Miracle-dz/UniFAR-FTUs huggingface dataset:
An Automatic Hybrid Segmentation Approach for Aligned Face Portrait Images

With the introduction of electronic personal documents (e.g. passports) in recent years the analysis of suitable photographs has become an important field of research. Such photographs for machine readable travel documents have to fulfill a set of minimal quality requirements defined by the International Civil Aviation Organization (ICAO). As some of the specified requirements are related to certain image regions only, these regions must be located in advance. In this work we present an automatic segmentation method for aligned color face images. The method is based on a convex variational energy formulation which is solved using weighted total variation. We apply constraints in the form of prior knowledge about the spatial configuration of typical passport photographs in order to solve for a global energy minimum. Several experiments on face images from two different datasets are presented to evaluate the performance of our algorithm. The obtained results demonstrate that our method is fairly robust and significantly outperforms other methods targeted at the same problem, in particular an expert system and an AdaBoost classifier.
A review of approaches to forestry research on structure, succession and biodiversity of undisturbed and semi-natural forests and woodlands in Europe

PREFACE Recently the interest in sustainable forest management in connection with biodiversity and nature conservation has increased rapidly. A large number of different organizations, science and research have emphasized the importance of the remaining untouched regions and ecosystems in different parts of the world. Especially virgin forests in various vegetation zones have received great attention. The high degree of biodiversity, the potential of genetic variability, the function as a control area for forest management and the naturalness and uniqueness of these areas have also made the political forum and the public aware of the present development. Many examples prove this fact, e.g. the clear cutting of virgin forests in Western Canada and the decline of tropical rain forests. A feasibility study implemented by Prof. Parviainen (Finnish Forest research Institute) was introduced and accepted as a project proposal by the European Forest Institute (EFI) in autumn 1993. The main goals of the study are to depict biodiversity indicators in undisturbed forests and implicate them to practical forest management. The proposed project was composed and submitted to AAIR-Programme in Brussels in January 1994. As the subject is of high interest for both research and nature conservation a large number of participants and collaborating institutions supported the proposal. Participants directly involved in the actions are The European Forest Institute in Joensuu and The Earlier in 1992 the IBN-DLO had accomplished a questionnaire on the forest reserves in Europe (Broekmeyer and Vos, 1993). As a result a Concerted Action proposal was submitted to the EU. The proposal, however, was not supported. The study by Broekmeyer and Vos (1993) has been of help to initiate the current project. This study can be regarded as a summary of background information on subjects concerning the history of forest reserves, research efforts and definitions of forest ecosystems and protected areas. The lack of time, however, did not allow to deal with all subjects and countries to a sufficient extent. The study has to be seen as background information on the ongoing project and on the creating of a network of forest reserves and conservation areas in Europe. It intends to give further suggestions for more detailed studies and literature reviews, which are of importance in this context. 4 In this context we would like to express our special thanks to Ms. Mirjam Broekmeyer for important information on forest reserves in Europe. We would also like to thank (WWF) …
The SWISS-MODEL Repository: new features and functionalities

The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. As of September 2005, the repository contained 675 000 models for 604 000 different protein sequences of the UniProt database. Regular updates ensure that the content of the repository reflects the current state of sequence and structure databases, integrating new or modified target sequences, and making use of new template structures. Each Repository entry consists of one or more 3D models accompanied by detailed information about the target protein and the model building process: functional annotation, a detailed template selection log, target-template alignment, summary of the model building and model quality assessment. The SWISS-MODEL Repository is freely accessible at .
New Environmental Line Feature-based Vision Navigation: Design and Analysis

Vision navigation using environmental features has been widely applied when satellite signals are not available. However, the matching performance of traditional environmental features such as keypoints degrades significantly in weakly textured areas, deteriorating navigation performance. Further, the user needs to evaluate and assure feature matching quality. In this paper, a new feature, named Line Segment Intersection Feature (LSIF), is proposed to solve the availability problem in weakly textured regions. Then a combined descriptor involving global structure and local gradient is designed for similarity comparison. To achieve reliable point-to-point matching, a coarse-to-fine matching algorithm is developed, which improves the performance of the point set matching algorithm. Finally, a framework of matching quality evaluation is proposed to assure matching performance. Through the comparison, it is demonstrated that the proposed new feature has superior overall performance especially on correctly matched numbers of keypoints and matching correctness. Also, using real image sets with weak texture, it is shown that the proposed LSIF can achieve improved navigation solutions with high continuity and accuracy.
Segmenting the Subthalamic Nucleus Using Narrow Band Limited Variational Level Set Method

We describe a novel variational level set based method for delineating the sub thalamic nucleus (STN) region of human brains from magnetic resonance (MR) images. Based on the understanding of specific imaging characteristic of STN, we apply a narrow band limitation in the region-based energy function for localizing the STN from initial contour information provided by doctors. The validity of the algorithm was tested on practical Parkinson's Patients' T1-weighted magnetic resonance images. Comparing to traditional edge-based and global region-based level set methods, our method achieves more reliable segmentation results. Also, our method is insensitive to the initial contour placement, making it applicable in practical surgical navigations.
An Improved Error Model for Noisy Channel Spelling Correction

The noisy channel model has been applied to a wide range of problems, including spelling correction. These models consist of two components: a source model and a channel model. Very little research has gone into improving the channel model for spelling correction. This paper describes a new channel model for spelling correction, based on generic string to string edits. Using this model gives significant performance improvements compared to previously proposed models.
Fast database restarts at facebook

Facebook engineers query multiple databases to monitor and analyze Facebook products and services. The fastest of these databases is Scuba, which achieves subsecond query response time by storing all of its data in memory across hundreds of servers. We are continually improving the code for Scuba and would like to push new software releases at least once a week. However, restarting a Scuba machine clears its memory. Recovering all of its data from disk --- about 120 GB per machine --- takes 2.5-3 hours to read and format the data per machine. Even 10 minutes is a long downtime for the critical applications that rely on Scuba, such as detecting user-facing errors. Restarting only 2% of the servers at a time mitigates the amount of unavailable data, but prolongs the restart duration to about 12 hours, during which users see only partial query results and one engineer needs to monitor the servers carefully. We need a faster, less engineer intensive, solution to enable frequent software upgrades. In this paper, we show that using shared memory provides a simple, effective, fast, solution to upgrading servers. Our key observation is that we can decouple the memory lifetime from the process lifetime. When we shutdown a server for a planned upgrade, we know that the memory state is valid (unlike when a server shuts down unexpectedly). We can therefore use shared memory to preserve memory state from the old server process to the new process. Our solution does not increase the server memory footprint and allows recovery at memory speeds, about 2-3 minutes per server. This solution maximizes uptime and availability, which has led to much faster and more frequent rollouts of new features and improvements. Furthermore, this technique can be applied to the in-memory state of any database, even if the memory contains a cache of a much larger disk-resident data set, as in most databases.
Diagnosis of Brain Abnormality Using both Structural and Functional MR Images

A number of neurological diseases are associated with structural and functional alterations in the brain. This paper presents a method of using both structural and functional MR images for brain disease diagnosis, by machine learning and high-dimensional template warping. First, a high-dimensional template warping technique is used to compute morphological and functional representations for each individual brain in a template space, within a mass preserving framework. Then, statistical regional features are extracted to reduce the dimensionality of morphological and functional representations, as well as to achieve the robustness to registration errors and inter-subject variations. Finally, the most discriminative regional features are selected by a hybrid feature selection method for brain classification, using a nonlinear support vector machine. The proposed method has been applied to classifying the brain images of prenatally cocaine-exposed young adults from those of socioeconomically matched controls, resulting in 91.8% correct classification rate using a leave-one-out cross-validation. Comparison results show the effectiveness of our method and also the importance of simultaneously using both structural and functional images for brain classification
Regulation of Yin Yang 1 by Tyrosine Phosphorylation*

Background: Yin Yang 1 is a transcription factor capable of activating or repressing its target genes, depending on context and cofactors. Results: YY1 is tyrosine-phosphorylated by Src family kinases, leading to down-regulation of its activity. Conclusion: Tyrosine phosphorylation of YY1 affects its ability to regulate gene expression. Significance: This is a novel post-translational modification of YY1 regulating its function. Yin Yang 1 (YY1) is a member of the GLI-Krüppel class of DNA and RNA binding transcription factors that can either activate or repress gene expression during cell growth, differentiation, and embryogenesis. Although much is known about YY1 interacting proteins and the target promoters regulated by YY1, much less is known about YY1 regulation through post-translational modifications. In this study we show that YY1 is tyrosine-phosphorylated in multiple cell types. Using a combination of pharmacological inhibition, kinase overexpression, and kinase knock-out studies, we demonstrate that YY1 is a target of multiple Src family kinases in vitro and in vivo. Moreover, we have identified multiple sites of YY1 phosphorylation and analyzed the effect of phosphorylation on the activity of YY1-responsive retroviral and cellular promoters. Phosphorylation of tyrosine 383 interferes with DNA and RNA binding, leading to the down-regulation of YY1 activity. Finally, we provide the first evidence that YY1 is a downstream target of epidermal growth factor receptor signaling in vivo. Taken together, the identification of YY1 as a target of Src family kinases provide key insights into the inhibitory role of tyrosine kinases in modulating YY1 activity.
Holocene floristic diversity and richness in northeast Norway revealed by sedimentary ancient DNA (sedaDNA) and pollen

We present a Holocene record of floristic diversity and environmental change for the central Varanger Peninsula, Finnmark, based on ancient DNA extracted from the sediments of a small lake (sedaDNA). The record covers the period c. 10 700 to 3300 cal. a BP and is complemented by pollen data. Measures of species richness, sample evenness and beta diversity were calculated based on sedaDNA sampling intervals and 1000‐year time windows. We identified 101 vascular plant and 17 bryophyte taxa, a high proportion (86%) of which are still growing within the region today. The high species richness (>60 taxa) observed in the Early Holocene, including representatives from all important plant functional groups, shows that modern shrub‐tundra communities, and much of their species complement, were in place as early as c. 10 700 cal. a BP. We infer that postglacial colonization of the area occurred prior to the full Holocene, during the Pleistocene‐Holocene transition, Younger Dryas stadial or earlier. Abundant DNA of the extra‐limital aquatic plant Callitriche hermaphroditica suggests it expanded its range northward between c. 10 200 and 9600 cal. a BP, when summers were warmer than present. High values of Pinus DNA occur throughout the record, but we cannot say with certainty if they represent prior local presence; however, pollen influx values >500 grains cm−2 a−1 between c. 8000 and 7300 cal. a BP strongly suggest the presence of pine woodland during this period. As the site lies beyond the modern tree limit of pine, it is likely that this expansion also reflects a response to warmer Early Holocene summers.
MemPype: a pipeline for the annotation of eukaryotic membrane proteins

MemPype is a Python-based pipeline including previously published methods for the prediction of signal peptides (SPEP), glycophosphatidylinositol (GPI) anchors (PredGPI), all-alpha membrane topology (ENSEMBLE), and a recent method (MemLoci) that specifically discriminates the localization of eukaryotic membrane proteins in: ‘cell membrane’, ‘internal membranes’, ‘organelle membranes’. MemLoci scores with accuracy of 70% and generalized correlation coefficient (GCC) of 0.50 on a rigorous homology-unbiased validation set and overpasses other predictors for subcellular localization. The annotation process is based both on inheritance through homology and computational methods. Each submitted protein first retrieves, when available, up to 25 similar proteins (with sequence identity ≥50% and alignment coverage ≥50% on both sequences). This helps the identification of membrane-associated proteins and detailed localization tags. Each protein is also filtered for the presence of a GPI anchor [0.8% false positive rate (FPR)]. A positive score of GPI anchor prediction labels the sequence as exposed to ‘Cell surface’. Concomitantly the sequence is analysed for the presence of a signal peptide and classified with MemLoci into one of three discriminated classes. Finally the sequence is filtered for predicting its putative all-alpha protein membrane topology (FPR <1%). The web server is available at: http://mu2py.biocomp. unibo.it/mempype.
Protein H encoded by plasmid CloDF13 is involved in excretion of cloacin DF13

Excretion of cloacin DF13 was studied in Escherichia coli cells harboring different CloDF13 insertion and deletion mutant plasmids. Insertions of a transposon at position 9.8 or 11.5% of the CloDF13 plasmid blocked the expression of gene H and strongly reduced the specific excretion of cloacin DF13 into the culture medium, but had no effect on the production of cloacin DF13. Insertions in or deletions of regions of the CloDF13 DNA upstream the cloacin operon did not affect the excretion or production of the bacteriocin. Introduction of a CloDF13 plasmid that encodes for the gene H product in cells harboring a CloDF13 plasmid with an insertion in gene H stimulated the excretion of cloacin DF13 significantly in mitomycin C-induced and in noninduced cultures. Cloacin DF13 in cloacinogenic cells that did not produce the gene H protein was found to be about 90% located in the cytoplasm. In cells that did produce the gene H product, about 30% of the cloacin DF13 molecules were found in the cytoplasm, about 18% were found in the periplasm, about 2% were in the membranes, and about 50% were located in the culture supernatant. Cyclic AMP stimulated the production but not the excretion of cloacin DF13 in cells cultivated in the presence of glucose.
Epigenetic Tailoring for the Production of Anti-Infective Cytosporones from the Marine Fungus Leucostoma persoonii

Recent genomic studies have demonstrated that fungi can possess gene clusters encoding for the production of previously unobserved secondary metabolites. Activation of these attenuated or silenced genes to obtain either improved titers of known compounds or new ones altogether has been a subject of considerable interest. In our efforts to discover new chemotypes that are effective against infectious diseases, including malaria and methicillin-resistant Staphylococcus aureus (MRSA), we have isolated a strain of marine fungus, Leucostoma persoonii, that produces bioactive cytosporones. Epigenetic modifiers employed to activate secondary metabolite genes resulted in enhanced production of known cytosporones B (1, 360%), C (2, 580%) and E (3, 890%), as well as the production of the previously undescribed cytosporone R (4). Cytosporone E was the most bioactive, displaying an IC90 of 13 µM toward Plasmodium falciparum, with A549 cytotoxicity IC90 of 437 µM, representing a 90% inhibition therapeutic index (TI90 = IC90 A459/IC90 P. falciparum) of 33. In addition, cytosporone E was active against MRSA with a minimal inhibitory concentration (MIC) of 72 µM and inhibition of MRSA biofilm at roughly half that value (minimum biofilm eradication counts, MBEC90, was found to be 39 µM).
Effort Estimation in Agile Software Development using Story Points

Agile software development has been gaining popularity and replacing the traditional methods of developing software. However, estimating the size and effort in Agile Software development still remains a challenge. This paper gives an overview of the different size estimation methods traditionally used and discusses in details the method based on Story Points, which is at present the most widely used estimation technique in Agile Software Development. The paper describes the steps followed in Story Point based method and highlights the area which needs to be looked into further.
Towards the design of fault-tolerant mixed-criticality systems on multicores

Mixed-criticality is a significant recent trend in the embedded system industry, where common computing platforms are utilized to host functionalities of varying criticality levels. To date, most scheduling techniques have focused on the timing aspect of this problem, while functional safety (i.e. fault-tolerance) is often neglected. This paper presents design methodologies to guarantee both safety and schedulability for real-time mixed-criticality systems on identical multicores. Assuming hardware/software transient errors, we model safety requirements on different criticality levels explicitly according to safety standards; based on this, we further propose fault-tolerant mixed-criticality scheduling techniques with task replication and re-execution to enhance system safety. To cope with runtime urgencies where critical tasks do not succeed after a certain number of trials, our techniques can perform system reconfigurations (task killing or service degradation) in those situations to reallocate system resources to the critical tasks. Due to explicit modeling of safety, we can quantify the impact of task killing and service degradation on system feasibility (safety and schedulability), enabling a rigorous design. To this end, we derive analysis techniques when reconfigurations are triggered either globally (synchronously) on all cores or locally (asynchronously) on each core. To our best knowledge, this is the first work on fault-tolerant mixed-criticality scheduling on multicores, matching theoretical insights with industrial safety standards. Our proposed techniques are validated with an industrial application and extensive simulations.
Morphologic and Morphometric Description of the Temporomandibular Joint in the Domestic Dog Using Computed Tomography

The temporomandibular joint (TMJ) in the domestic dog is a synovial joint with 2 articular surfaces, the mandibular fossa of the squamous portion of the temporal bone and the articular head of the condylar process of the mandible. Although different diagnostic imaging techniques have been used to study the TMJ in dogs, morphologic and morphometric studies based on computed tomography (CT) are scarce. The purpose of the present study was to describe the morphologic and morphometric features of the TMJ in domestic dogs using CT. Width and depth of the mandibular fossa and 2 different angles between the mandibular fossa and the condylar process were measured in 96 TMJs of 48 dogs of different breeds (Labrador retriever, German shepherd, cocker spaniel, boxer, English bulldog, pug, shih tzu, and Cavalier King Charles spaniel). Temporomandibular joint conformation differed between breeds. Mid- and small-sized dogs had mandibular fossae that were more shallow, less developed retroarticular processes, and irregularly shaped condylar processes. The TMJs were more congruent in large dogs, presenting with deeper mandibular fossae, prominent retroarticular processes, and more uniform condylar processes. The measurements proposed in this study demonstrated 3 different morphologic conformations for the TMJ in the dogs of this study.