired and used to shape perception. The theoretical work extends previous Bayesian models of sensory processing, to understand how visual neural responses are altered by the behavioural context of presetned stimuli. Finally, these studies provide a unified description of ‘expectations’ and ‘goal-orientated attention’, as corresponding to continuous adaptation of an internal generative model of the world to account for newly received contextual information.
Gender and BAC: A Predictor of Risky Behavior Among College Students?

Risky behaviors related to alcohol consumption are a prevalent issue on college campuses, compelling universities across the nation to intervene. While excessive alcohol consumption has become common on campuses, it is associated with many negative consequences such as trouble with academics, relationships and the legal system (Park, 2004). College “binge drinking” has received significant attention; however, there has been less focus on the increasing levels of negative consequences resulting from alcohol consumption (Grant et al., 2005). Young adults who binge drink are more likely to partake in risk-taking, not because they desire to, but because they see no perceived risk at the time (Leigh, 1999). While there is a positive relationship between the number of risky behaviors and higher BAC (blood alcohol content), this correlation is reinforced when gender is accounted for. The purpose of the present study is to examine the consequences of alcohol consumption and if gender in conjunction with BAC accounts for the resulting number of risky behaviors. The sample consists of 200 undergraduate students at a midsized, Midwestern public university with an average age of 20.35 years. 54% of the participants were male and 46% female, the majority being white/Caucasian (92.5%). Many of the students came from middle to upper class backgrounds with 54.80% reporting an annual family income of $100,000 or greater. Data was collected through a survey, which requested information on the student’s drinking behavior that evening and contact information via each student’s email. After the initial survey the students were breathalyzed. Students then proceeded to a more extensive questionnaire, which assessed the effect of alcohol consumption on risky behavior. The study found that gender alone was not enough to predict the number risky behaviors occurring upon each session of alcohol consumption; however, gender in combination with BAL was effective in predicting number of risky behaviors.
The significance of cysteine synthesis for acclimation to high light conditions

Situations of excess light intensity are known to result in the emergence of reactive oxygen species that originate from the electron transport chain in chloroplasts. The redox state of glutathione and its biosynthesis contribute importantly to the plant's response to this stress. In this study we analyzed the significance of cysteine synthesis for long-term acclimation to high light conditions in Arabidopsis thaliana. Emphasis was put on the rate-limiting step of cysteine synthesis, the formation of the precursor O-acetylserine (OAS) that is catalyzed by serine acetyltransferase (SERAT). Wild type Arabidopsis plants responded to the high light condition (800 μmol m−2 s−1 for 10 days) with synthesis of photo-protective anthocyanins, induction of total SERAT activity and elevated glutathione levels when compared to the control condition (100 μmol m−2 s−1). The role of cysteine synthesis in chloroplasts was probed in mutant plants lacking the chloroplast isoform SERAT2;1 (serat2;1) and two knock-out alleles of CYP20-3, a positive interactor of SERAT in the chloroplast. Acclimation to high light resulted in a smaller growth enhancement than wild type in the serat2;1 and cyp20-3 mutants, less induction of total SERAT activity and OAS levels but similar cysteine and glutathione concentrations. Expression analysis revealed no increase in mRNA of the chloroplast SERAT2;1 encoding SERAT2;1 gene but up to 4.4-fold elevated SERAT2;2 mRNA levels for the mitochondrial SERAT isoform. Thus, lack of chloroplast SERAT2;1 activity or its activation by CYP20-3 prevents the full growth response to high light conditions, but the enhanced demand for glutathione is likely mediated by synthesis of OAS in the mitochondria. In conclusion, cysteine synthesis in the chloroplast is important for performance but is dispensable for survival under long-term exposure to high light and can be partially complemented by cysteine synthesis in mitochondria.
Introducing redundant computations in a behavior for reducing BIST resources

The degree of freedom that can be exploited during scheduling and assignment to minimize BIST resources is often limited by the data dependencies of a behavior. We propose transformation of a behavior by introducing redundant computations such that the resulting data path requires few BIST resources. The transformation makes use of spare capacity of modules to add redundancy that enables test paths to be shared among the modules. A technique is presented for introducing redundant computations that reduce the BIST resource requirements of a data path without compromising the latency and functional resource constraints.
Modelling Distributed Multiscale Simulation Performance: An Application to Nanocomposites

Clay polymer nanocomposites are a new range of particle filled composite material which interact over many different length scales, ranging from the quantum mechanical level to macroscopic. Multiscale simulation is therefore an important technique to understand and, ultimately, predict the properties of the composites from their individual components. We describe two multiscale simulation scenarios in which we couple simulations running on different levels of scale: in the loosely-coupled scheme we have a unidirectional coupling of one level to the next level, while in the tightly-coupled scheme we have simulations creating multiple inputs and parameters for simulations at different levels, running concurrently. We present a performance model that predicts the multiscale efficiency of our multiscale application. Here the multiscale efficiency constitutes the fraction of runtime spent on executing the simulation codes, and not on operations facilitating the coupling between the simulations. We find that the efficiency is high (greater than 90 %) until the number of sub-simulations exceeds a critical number (> 10 in our examples).
Bir Üniversite Hastanesinde Çalışan Hemşirelerin Tükenmişlik Düzeyleri ve Aile Desteğinin Etkisi

Amac: Bu calisma Samsun OMU Tip Fakultesi Hastanesinde calisan hemsirelerde tukenme ve aile destek duzeylerinin bazi demografik ozellikler ve mesleksel degiskenlerle iliskisini arastirmak amaciyla planlanmistir. Gerec ve Yontemler: Tanimlayici tipteki bu calismanin verileri 15 subat- 15 mart 2008 tarihleri arasinda toplanmistir. Veriler Ic Hastaliklari ve Cerrahi Servisi'nde calisan 191 hemsireden, Sosyo-demografik Veri Toplama Formu, Maslach Tukenmislik Olcegi ve Algilanan Aile Destek Olcegi uygulanarak toplanmistir. Arastirmadan elde edilen verilerin istatistiksel analizleri icin SPSS paket programinin 10.0 surumu kullanilmis, ANOVA ve t testinden yararlanilmistir. Bulgular: Calisma grubunun ADO puan ortalamasi 33.17±6.07, duygusal tukenmislik puan ortalamalari 28.18±10.96 duyarsizlasma alt olceginin puan ortalamalari 7.25±6.21 kisisel basarisizlik alt olceginin puan ortalamalari 36.32±7.55 olarak belirlenmistir. Yas degiskenine gore, hemsirelerin, kisisel basari puan ortalamalarinda anlamli duzeyde farklilasma gorulmustur. Mezun olunan okul, calisma suresi, ve medeni durum ile tukenmislik ve aile destek olcegi puanlari arasinda anlamli bir iliski olmadigi saptanmistir. Meslek secimi degiskenine gore, duyarsizlasma, kisisel basarisizlik ve aile destek puanlari anlamli duzeyde farklilasmamistir. Diger taraftan meslek secimi degiskenine gore duygusal tukenme duzeyleri arasinda anlamli duzeyde farklilasma gorulmustur. Sonuc: Hemsirelerin “duygusal tukenme” ile “duyarsizlasma” ve kisisel basari alt boyutlarinin ve Aile Destegi puan ortalamalarinda anlamli duzeyde farklilasma bulunmamistir. Hemsirelerde MTO alt olcek puan ortalamalarinin duygusal tukenme alaninda "ust" sinirda yer aldigi ayrica, duyarsizlasma ve bireysel basari alt olcek puanlarinin orta derecede oldugu saptanmistir.
Neuroimaging in Alzheimer's disease: current role in clinical practice and potential future applications

Alzheimer's disease is the most common cause of dementia and its prevalence is expected to increase in the coming years. Therefore, accurate diagnosis is crucial for patients, clinicians and researchers. Neuroimaging techniques have provided invaluable information about Alzheimer's disease and, owing to recent advances, these methods will have an increasingly important role in research and clinical practice. The purpose of this article is to review recent neuroimaging studies of Alzheimer's disease that provide relevant information to clinical practice, including a new modality: in vivo amyloid imaging. Magnetic resonance imaging, single photon emission computed tomography and 18F-fluorodeoxyglucose-positron emission tomography are currently available for clinical use. Patients with suspected Alzheimer's disease are commonly investigated with magnetic resonance imaging because it provides detailed images of brain structure and allows the identification of supportive features for the diagnosis. Neurofunctional techniques such as single photon emission computed tomography and 18F-fluorodeoxyglucose-positron emission tomography can also be used to complement the diagnostic investigation in cases of uncertainty. Amyloid imaging is a non-invasive technique that uses positron emission tomography technology to investigate the accumulation of the β-amyloid peptide in the brain, which is a hallmark of Alzheimer's disease. This is a promising test but currently its use is restricted to very few specialized research centers in the world. Technological innovations will probably increase its availability and reliability, which are the necessary steps to achieve robust clinical applicability. Thus, in the future it is likely that amyloid imaging techniques will be used in the clinical evaluation of patients with Alzheimer's disease.
Management of Antithrombotic Therapy in Atrial Fibrillation Patients Presenting with Acute Coronary Syndrome and/or Undergoing Percutaneous Coronary Intervention/ Stenting

Summary There remains uncertainty over optimal antithrombotic management strategy for patients with atrial fibrillation (AF) presenting with an acute coronary syndrome and/or undergoing percutaneous coronary intervention/stenting. Clinicians need to balance the risk of stroke and thromboembolism against the risk of recurrent cardiac ischaemia and/ or stent thrombosis, and the risk of bleeding. This consensus document comprehensively reviews the published evidence and presents a consensus statement on a ‘best practice’ antithrombotic therapy guideline for the management of antithrombotic therapy in such AF patients.
The Effectiveness of Systematic and Engaging Early Literacy (SEEL) Intervention on Word Reading in Kindergarten Students Receiving Tier 3 Services

The Effectiveness of Systematic and Engaging Early Literacy (SEEL) Intervention on Word Reading in Kindergarten Students Receiving Tier 3 Services C. Haley Cole Department of Communication Disorders Master of Science This study, a modification of Marshall (2011), evaluated the effectiveness of the Systematic and Engaging Early Literacy (SEEL) intervention method to improve consonantvowel-consonant (CVC) reading in four students receiving Tier 3 services. The SEEL intervention method was also combined with the use of digital books on an iPad to investigate the effects of using technology in reading intervention sessions. Previous research indicates effectiveness for the foundational principles of SEEL, which include instruction in engaging, meaningful contexts that provide frequent and intense opportunities to practice. This research involved 4 kindergarten students who qualified for Tier 3 services based on their performance on an index of difficulty in early literacy skills. The study contrasted trained with untrained literacy targets of comparable difficulty and was conducted as a single-subject multiple-baseline-acrossbehaviors design. Intervention was delivered three times a week for 15-20 minutes, depending on the engagement of the participants. An analysis of the results showed improvement in three out of four participants in their reading ability of the target CVC words. It gave mixed results as to the effects of using technology in combination with the reading intervention. The analysis also looked at student engagement during both the hands-on manipulation of the materials and the reading and writing tasks performed on the iPad. It found that the engagement between these two parts of each session was similar; if a student had poor engagement for the SEEL intervention, he or she also had poor engagement for the iPad portion, and vice versa. This study provides further insight into the efficacy of SEEL and the use of technology; it also provides suggestions for future research in the area of reading intervention.
Open Effects: Programmer-guided Effects for Open World Concurrent Programs

The open world assumption makes the design of a type-and-effect system challenging, especially in concurrent object-oriented languages. The main problem is in the computation of the effects of a dynamically dispatched method invocation, because all possible dynamic types of its receiver are not known statically. Previous work proposes effect annotations that provide a static upper bound on the effects of a dynamically dispatched method, conservative enough to cover the effects of all methods which could possibly be executed upon its invocation. For two dynamically dispatched methods, a typical type-and-effect system may disallow concurrent execution of their invocations because their conservatively specified static effects conflict. However, such a conflict may not actually happen at runtime, depending on the dynamic types of their receivers. This work proposes open effects, a sound trust-but-verify type-and-effect system, to better enable concurrent execution of dynamically dispatched method invocations. If a programmer annotates the receiver of a certain method invocation as open, then the type system trusts the programmer and assigns an open effect to the method. The open effect is supposed, optimistically, not to conflict with other effects. Such optimistic assumptions are verified statically, if possible, or at runtime otherwise. Open effects is complementary to previously proposed static and dynamic effect analyses and combines them such that the accuracy of static analysis could help decrease the overhead of the dynamic analysis. Performance evaluations of an implementation of open effects, on various benchmarks, show that: open effects incurs negligible annotation and runtime overheads such that code with open effects does almost as well as its manually tuned concurrent version.
Using Example-Based Machine Translation to translate DVD Subtitles

Audiovisual Translation (AVT), and in particular subtitling, has been recognised as an area that could potentially benefit from the introduction of machine translation (followed by post-editing) [1],[2],[10],[15],[27],[28]. In recent years the demands on subtitlers have increased, while the payment to subtitlers and time allotted to produce the subtitles have both decreased. Therefore this market is recognised as a potential real-world application of MT. Recent publications have introduced Corpus-Based MT approaches to translate subtitles [15],[27],[28]. An SMT system has been implemented in a Swedish subtitling company to translate between Swedish and Danish and Swedish and Norwegian subtitles, with the company already reporting a successful return on their investment [27]. The hybrid EBMT/SMT system used in the current research, on the other hand, remains within the confines of academic research, and the real potential of the system is not fully known. In this paper we report on the success to date of using this hybrid system to translate English-German DVD subtitles, based on a human evaluation of the system output using real end-users of the subtitles. The subtitles are evaluated in terms of intelligibility and acceptability. We then comment on the developments that are required to make the EBMT/SMT system more accessible for use within the AVT industry, and to put the system in a position where it could compete commercially with the SMT approach.