Miracle-dz/UniFAR-FTUs huggingface dataset:
Animals between Nature and Culture: The Story of Archaeozoology

The paper aims to tell the story of archaeozoology and utilize it to point out changes in the perception of nature and culture, the perception of animals as organisms that belong entirely to the domain of nature (unlike people who ‘build’ culture onto their nature), as well as display how these perceptions shaped the discipline of archaeozoology and influenced its position within archaeology. Animal remains, almost as a rule, represent some of the most common findings at archaeological sites; however, the attention which has been given to them in archaeological analysis and interpretation was largely dependent on the dominant paradigms in science. With the appearance of the ‘new’ or processual paradigm in archaeology and the concurrent development of archaeozoology, findings like these became the object of study and an important ‘key’ for understanding questions of sustenance, economy and strategies of survival in the past. The strict divide between the natural sciences and humanities (which is a consequence of the wider modernist narrative about the dichotomy of nature and culture), meant that only specialized experts could study animal remains, and that animal remains should be viewed, studied and published on separately from studies on architecture, sculptures and figurines, tools and other artifacts. Thus, archaeozoological reports long represented merely a kind of ‘addition’ to archaeological publications and rarely figured significantly in interpretations. With the paradigm shift brought on by post-processual archaeology, the research focus shifted from economic and functionalist explanations of social phenomena to the study of the influence of culture on shaping human behavior and values. Social theories of cultural constructivism indicate that concepts of ‘humanity’ and ‘animality’ are culturally shaped and a product of discourse, but they often ignore osteological analyses of human and animal remains in the process. Even though at first glance it may seem that constructivist studies and the positivist scientific method on which osteology is based are mutually exclusive in contemporary archaeology, their integration can provide a more detailed picture of how animals shape the way in which humans experience the world, of meanings ascribed to animals, as well as of the very nature of boundaries between people and animals in different cultural contexts.
Brain-implantable biomimetic electronics as the next era in neural prosthetics

An interdisciplinary multilaboratory effort to develop an implantable neural prosthetic that can coexist and bidirectionally communicate with living brain tissue is described. Although the final achievement of such such a goal is many years in the future, it is proposed that the path to an implantable prosthetic is now definable, allowing the problem to be solved in a rational, incremental manner. Outlined in this report is our collective progress in developing the underlying science and technology that will enable the functions of specific brain damaged regions to be replaced by multichip modules consisting of novel hybrid analog/digital microchips. The component microchips are "neurocomputational" incorporating experimentally based mathematical models of the nonlinear dynamic and adaptive properties of biological neurons and neural networks. The hardware developed to date, although limited in capacity, can perform computations supporting cognitive functions such as pattern recognition, but more generally will support any brain function for which there is sufficient experimental information. To allow the "neurocomputational" multichip module to communicate with existing brain tissue, another novel microcircuitry element has been developed-silicon-based multielectrode arrays that are "neuromorphic," i.e., designed to conform to the region-specific cytoarchitecture of the brain, When the "neurocomputational" and "neuromorphic" components are fully integrated, our vision is that the resulting prosthetic, after intracranial implantation, will receive electrical impulses from targeted subregions of the the brain, process the information using the hardware model of that brain region, and communicate back to the functioning brain. The proposed prosthetic microchips also have been designed with parameters that can be optimized after implantation, allowing each prosthetic to adapt to a particular user/patient.
A Q Methodological Investigation of the Kurdish Conflict Frames among Parliamentarians, Experts and Lay People in Turkey

Many societies in different parts of the world have witnessed intractable conflicts. People living in these societies construct conflict frames to understand the ongoing conflicts. Based on Lederach’s (1999) pyramid approach to peace building, the current study investigates how people understand the Kurdish conflict in Turkey in three segments of society: a) politicians, b) scholars and journalists and c) lay people. The Kurdish conflict was approached based on the frame analysis of Entman (1993), which includes four domains: a) problem definition, b) causal interpretation, c) moral evaluation, and d) treatment recommendation. In a first phase, focus group discussions and open-ended questionnaires were used to explore alternative conflict understandings among lay people. In a second phase, Q methodology, a method suitable to uncover socially shared viewpoints, was used to understand the conflict frames of parliamentarians, experts and lay people. In a third phase, after analyzing each participant group’s frames separately, a second-order analysis was performed to see the similarities and differences between the different segments. Five different frames of the Kurdish conflict could be distinguished. In general, the meaning of the different frames, differences and commonalities within and between the segments, the usefulness of Q methodology to explore representations of conflict, and implications for conflict resolution will be discussed.
Acutely increasing δGABAA receptor activity impairs memory and inhibits synaptic plasticity in the hippocampus

Extrasynaptic γ-aminobutyric acid type A (GABAA) receptors that contain the δ subunit (δGABAA receptors) are expressed in several brain regions including the dentate gyrus (DG) and CA1 subfields of the hippocampus. Drugs that increase δGABAA receptor activity have been proposed as treatments for a variety of disorders including insomnia, epilepsy and chronic pain. Also, long-term pretreatment with the δGABAA receptor–preferring agonist 4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridin-3-ol (THIP) enhances discrimination memory and increases neurogenesis in the DG. Despite the potential therapeutic benefits of such treatments, the effects of acutely increasing δGABAA receptor activity on memory behaviors remain unknown. Here, we studied the effects of THIP (4 mg/kg, i.p.) on memory performance in wild-type (WT) and δGABAA receptor null mutant (Gabrd−/−) mice. Additionally, the effects of THIP on long-term potentiation (LTP), a molecular correlate of memory, were studied within the DG and CA1 subfields of the hippocampus using electrophysiological recordings of field potentials in hippocampal slices. The results showed that THIP impaired performance in the Morris water maze, contextual fear conditioning and object recognition tasks in WT mice but not Gabrd−/− mice. Furthermore, THIP inhibited LTP in hippocampal slices from WT but not Gabrd−/− mice, an effect that was blocked by GABAA receptor antagonist bicuculline. Thus, acutely increasing δGABAA receptor activity impairs memory behaviors and inhibits synaptic plasticity. These results have important implications for the development of therapies aimed at increasing δGABAA receptor activity.
Reliable and Enhanced Stiffness Perception in Soft-tissue Telemanipulation

Haptic feedback is one of the missing links in robotized minimally invasive telesurgery. The teleoperation controllers are optimized so as to offer the surgeon a reliable perception of the stiffness of soft tissue, rather than following the traditional approach where tracking and force reflection fidelity are considered. The experimental results show that optimization allows for better focus on the quality of the haptic information in the performance-stability trade-off. A force sensor to measure the interaction forces with the environment is found to be indispensable for high-quality touch feedback. Next to optimization for realistic feedback of the environment stiffness, in this paper we describe how to extend human perception beyond differential thresholds and thus enhance sensitivity. Experiments on a one-dimensional system demonstrate that the operator is able to discriminate tinier differences using a telemanipulation system with enhanced sensitivity than through direct manipulation.
A general framework for building noise-free homomorphic cryptosystems

We present a general framework for developing and analyzing homomorphic cryptosystems whose security relies on the difficulty of solving systems of nonlinear equations over Zn, n being an RSA modulus. In this framework, many homomorphic cryptosystems can be conceptualized. Based on symmetry considerations, we propose a general assumption that ensures the security of these schemes. To highlight this, we present an additive homomorphic private-key cryptosystem and we prove its security. Finally, we propose two motivating perspectives of this work. We first propose an FHE based on the previous scheme by defining a simple multiplicative operator. Secondly, we propose ways to remove the factoring assumption in order to get pure multivariate schemes.
ART AND TECHNOLOGY PERSPECTIVES ON BRAIN ATLASES

The research presented in this thesis explores an approach to neuroimaging which concerns the use of Brain Atlases and Neuronavigation techniques. The main focus has been to perform investigations regarding the methods, validity and scope of current visualisations of the brain. Although it is presented at the faculty of Information Technology, Mathematics and Electrical Engineering, this thesis does not focus on a technical research. The thesis does not aim at refining, advancing nor improving the state of the art of neuroimaging technologies but, instead, rethink the methods in order to find unexplored points of view which could ultimately impact and question current neuroimaging practices. Therefore, this thesis has both technical and reflective objectives, and it delivers its materials through practice based research. The hypothesis thesis is pursued with the following research questions: RQ1: Can an interactive installation provoke the reflection on the current scope of brain atlases and neuronavigation? RQ2: Can neurosciences benefit from an interactive installation provoking the reflection on the scope of brain atlases? Each of the research questions has been approached with a contribution (C1 and C2) which consequently produced a number of scientific publications, art exhibitions, with their correspondent art catalogues, documentation and press articles, and also software implementations which are open to the public domain. In our research we explore uses of vision technologies to mediate neuronavigation as well as series of prototypes conceiving tools to support neuroscience cooperation. Following are the descriptions of the mentioned contributions: C1: A-me The first contribution of the thesis focuses on how visualisation and navigation technologies used in the surgical environment can have diverging social, cultural, and ethical implications when used in the exhibition space. The aim of this study is to analyse the state
An XQuery-based trigger service to bring consistency management to data integration systems

Nowadays XML-based data integration systems are accepted as data service providers on the web. In order to make such a data integration system fully equipped with data manipulation capabilities, programming frameworks which support update at the integration level are being developed. When the user is permitted to submit updates, it is necessary to establish the best possible data consistency in the whole data integration system. To that extend, we present an approach based on an XQuery trigger service. We define an XQuery trigger model together with its semantics. We report on the integration of the XQuery trigger service into the overall architecture and discuss details of the execution model. Experiments show that data consistency is enforced easily, efficiently and conveniently at the global level.
Global proteomic profiling in multistep hepatocarcinogenesis and identification of PARP1 as a novel molecular marker in hepatocellular carcinoma

The more accurate biomarkers have long been desired for hepatocellular carcinoma (HCC). Here, we characterized global large-scale proteomics of multistep hepatocarcinogenesis in an attempt to identify novel biomarkers for HCC. Quantitative data of 37874 sequences and 3017 proteins during hepatocarcinogenesis were obtained in cohort 1 of 75 samples (5 pooled groups: normal livers, hepatitis livers, cirrhotic livers, peritumoral livers, and HCC tissues) by iTRAQ 2D LC-MS/MS. The diagnostic performance of the top six most upregulated proteins in HCC group and HSP70 as reference were subsequently validated in cohort 2 of 114 samples (hepatocarcinogenesis from normal livers to HCC) using immunohistochemistry. Of seven candidate protein markers, PARP1, GS and NDRG1 showed the optimal diagnostic performance for HCC. PARP1, as a novel marker, showed comparable diagnostic performance to that of classic markers GS and NDRG1 in HCC (AUCs = 0.872, 0.856 and 0.792, respectively). A significant higher AUC of 0.945 was achieved when three markers combined. For diagnosis of HCC, the sensitivity and specificity were 88.2% and 81.0% when at least two of the markers were positive. Similar diagnostic values of PARP1, GS and NDRG1 were confirmed by immunohistochemistry in cohort 3 of 180 HCC patients. Further analysis indicated that PARP1 and NDRG1 were associated with some clinicopathological features, and the independent prognostic factors for HCC patients. Overall, global large-scale proteomics on spectrum of multistep hepatocarcinogenesis are obtained. PARP1 is a novel promising diagnostic/prognostic marker for HCC, and the three-marker panel (PARP1, GS and NDRG1) with excellent diagnostic performance for HCC was established.
Analysis of Data Mining Based Software Defect Prediction Techniques

Software bug repository is the main resource for fault prone modules. Different data mining algorithms are used to extract fault prone modules from these repositories. Software development team tries to increase the software quality by decreasing the number of defects as much as possible. In this paper different data mining techniques are discussed for identifying fault prone modules as well as compare the data mining algorithms to find out the best algorithm for defect prediction.
SystemC Simulation of Continuous-Time Σ − ∆ Analog-Digital Converters in the Presence of Nonlinearities

This paper presents a method for SystemC simulation of analog systems with nonlinear parameters. Specifically, the paper focuses on Σ−∆ analog-to-digital converters (ADC). The method generates compiled-code simulators based on symbolic analysis. Code is optimized using loop invariant elimination, and constant folding. Circuits are described as structural macromodels. Non-linear parameters are expressed using piecewise linear (PWL) models.
Multimodal Visualization with Interactive Closeups

Closeups are used in illustrations to provide detailed views on regions of interest. They are integrated into the rendering of the whole structure in order to reveal their spatial context. In this paper we present the concept of interactive closeups for medical reporting. Each closeup is associated with a region of interest and may show a single modality or a desired combination of the available modalities using different visualization styles. Thus it becomes possible to visualize multiple modalities simultaneously and to support doctor-to-doctor communication on the basis of interactive multimodal closeup visualizations. We discuss how to compute a layout for 2D and 3D closeups, and how to edit a closeup configuration to prepare a presentation or a subsequent doctor-to-doctor communication. Furthermore, we introduce a GPU-based rendering algorithm, which allows to render multiple closeups at interactive frame rates. We demonstrate the application of the introduced concepts to multimodal PET/CT data sets additionally co-registered with MRI.
Would We Know It If We Saw It? Assessing Quality of Care in Group Homes for Youth

This article proposes and examines a parsimonious framework for assessing quality in therapeutic residential care. The synthesized conceptual framework includes four potentially critical domains of quality: setting, staffing, safety, and treatment. Data from a recently completed quasi-experimental study of group homes were used to examine prevalence of various key indicators within each of these domains and to explore relationships between these indicators and youth-level outcomes. Findings suggest that, among this sample of licensed homes in a southeastern state, licensure may be an initial indicator of baseline quality. Beyond this most basic level, utilization of an evidence-informed model (in this case, the teaching family model) was associated with better outcomes. Net of model, findings suggest that positively focused motivational systems, youth’s perceptions of staff’s fairness and helpfulness, provision of age/interest-appropriate toys/books/games, more preservice training, and prohibition of physical restraint were all associated with better outcomes for youth. Additional work is needed to assess the generalizability and utility of this framework for assessing quality in group homes.
The GOLPH3 pathway regulates Golgi shape and function and is activated by DNA damage

The Golgi protein GOLPH3 binds to PtdIns(4)P and MYO18A, linking the Golgi to the actin cytoskeleton. The GOLPH3 pathway is essential for vesicular trafficking from the Golgi to the plasma membrane. A side effect of GOLPH3-dependent trafficking is to generate the extended ribbon shape of the Golgi. Perturbation of the pathway results in changes to both Golgi morphology and secretion, with functional consequences for the cell. The cellular response to DNA damage provides an example of GOLPH3-mediated regulation of the Golgi. Upon DNA damage, DNA-PK phosphorylation of GOLPH3 increases binding to MYO18A, activating the GOLPH3 pathway, which consequently results in Golgi fragmentation, reduced trafficking, and enhanced cell survival. The PtdIns(4)P/GOLPH3/MYO18A/F-actin pathway provides new insight into the relationship between Golgi morphology and function, and their regulation.
Melatonin: therapeutic and clinical utilization

Melatonin, acting through melatonin receptors, is involved in numerous physiological processes including circadian entrainment, blood pressure regulation, oncogenesis, retinal physiology, seasonal reproduction, ovarian physiology, immune function and most recently in inducing osteoblast differentiation. Moreover, melatonin was proved to be a potent‐free radical scavenger and a broad‐spectrum antioxidant. More research is required into the effects of therapeutically modulating the melatoninergic system on circadian haemodynamics and rhythm under varying physiopathological conditions and the possible impact on morbidity and mortality in humans.
Chandra Observations and Optical Identification of Hard X-Ray Sources Discovered with ASCA

We present the first results of the Chandra and optical follow-up observations of hard X-ray sources detected in the ASCA Medium Sensitivity Survey (AMSS). Optical identifications are made for five objects. Three of them show either weak or absent optical narrow emission lines and are at low redshift ~0.06. One of them is a broad line object at z=0.910 and one is a z=0.460 object with only narrow lines. All the narrow line objects show strong evidence for absorption in their X-ray spectra. Their line ratios are consistent with a Seyfert II/LINER identification as are the line widths. The three low redshift objects have the colors of normal galaxies and apparently the light is dominated by stars. This could be due to the extinction of the underlying nuclear continuum by the same matter that absorbs X-rays and/or due to the dilution of the central source by starlight. These results suggest that X-ray sources that appear as ``normal'' galaxies in optical and near-IR bands significantly contribute to the hard X-ray background. This population of objects has a high space density and probably dominates the entire population of active galaxies.
Localization of RAP1 and topoisomerase II in nuclei and meiotic chromosomes of yeast

Topoisomerase II (topoII) and RAP1 (Repressor Activator Protein 1) are two abundant nuclear proteins with proposed structural roles in the higher-order organization of chromosomes. Both proteins co-fractionate as components of nuclear scaffolds from vegetatively growing yeast cells, and both proteins are present as components of pachytene chromosome, co-fractionating with an insoluble subfraction of meiotic nuclei. Immunolocalization using antibodies specific for topoII shows staining of an axial core of the yeast meiotic chromosome, extending the length of the synaptonemal complex. RAP1, on the other hand, is located at the ends of the paired bivalent chromosomes, consistent with its ability to bind telomeric sequences in vitro. In interphase nuclei, again in contrast to anti-topoII, anti-RAP1 gives a distinctly punctate staining that is located primarily at the nuclear periphery. Approximately 16 brightly staining foci can be identified in a diploid nucleus stained with anti-RAP1 antibodies, suggesting that telomeres are grouped together, perhaps through interaction with the nuclear envelope.
Genome scan meta-analysis of schizophrenia and bipolar disorder, part II: Schizophrenia.

Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to data from 20 schizophrenia genome scans. Each marker for each scan was assigned to 1 of 120 30-cM bins, with the bins ranked by linkage scores (1 = most significant) and the ranks averaged across studies (R(avg)) and then weighted for sample size (N(sqrt)[affected casess]). A permutation test was used to compute the probability of observing, by chance, each bin's average rank (P(AvgRnk)) or of observing it for a bin with the same place (first, second, etc.) in the order of average ranks in each permutation (P(ord)). The GSMA produced significant genomewide evidence for linkage on chromosome 2q (PAvgRnk<.000417). Two aggregate criteria for linkage were also met (clusters of nominally significant P values that did not occur in 1,000 replicates of the entire data set with no linkage present): 12 consecutive bins with both P(AvgRnk) and P(ord)<. 05, including regions of chromosomes 5q, 3p, 11q, 6p, 1q, 22q, 8p, 20q, and 14p, and 19 consecutive bins with P(ord)<. 05, additionally including regions of chromosomes 16q, 18q, 10p, 15q, 6q, and 17q. There is greater consistency of linkage results across studies than has been previously recognized. The results suggest that some or all of these regions contain loci that increase susceptibility to schizophrenia in diverse populations.