Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level

Background: With more and more genomes being sequenced, detecting synteny between genomes becomes more and more important. However, for microorganisms the genomic divergence quickly becomes large, resulting in different codon usage and shuffling of gene order and gene elements such as exons. Results: We present Proteny, a methodology to detect synteny between diverged genomes. It operates on the amino acid sequence level to be insensitive to codon usage adaptations and clusters groups of exons disregarding order to handle diversity in genomic ordering between genomes. Furthermore, Proteny assigns significance levels to the syntenic clusters such that they can be selected on statistical grounds. Finally, Proteny provides novel ways to visualize results at different scales, facilitating the exploration and interpretation of syntenic regions. We test the performance of Proteny on a standard ground truth dataset, and we illustrate the use of Proteny on two closely related genomes (two different strains of Aspergillus niger) and on two distant genomes (two species of Basidiomycota). In comparison to other tools, we find that Proteny finds clusters with more true homologies in fewer clusters that contain more genes, i.e. Proteny is able to identify a more consistent synteny. Further, we show how genome rearrangements, assembly errors, gene duplications and the conservation of specific genes can be easily studied with Proteny. Availability and implementation: Proteny is freely available at the Delft Bioinformatics Lab website http://bioinformatics.tudelft.nl/dbl/software. Contact: t.gehrmann@tudelft.nl Supplementary information: Supplementary data are available at Bioinformatics online.
Hex-utils: A Tool Set Supporting HexASCII Hexagonal rasters

The advantages of hexagonal meshes over squared grids in discretising spatial variables have been known for long. Notwithstanding, the raster data formats used in geo-spatial disciplines to this purpose are still today almost exclusively reliant on squared grids. The HexASCII file format is a core element in an attempt to introduce hexagonal rasters to mainstream GIS, defining a simple vehicle to store and share such data structures. This article describes the hex-utils tool-kit, an Application Programming Interface (API) and a set of command line tools enabling the use of HexASCII rasters. Basic operations are supported: creation of new hexagonal rasters from different inputs and transformation into file formats readable by desktop GIS programmes. The API sets a framework for the development of further functionality.
Task Partitioning in Swarm Robotics as a Multi-Armed Bandit Problem

The information provided is the sole responsibility of the authors and does not necessarily reflect the opinion of the members of IRIDIA. The authors take full responsibility for any copyright breaches that may result from publication of this paper in the IRIDIA – Technical Report Series. IRIDIA is not responsible for any use that might be made of data appearing in this publication.
Policy Is Personal: Sex, Gender, and Informal Care

The last ten years have seen an enormous upsurge in interest in policies for community care in all countries of the developed world. They all have ageing populations and most have governments committed to tight control of welfare expenditure. A major consequence has been the growing attention paid to the position of 'carers' - those who find themselves caring for their relatives in their own homes and for no pay. A considerable academic literature now exists documenting the problems of such carers, and pointing out that it is women who largely bear the burden of care. This book looks at the problem of care from a different angle and asks the question 'Why do people care? '. Using findings from her study of carers living in Canterbury, England, Clare Ungerson discusses the many different kinds of answer to that question. In particular she draws attention to how men and women carers explain their motivation differently, how women, especially, are 'negotiated' into caring by their relatives, and how men and women make sense of the caring they do using different kinds of language. The book develops our understanding of the complicated issues of familial love, duty, and kinship-based responsibility, and of masculine and feminine identity in the context of informal care. It will appeal to a wide audience, including students and teachers of social policy, sociology, women's studies, community care planners, social workers, and carers themselves.
Unlateral total deafness in children. Clinical problems with a special view to vestibular function.

Routine examination of about 183,000 school pupils through 10 years revealed total deafness in one ear with normal hearing in the other ear in 1 in 1000. From among these subjects, the author made a thorough study of 122 selected at random.The abnormality was found to be commoner in boys than in girls. It seldom involves an actual handicap, and frequently it is not recognized. The diagnosis of unilateral total deafness in this series as well as the shadow curve and bone conduction findings are discussed in some detail. X-rays revealed abnormal labyrinthine appearances in 18%, usually in the form of obliterated semicircular canals. In 2 cases the vestibule and the lateral semicircular canal made up one large cavity.Vestibular function was absent on the deaf side in 28% and preserved in 72%, including one case with impaired and all the others with normal function. Two patients presented so-called “pseudocaloric nystagmus”; in one of these cases the labyrinthine loss was acquired, while in the other one it w.
School-Based Mental Health Services: Funding Options and Issues

Approximately 18% to 22% of youngsters experience mental health problems and, of those, 5% to 8% have diagnosable mental disorders or serious emotional disturbance. Children in foster care experience even higher levels of mental health problems. Unfortunately, only 7% to 16% of those children actually receive mental health services—typically provided by schools. Consequently, school-based mental health services have moved in new directions in recent years, including increased training for teachers, infusion of more mental health practitioners, and renewed commitment to the wraparound approach. However, all of these require time and money. An often neglected area is the availability of federal funding intended to provide children and adolescents with access to mental health services in schools. The purpose of this article is to describe federal legislative mandates and initiatives that have funding mechanisms to provide mental health services to children in schools. The challenges schools face in implementing these services are also addressed.
Memory Performance Profiling via Sampled Performance Monitor Event Traces

Memory performance can be studied, process behavior can be characterized, and application performance can be improved through the use of sampled performance monitor event traces. As an example, this paper demonstrates how sampled traces of the TPC-C benchmark executed on eightand 32-processor configurations of the IBM eServer pSeries 690 (p690) are analyzed to identify the resolution sites of level-two (L2) cache data-load misses and study the heavily-hit resolution sites, i.e., level-three (L3) caches and main memory, with the goal of recognizing the heavily-hit regions of the application’s address space, segments, pages, cache blocks, routines, instructions, and data structures. Preliminary data analysis of the traces, using a powerful and flexible performance evaluation framework, indicates that data-load hits at heavily-hit resolution sites have high locality of reference within regions of the address space, segments, and pages. Specifically, the buffer pool and heap regions of the TPCC address space dominate as the effective address regions for data loads satisfied by local L3 caches and main memory. Furthermore, for the data loads satisfied by local L3 caches, the segments, pages, and cache blocks that comprise the buffer pool exhibit a dense distribution. Work continues to characterize related process behaviors as well as other workloads, and to define ways to remedy the performance degradation associated with L2-cache data-load misses serviced at high-penalty levels of the p690 memory hierarchy.
Relaxation kinetics of DNA–ligand binding including direct transfer

The relaxation kinetics of binding of ethidium to calf‐thymus DNA as studied previously by the temperature‐jump method with absorption detection [Bresloff, J. & Crothers, D. M. (1975) J. Mol. Biol. 95, 103] is reanalyzed in terms of a series of models for DNA‐ligand interactions that include cases with and without internal and bimolecular direct transfer of ligands between different binding modes or different binding sites. The experimental results are shown to be consistent with two alternative binding mechanisms. Both models include bimolecular “direct transfer” steps and a site size of two base pairs per site. In the first model, there exist two distinct modes of binding to the DNA double helix at each binding site. In the second model, sites containing at least one GC base pair constitute a different and stronger class of binding sites than those containing only AT base pairs. The existence of a direct transfer pathway between two classes of bound ligands is supported by the linear increase of reciprocal relaxation times far beyond the concentration regions, where off‐rates should have become rate limiting. The second model, incorporating the notion of base selectivity, is in quantitative agreement with published work on ethidium binding to DNAs of different base compositions and with nmr measurements of bound ligand lifetimes.
Mixing Methods: A Multistage Strategy for Studying Patriotism and Citizen Participation

We propose a methodological strategy that addresses some of the widespread criticisms of survey research. Traditional survey research has, to a great extent, neglected the role of contested concepts in politics and respondents' subjectivity. Our mix of methods—including conceptual analysis, Q-methodology, and survey research—enables us to measure people's subjective understandings of contested concepts while allowing us to reap the benefits of survey research. In two case studies, one on patriotism and the other on participatory citizenship, we demonstrate that the mixed method more accu rately measures respondents' subjectivity and leads to greater predictive abil ity through more accurate measures.
System simulation for availability of weapon systems under various missions

In this paper, estimates for availability of weapon systems (fighter aircraft and weapons) during battles are obtained by system simulation. The weapon system is viewed as a system with fighter aircraft that includes both fixed wing aircraft (called simply aircraft) and rotary wing aircraft (helicopter) and weapons as its entities. The functions of the system are basically the military missions. The system is modeled statistically with various probability distributions. The parameters of the probability distributions considered are the system characteristics, which are being inputted. The outputs are the number of fighter aircraft attrited, the number of serviceable fighter aircraft available, and the tons of weapons available for use at the end of each day. The availability of fighter aircraft is obtained as the ratio of the number of fighter aircraft available at the end of each day to the number considered on the first day of the battle. The factors that affect the availability are: the number of missions, the number of sorties in each mission, the tonnage of weapons used in each mission, the battle damage rate considered for each mission, the unreliability of each fighter aircraft, and the repair rate. Further, the admin and logistic delays may affect the repair process. The logistic delay includes delay in transportation due to variations in terrain and weapons replenishment. The availability of weapons is calculated as the ratio of the tonnage of weapons available for use at the end of each day to the tonnage available at the start of each battle day. The availability of weapon system is obtained as the product of the availability of fighter aircraft and the availability of weapons. The results are analyzed in terms of graphs of availability for battle days along with certain statistical measures. From the results of this simulation it is possible to plan combat missions based on criteria such as high priority targets to be attacked and effectiveness of missions for specific air-battle scenarios. Further, the simulation will help towards the design of an improved system which could focus on the factors affecting the availability as brought out in this simulation and their relative significance. © 2005 Wiley Periodicals, Inc. Syst Eng 8: 309–322, 2005
Scandinavian Journal of Information Systems a Conceptual Map of Software Process Improvement a Conceptual Map of Software Process Improvement Aaen Et Al.: a Conceptual Map of Software Process Improvement Special Issue Article -a Conceptual Map of Software Process Improvement

Software organisations have for many years struggled to mature engineering practices using a variety of approaches. Over the last decade a new approach, known as software process improvement (SPI), has emerged and become widely used in the software industry. In this paper we position SPI in the landscape of initiatives that can be used in software organisations to mature their operations. A map is offered describing the characteristic features of SPI initiatives, the benefits and risks related to such initiatives, and the relations to complementary approaches to professionalise the industry. The map highlights management, approach, and perspective as three main concerns of SPI and lists three key ideas for each of these concerns. The map is based on an extensive survey of the SPI literature combined with experiences from SPI practice. Practitioners can use the map strategically to make decisions on whether to initiate SPI initiatives, to integrate SPI efforts with other improvement initiatives, and, more generally, to create and manage improvement programs based on SPI ideas. Researchers can use the map to identify key questions and areas of knowledge that can fruitfully inform SPI theory and practice.
Becoming a wise old woman: resilience and wellness in later life

Abstract Older women often describe themselves as well in spite of being objectively in poor health. Such a view of self as resilient can sustain women through the process of becoming older. Drawing on recent research, I discuss how a sense of resilience in later life may be informed by memories of loss and coping in the past. Through selective memories, women informants constructed a story of coping, one that provided a buffer against the challenges of ageing, including deleterious changes in health status. The concept of ‘resilient ageing’ is contrasted with that of ‘successful ageing’, with the former providing a way of understanding how an older woman can come to view herself as well in spite of illness or disability. In contrast to the reductionism of the concept of successful ageing, resilient ageing enriches the understanding of the complexity of later life and the wisdom that can accompany that understanding.
Instigation to aggress and escalation of aggression examined from a personological perspective: The role of irritability and of emotional susceptibility

Two studies were conducted using Buss hostility machine paradigm to investigate the role of individual differences in irritability and emotional susceptibility on the instigation to aggress by a self-esteem lowering manipulation and on the hypothesized escalation of aggression over trials. The role of sex was also examined. In the first study, 60 highly irritable and 60 low irritable subjects were given the opportunity to deliver electric shocks to an experimental confederate, half after being provoked by a negative judgement on their performance in a learning task, half without such an experience. Each group of subjects was divided equally between males and females. It was found that highly irritable subjects, both males and females, delivered higher shocks after provocation than low irritable subjects under similar circumstances. An upward drift of shock level over trials was found only in provoked males and only in highly irritable females. In the second study, 60 highly emotionally susceptible and 60 low emotionally susceptible males and females were given the opportunity to deliver electric shocks to an experimental confederate, half after experiencing provocation, half without such an experience. It was found that provoked subjects delivered higher shocks than unprovoked subjects and that highly emotionally susceptible subjects delivered higher shocks than low emotionally susceptible subjects. Whereas an upward drift of shock levels over trials was found only in provoked males, the same effect was found in females, whether provoked or not. These findings are discussed in terms of the importance of stable personality characteristics that may mediate aggressive response.
An Efficient Anonymous Batch Authentication Scheme Based on HMAC for VANETs

In vehicular ad hoc networks (VANETs), when a vehicle receives a message, the certificate revocation list (CRL) checking process will operate before certificate and signature verification. However, large communication sources, storage space, and checking time are needed for CRLs that cause the privacy disclosure issue as well. To address these issues, in this paper, we propose an efficient anonymous batch authentication scheme (ABAH) to replace the CRL checking process by calculating the hash message authentication code (HMAC). In our scheme, we first divide the precinct into several domains, in which road-side units (RSUs) manage vehicles in a localized manner. Then, we adopt pseudonyms to achieve privacy-preserving and realize batch authentication by using an identity-based signature (IBS). Finally, we use HMAC to avoid the time-consuming CRL checking and to ensure the integrity of messages that may get loss in previous batch authentication. The security and performance analysis are carried out to demonstrate that ABAH is more efficient in terms of verification delay than the conventional authentication methods employing CRLs. Meanwhile, our solution can keep conditional privacy in VANETs.
Systemic to Pulmonary Collaterals in Very Low Birth Weight Infants: Color Doppler Detection of Systemic to Pulmonary Connections During Neonatal and Early Infancy Period

Objective. Angiographic visualization of systemic to pulmonary collaterals (SPC) has been documented in premature infants needing prolonged ventilatory support. Noninvasive identification of such communications in premature infants was reported recently. The purpose of this study was to describe: 1) incidence, 2) clinical findings and implications, and 3) short-term follow-up of SPC diagnosed by echocardiography in very low birth weight (VLBW) infants admitted to the neonatal intensive care unit. Methods. From December 1, 1994 to August 31, 1996, 196 infants with birth weight <1500 g were admitted to the neonatal intensive care unit; 133 of them received serial echocardiographic evaluations at 1 to 2 days, at 2 weeks, and at 1, 2, and 3 months of life. Follow-up echocardiograms were scheduled at 6 months and 1 year of age for patients with SPC persisting at 3 months of age. Results. SPC were demonstrated in 88 patients (66%) at 1 to 90 days of life (mean 28 days). In most cases, the SPC originated at the distal aortic arch or the proximal descending aorta. Ten patients (11%) were treated for congestive heart failure. The symptoms improved and anticongestive therapy was discontinued in 9. One patient with persistent congestive heart failure underwent therapeutic cardiac catheterization and 1 prominent SPC was embolized. Conclusions. The incidence of SPC in VLBW infants is much higher than previously reported. We postulate that SPC are bronchopulmonary communications that enlarge and/or proliferate in response to a given stimulus. These communications are associated with increased time on positive pressure ventilation and length of stay in the hospital. SPC may lead to pulmonary edema and should be searched for in VLBW infants with a more complicated course. Echocardiographic examination with color Doppler performed in premature infants to evaluate left to right shunts should include careful search for systemic to pulmonary collaterals. echocardiography, systemic to pulmonary collaterals, aortopulmonary collaterals, prematurity, pulmonary edema.
Detection of anti-type 3 muscarinic acetylcholine receptor autoantibodies in the sera of Sjögren's syndrome patients by use of a transfected cell line assay.

OBJECTIVE Sjögren's syndrome (SS) is an autoimmune disease affecting primarily the salivary and lacrimal glands, leading to dry mouth and dry eyes. Recent studies have suggested that autoantibodies reactive with the type 3 muscarinic acetylcholine receptors (M3Rs) expressed on salivary and lacrimal gland cells may be highly specific for SS. To test this hypothesis, we constructed a cell line expressing the human M3R gene in order to screen for anti-M3R autoantibodies in sera from SS patients. METHODS Complementary DNA encoding the open-reading frame (ORF) of the human M3R gene was amplified, ligated into the pcDNA5/FRT/V5-His-TOPO TA vector, and then used to transform Escherichia coli bacteria. Plasmid DNA containing the M3R ORF with the correct orientation was transfected into Flp-In Chinese hamster ovary (CHO) cells using Flp recombinase-mediated site-specific recombination. An M3R-transfected CHO cell line, selected and propagated in hygromycin, was used to detect anti-M3R autoantibodies in SS patient and healthy control sera by flow cytometry. RESULTS Testing of sera for the presence of anti-M3R autoantibodies bound to CHO-transfected cells revealed the presence of anti-M3R autoantibodies in SS patients (9 of 11) but not in healthy controls (0 of 11). Although the anti-M3R autoantibodies detected in patient sera were of multiple isotypes, the most consistently detected were IgG1, IgG3, and IgA. CONCLUSION Using a newly constructed cell line expressing human M3R, anti-M3R autoantibodies were easily detected in sera from SS patients. These autoantibodies were skewed toward the IgG1, IgG3, and IgA isotypes, probably recognizing a tertiary epitope created by extracellular domains of the receptor protein. Anti-M3R autoantibodies represent a highly promising clinical marker for the identification of SS.