Miracle-dz/UniFAR-FTUs huggingface dataset:
The evolution of genomic islands by increased establishment probability of linked alleles

Genomic islands are clusters of loci with elevated divergence that are commonly found in population genomic studies of local adaptation and speciation. One explanation for their evolution is that linkage between selected alleles confers a benefit, which increases the establishment probability of new mutations that are linked to existing locally adapted polymorphisms. Previous theory suggested there is only limited potential for the evolution of islands via this mechanism, but involved some simplifying assumptions that may limit the accuracy of this inference. Here, we extend previous analytical approaches to study the effect of linkage on the establishment probability of new mutations and identify parameter regimes that are most likely to lead to evolution of islands via this mechanism. We show how the interplay between migration and selection affects the establishment probability of linked vs. unlinked alleles, the expected maximum size of genomic islands, and the expected time required for their evolution. Our results agree with previous studies, suggesting that this mechanism alone is unlikely to be a general explanation for the evolution of genomic islands. However, this mechanism could occur more readily if there were other pre‐adaptations to reduce local rates of recombination or increase the local density of mutational targets within the region of the island. We also show that island formation via erosion following secondary contact is much more rapid than island formation from de novo mutations, suggesting that this mechanism may be more likely.
Phase II Trial of XELOX as First-Line Treatment for Patients with Advanced Gastric Cancer

Background: The prognosis of patients with advanced gastric cancer (AGC) remains poor, and no single chemotherapy regimen is recognized as a global standard. A phase II trial was conducted to determine the efficacy and tolerability of capecitabine and oxaliplatin (XELOX) given every 3 weeks in combination in patients with AGC. Methods: Patients with previously untreated AGC received intravenous oxaliplatin 130 mg/m2 over 2 h on day 1 plus oral capecitabine 1,000 mg/m2 twice daily on days 1–14, every 3 weeks. Treatment was continued for 8 cycles or until disease progression or intolerable toxicity. Results: Fifty patients were enrolled. In total, 210 cycles of XELOX were delivered. The OVERALL response rate was 42% (95% CI 28.6–56.7), with 2 complete and 19 partial responses. At 15.2 months of median follow-up, median time to progression and overall survival were 5.8 (95% CI 3.4–8.2) and 11.1 (95% CI 5.6–16.5) months, respectively. The most common hematological adverse event was neutropenia (56% of patients); grade 3–4 neutropenia was observed in 6 patients, with neutropenic fever in only 2 patients. The most common non-hematological toxicities were vomiting (34%), hand-foot syndrome (26%), diarrhea (24%) and neurosensory toxicity (22%). There were no treatment-related deaths. Conclusions: XELOX is active for the first-line treatment of AGC with a manageable tolerability profile.
Searching the Integers

Consider an ordered universe U , and a set T ⊂ U with |T | = n. The goal is to preprocess T , such that the following query can be answered efficiently: given x ∈ U , report the predecessor of x, i.e. max{y ∈ T | y < x}. We can also consider the dynamic problem, where elements are inserted and deleted into T . Let tq be the query time, and tu the update time. This is a fundamental search problem, with an impressive number of applications. Later, we will discuss IP lookup (forwarding packets on the Internet), orthogonal range queries and persistent data structures as examples. The problem was considered in many computational models. In fact, most models below were initially defined to study the predecessor problem.
Programming the Brain and Behaviour by Early‐Life Stress: A Focus on Neuroactive Steroids

Animal studies have amply demonstrated that stress exposure during pregnancy or in early postnatal life can adversely influence brain development and have long‐term ‘programming’ effects on future brain function and behaviour. Furthermore, a growing body of evidence from human studies supports the hypothesis that some psychiatric disorders may have developmental origins. Here, the focus is on three adverse consequences of early‐life stress: dysregulation of the hypothalamic‐pituitary‐adrenal (HPA) axis, heightened anxiety behaviour and cognitive impairments, with review of what is known about the underlying central mechanisms. Neuroactive steroids modulate neuronal activity and play a key role in neurodevelopment. Moreover they can negatively modulate activity of the HPA axis, exert anxiolytic actions and influence cognitive performance. Thus, neuroactive steroids may provide a link between early‐life stress and the resultant adverse effects on the brain and behaviour. Here, a role for neuroactive steroids, in particular the 5α‐reduced/3α‐hydroxylated metabolites of progesterone, testosterone and deoxycorticosterone, is discussed in the context of early‐life stress. Furthermore, the impact of early‐life stress on the brain's capacity to generate neurosteroids is considered and the evidence for an ability of neuroactive steroids to over‐write the negative effects of early‐life stress on the brain and behaviour is examined. An enhanced understanding of the influence of early‐life stress on brain neurosteroid systems could aid the identification of new targets for developing treatments for stress‐related conditions in humans.
Preservation of hippocampal neuron numbers and hippocampal subfield volumes in behaviorally characterized aged tree shrews

Aging is associated with a decreased ability to store and retrieve information. The hippocampal formation plays a critical role in such memory processes, and its integrity is affected during normal aging. We used tree shrews (Tupaia belangeri) as an animal model of aging, because in many characteristics, tree shrews are closer to primates than they are to rodents. Young and aged male tree shrews performed a holeboard spatial memory task, which permits assessment of reference and working memory. Upon completion of the behavioral measurements, we carried out modified stereological analyses of neuronal numbers in various subdivisions of the hippocampus and used the Cavalieri method to calculate the volumes of these subfields. Results showed that the working memory of aged tree shrews was significantly impaired compared with that of young animals, whereas the hippocampus‐dependent reference memory remained unchanged by aging. Estimation of the number of neurons revealed preserved neuron numbers in the subiculum, in the subregions CA1, CA2, CA3, and in the hilus of the dentate gyrus. Volume measurements showed no aging‐related changes in the volume of any of these hippocampal subregions, or in the molecular and granule cell layers of the dentate gyrus of tree shrews. We conclude that the observed changes in memory performance in aging tree shrews are not accompanied by observable reductions of hippocampal neuron numbers or hippocampal volume, rather, the changes in memory performance are more likely the result of modified subcellular mechanisms that are affected by the aging process. J. Comp. Neurol. 468:509–517, 2004. © 2003 Wiley‐Liss, Inc.
Heuristic Transformation of Well-Constructed Conceptual Maps into OWL Preliminary Domain Ontologies

Ontologies are a form of knowledge representation that is meant for software systems, or agents, as well as for human users. Building an ontology consists of, in short, formally specifying concepts and their relations concerning a certain knowledge domain. Such specification should convey an interpretation of the domain as agreed by experts and requires specific ontology engineering skills. In relation to ontologies, conceptual maps are a more informal, simple and, thus, accessible form of knowledge representation. However, the freedom enjoyed in defining concepts and their links makes it difficult to directly draw formal representations from conceptual maps. This work presents heuristics that are able to transform conceptual maps into ontologies specified in OWL (Web Ontology Language). In this way, the ease of construction of conceptual maps can be taken advantage of to alleviate the knowledge acquisition bottleneck that is inherent in ontology engineering.
An epitope in hepatitis C virus core region recognized by cytotoxic T cells in mice and humans

Several cytotoxic T-lymphocyte (CTL) epitopes have been defined in hepatitis C virus (HCV) proteins. CTL may play an important role in the control of infection by HCV. Here, we identify a highly conserved antigenic site in the HCV core recognized by both murine and human CTL. Spleen cells from mice immunized with a recombinant vaccinia virus expressing the HCV core gene were restimulated in vitro with 11 peptides from the core protein. CTL from H-2d mice responded to a single 16-residue synthetic peptide (HCV 129-144). This conserved epitope was presented by a murine class I major histocompatibility molecule (H-2Dd) to conventional CD4- CD8+ CTL mapped by using transfectants expressing Dd, Ld, or Kd, but was not seen by CTL restricted by H-2b. The murine epitope was mapped to the decapeptide LMGYIPLVGA. The same 16-residue peptide was recognized by CTL from two HCV-seropositive patients but not by CTL from any seronegative donors. CTL from two HLA-A2-positive patients with acute and chronic hepatitides C recognized a 9-residue fragment (DLMGYIPLV) of the peptide presented by HLA-A2 and containing an HLA-A2-binding motif, extending only 1 residue beyond the murine epitope. Therefore, this conserved peptide, seen with murine CTL and human CTL with a very prevalent HLA class I molecule, may be a valuable component of an HCV vaccine against a broad range of HCV isolates. This study demonstrates that the screening for CTL epitopes in mice prior to human study may be useful.
ASSESMENT OF PALM KERNEL SHELL AS A COMPOSITE AGGREGATE IN CONCRETE

This manuscript presents a report on the physical properties of palm kernel shell used here as a coarse aggregate and their effect on the strength properties of palm kernel shell concrete. Laboratory research was carried out to observe the effects of replacing crushed granite with palm kernel shell on the compressive strength and density of palm kernel shell concrete. Mix design of 1:2:4 and a water-cement ratio of 0.6 were used to produce concrete specimen cubes of size 150mm 3 . A total of 60 cubes were made and wholly submerged in water to cure for 28days at intervals of 7days i.e. 7, 14, 21 and 28 days after which their densities and compressive strengths were determined. Granite was replaced with palm kernel shell in the mix at 25% interval resulting in three replicates of specimen cubes at each curing age. Compressive strength and density decreased continuously as palm kernel shell was added to the mix for all the Curing ages tested. The 28day compressive strength of the palm kernel shell concrete ranged from 12.71 to 16.63N/mm 2 , whereas the density ranged between 1562 to 2042 kg/m 3 . Physical properties tests conducted include sieve analysis, bulk density, moisture content and specific gravity to describe aggregates. The Specific gravities of Sharp Sand, Crushed Granite and Palm Kernel Shell were found to be 2.5, 2.76 and1.301 while their bulk densities are 1650, 1545, and 634 kg/m 3 respectively. Water absorption capability tests on crushed granite and palm kernel shell were observed to be 6% in both 1hr and 24hrs and 11% in 1hr and 21.5% in 24hrs respectively. All the aggregates utilized in this research work demonstrated their suitability in concrete production given the observations and physical properties result present.
Site-specific labeling of the ribosome for single-molecule spectroscopy

Single-molecule fluorescence spectroscopy can reveal mechanistic and kinetic details that may not be observed in static structural and bulk biochemical studies of protein synthesis. One approach requires site-specific and stable attachment of fluorophores to the components of translation machinery. Fluorescent tagging of the ribosome is a prerequisite for the observation of dynamic changes in ribosomal conformation during translation using fluorescence methods. Modifications of the ribosomal particle are difficult due to its complexity and high degree of sequence and structural conservation. We have developed a general method to label specifically the prokaryotic ribosome by hybridization of fluorescent oligonucleotides to mutated ribosomal RNA. Functional, modified ribosomes can be purified as a homogenous population, and fluorescence can be monitored from labeled ribosomal complexes immobilized on a derivatized quartz surface.
Developing a Preceptorship/Mentorship Model for Home Health Care Nurses

Preceptorship and mentorship programs are used in the health care sector to educate nurses, enhance their leadership skills, and improve their quality of work life. Recognizing the importance of these initiatives, Saint Elizabeth Health Care sought funding to create an innovative model of preceptorship/mentorship that meets the unique needs of home health care nurses. The methods utilized included focus groups, key informant interviews, and a workflow analysis. Factors that influence preceptorship such as nursing workload, preceptor training and remuneration were examined to develop a new model that offers career enhancement and leadership opportunities for preceptors and mentors, and promotes a welcoming environment for preceptees. Reward and recognition programs were created for preceptors to acknowledge their leadership contribution at the front line. This study demonstrates how evidence and innovation were used to create a preceptorship/mentorship model to develop community nursing leaders of the future.
Improving Computational Efficiency of Prediction in Model-based Prognostics Using the Unscented Transform

Model-based prognostics captures system knowledge in the form of physics-based models of components, and how they fail, in order to obtain accurate predictions of end of life (EOL). EOL is predicted based on the estimated current state distribution of a component and expected profiles of future usage. In general, this requires simulations of the component using the underlying models. In this paper, we develop a simulation-based prediction methodology that achieves computational efficiency by performing only the minimal number of simulations needed in order to accurately approximate the mean and variance of the complete EOL distribution. This is performed through the use of the unscented transform, which predicts the means and covariances of a distribution passed through a nonlinear transformation. In this case, the EOL simulation acts as that nonlinear transformation. In this paper, we review the unscented transform, and describe how this concept is applied to efficient EOL prediction. As a case study, we develop a physics-based model of a solenoid valve, and perform simulation experiments to demonstrate improved computational efficiency without sacrificing prediction accuracy
4 × 2 MIMO field test of advanced SFN using space-time coding for 8K transmission

Japan Broadcasting Corporation (NHK) is aiming to broadcast ultra high definition television (UHDTV), such as 8K, terrestrially. To evaluate a next-generation terrestrial network, two experimental stations composed of an advanced single frequency network (SFN) using space-time coding technology were set up in the Hitoyoshi area of Kumamoto, Japan. The transmission capacity of each experimental station is a maximum of 91.8 Mbps when using dual-polarized multi-input multi-output (MIMO) and 4096QAM modulation. To evaluate an advanced SFN with a 4 × 2 MIMO system, we conducted experiments in a field test in the Hitoyoshi area to compare three SFN schemes: conventional SFN without coding, space-time coding (STC), and space-frequency coding (SFC). The results of the field tests show that the required received power of the STC-SFN and SFC-SFN are lower than those of the conventional SFN, and the amount of improvement averaged 2 dB. In this paper, we report on this field test.
Treatment of insomnia in depressed insomniacs: effects on health-related quality of life, objective and self-reported sleep, and depression.

STUDY OBJECTIVES Insomnia is associated with poor health related quality of life (HRQOL) in depressed patients. Prior clinical trials of hypnotic treatment of insomnia in depressed patients have shown improvement in HRQOL, but in these studies HRQOL was relegated to a secondary outcome, and objective measures of sleep were not undertaken. DESIGN Double-blind, randomized, placebo-controlled clinical trial. SETTING Outpatient clinic and sleep laboratory. PATIENTS 60 depressed, insomniac outpatients. INTERVENTIONS One week of open-label fluoxetine (FLX), followed by 8 more weeks of FLX combined with either eszopiclone (ESZ) 3 mg or placebo at bedtime. MEASUREMENTS The primary HRQOL measure was the daily living and role functioning subscale (DLRF) of the Basis-32. Other measures included the Q-LES-Q, self-reported sleep, PSG, actigraphy, depression severity (HRSD). RESULTS At the end of randomized treatment, patients receiving ESZ had lower (better) DLRF scores (0.81 +/- 0.64) than those receiving placebo (1.2 +/- 0.72), p = 0.01. The effect size for DLRF was 0.62, indicating a moderate effect. An advantage for ESZ was also seen in other measures of HRQOL, and most assessments of antidepressant efficacy and sleep. Women reported better end of treatment HRQOL scores than men. CONCLUSIONS ESZ treatment of insomnia in depressed patients is associated with multiple favorable outcomes, including superior improvement in HRQOL, depression severity, and sleep.
Nonparametric predictive inference for voting systems

We present upper and lower probabilities for reliability of voting systems, also known as k-outof-m systems, which include seriesand parallel-systems. We restrict attention to systems with identical components. These interval probabilities are based on the nonparametric predictive inferential (NPI) approach for Bernoulli data presented by Coolen (1998). In this approach, it is assumed that test data are available on the components, and that the future components to be used in the system are exchangeable with these. This approach fits into the general framework of Imprecise Reliability, which has received increasing attention in recent years (Utkin and Coolen 2007). An early overview of NPI in Reliability was presented by Coolen, Coolen-Schrijner and Yan (2002), in recent years NPI has been further developed and presented as an attractive statistical theory for situations where one aims at inference for future observables on the basis of available data, adding only rather limited additional assumptions (Coolen 2006a). A particularly attractive feature of NPI in Reliability, with lower and upper probabilities, is that data containing zero failures can be dealt with in an attractive manner, which will also be illustrated in this paper for reliability of voting systems.
Why users (fail to) read computer usage policies

Purpose – This paper aims to improve understanding of individuals' awareness and perceptions of computer usage policies (CUPs) and why individuals elect not to read these policies.Design/methodology/approach – MBA students were asked to complete an online survey evaluating their behavioral intention to read CUPs, as well as their performance of this behavior. Factors contributing to the intention to read policies were also examined. The resulting data were analyzed with Smart PLS.Findings – Results suggest that three factors influence individual intention to read CUPs. These factors include attitude, apathy, and social trust. The model explained about 70 percent of individual intention to read CUPs and about 44 percent of the variability in actually reading these policies.Research limitations/implications – The sample is limited to MBA students from a single university.Practical implications – Although written policy statements are often considered the cornerstone of computer security, many individuals el.
The distributed interoperable object model and its application to large-scale interoperable database systems

A large-scale interoperable database system operating in a dynamic environment should provide uniform access user interface to its components, scalability to larger networks, evolution of database schema and applications, composability of client and server components, and preserve component autonomv. To address the research issues rxesented by such systems, we introduce the Distributed I;teroperable Object Model (DIOM). DIOM’S main features include the explicit representation of and access to semantics in data sources through the D1OM base interfaces, the use of interface abstraction mechanisms such as import, specialization, generalization, and aggregation.
Leishmania-Specific Surface Antigens Show Sub-Genus Sequence Variation and Immune Recognition

Background A family of hydrophilic acylated surface (HASP) proteins, containing extensive and variant amino acid repeats, is expressed at the plasma membrane in infective extracellular (metacyclic) and intracellular (amastigote) stages of Old World Leishmania species. While HASPs are antigenic in the host and can induce protective immune responses, the biological functions of these Leishmania-specific proteins remain unresolved. Previous genome analysis has suggested that parasites of the sub-genus Leishmania (Viannia) have lost HASP genes from their genomes. Methods/Principal Findings We have used molecular and cellular methods to analyse HASP expression in New World Leishmania mexicana complex species and show that, unlike in L. major, these proteins are expressed predominantly following differentiation into amastigotes within macrophages. Further genome analysis has revealed that the L. (Viannia) species, L. (V.) braziliensis, does express HASP-like proteins of low amino acid similarity but with similar biochemical characteristics, from genes present on a region of chromosome 23 that is syntenic with the HASP/SHERP locus in Old World Leishmania species and the L. (L.) mexicana complex. A related gene is also present in Leptomonas seymouri and this may represent the ancestral copy of these Leishmania-genus specific sequences. The L. braziliensis HASP-like proteins (named the orthologous (o) HASPs) are predominantly expressed on the plasma membrane in amastigotes and are recognised by immune sera taken from 4 out of 6 leishmaniasis patients tested in an endemic region of Brazil. Analysis of the repetitive domains of the oHASPs has shown considerable genetic variation in parasite isolates taken from the same patients, suggesting that antigenic change may play a role in immune recognition of this protein family. Conclusions/Significance These findings confirm that antigenic hydrophilic acylated proteins are expressed from genes in the same chromosomal region in species across the genus Leishmania. These proteins are surface-exposed on amastigotes (although L. (L.) major parasites also express HASPB on the metacyclic plasma membrane). The central repetitive domains of the HASPs are highly variant in their amino acid sequences, both within and between species, consistent with a role in immune recognition in the host.