Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphorylation Site Mutations Affect Herpes Simplex Virus Type 1 ICP0 Function

ABSTRACT The herpes simplex virus type 1 (HSV-1) immediate-early (IE) regulatory protein infected-cell protein 0 (ICP0) is a strong and global transactivator of both viral and cellular genes. In a previous study, we reported that ICP0 is highly phosphorylated and contains at least seven distinct phosphorylation signals as determined by phosphotryptic peptide mapping (D. J. Davido et al., J. Virol. 76:1077-1088, 2002). Since phosphorylation affects the activities of many viral regulatory proteins, we sought to determine whether the phosphorylation of ICP0 affects its functions. To address this question, it was first necessary to identify the regions of ICP0 that are phosphorylated. For this purpose, ICP0 was partially purified, and phosphorylation sites were mapped by microcapillary high-pressure liquid chromatography tandem mass spectrometry. Three phosphorylated regions containing 11 putative phosphorylation sites, all within or adjacent to domains important for the transactivating activity of ICP0, were identified. The 11 sites were mutated to alanine as clusters in each of the three regions by site-directed mutagenesis, generating plasmids expressing mutant forms of ICP0: Phos 1 (four mutated sites), Phos 2 (three mutated sites), and Phos 3 (four mutated sites). One-dimensional phosphotryptic peptide analysis confirmed that the phosphorylation state of each Phos mutant form of ICP0 is altered relative to that of wild-type ICP0. In functional assays, the ICP0 phosphorylation site mutations affected the subcellular and subnuclear localization of ICP0, its ability to alter the staining pattern of the nuclear domain 10 (ND10)-associated protein PML, and/or its transactivating activity in Vero cells. Only mutations in Phos 1, however, impaired the ability of ICP0 to complement the replication of an ICP0 null mutant in Vero cells. This study thus suggests that phosphorylation is an important regulator of ICP0 function.
Development and Psychometric Evaluation of the Patient Safety Violation Scale in Medical Oncology Units in Iran.

BACKGROUND Patient safety is one of the key components of nursing care for cancer cases. Valid and reliable context-based instruments are necessary for accurate evaluation of patient safety in oncology units. The aim of the present study was to develop and evaluate the psychometric properties of the Patient Safety Violation Scale in medical oncology units in Iran. MATERIALS AND METHODS In this methodological study, a pool of 58 items was generated through reviewing the existing literature. The validity of the 58-item scale was assessed through calculating impact score, content validity ratio, and content validity index for its items as well as conducting exploratory factor analysis. The reliability of the scale was evaluated by assessing its internal consistency and test- retest stability. Study sample consisted of 300 oncology nurses who were recruited from thirteen teaching hospitals affiliated to Tehran University of Medical Sciences, Tehran, Iran. RESULTS Sixteen items were excluded from the scale due to having low impact scores, content validity ratios, or content validity indices. In exploratory factor analysis, the remaining 42 items were loaded on five factors including patient fall, verification of patientidentity, harm during care delivery, delay in care delivery, and medication errors. These five factors explained 62% of the total variance. The Cronbach's alpha of the scale and the test-retest interclass correlation coefficient were equal to 0.933 and 0.92, respectively. CONCLUSIONS The 42-item Patient Safety Violation Scale is a simple and short scale which has acceptable validity and reliability. Consequently, it can be used for assessing patient safety in clinical settings such as medical oncology units and for research projects.
Avalanche-size distribution at the depinning transition: A numerical test of the theory

We calculate numerically the sizes $S$ of jumps (avalanches) between successively pinned configurations of an elastic line $(d=1)$ or interface $(d=2)$, pulled by a spring of (small) strength ${m}^{2}$ in a random-field landscape. We obtain strong evidence that the size distribution, away from the small-scale cutoff, takes the form $P(S)=\frac{⟨S⟩}{{S}_{m}^{2}}p(S/{S}_{m})$ where ${S}_{m}\ensuremath{\mathrel{:=}}\frac{⟨{S}^{2}⟩}{2⟨S⟩}\ensuremath{\sim}{m}^{\ensuremath{-}d\ensuremath{-}\ensuremath{\zeta}}$ is the scale of avalanches, and $\ensuremath{\zeta}$ the roughness exponent at the depinning transition. Measurement of the scaling function $f(s)\ensuremath{\mathrel{:=}}{s}^{\ensuremath{\tau}}p(s)$ is compared with the predictions from a recent Functional RG (FRG) calculation, both at mean-field and one-loop level. The avalanche-size exponent $\ensuremath{\tau}$ is found in good agreement with the conjecture $\ensuremath{\tau}=2\ensuremath{-}2/(d+\ensuremath{\zeta})$, recently confirmed to one loop via the FRG. The function $f(s)$ exhibits a shoulder and a stretched exponential decay at large $s$, $\text{ln}\text{ }f(s)\ensuremath{\sim}\ensuremath{-}{s}^{\ensuremath{\delta}}$, with $\ensuremath{\delta}\ensuremath{\approx}7/6$ in $d=1$. The function $f(s)$, universal ratios of moments, and the generating function $⟨{e}^{\ensuremath{\lambda}s}⟩$ are found in excellent agreement with the one-loop FRG predictions. The distribution of local avalanche sizes ${S}_{\ensuremath{\phi}}$, i.e., of the jumps of a subspace of the manifold of dimension ${d}_{\ensuremath{\phi}}$, is also computed and compared to our FRG predictions, and to the conjecture ${\ensuremath{\tau}}_{\ensuremath{\phi}}=2\ensuremath{-}2/({d}_{\ensuremath{\phi}}+\ensuremath{\zeta})$.
Bleomycin induces caveolin-1 and -2 expression in epithelial lung cancer A549 cells.

BACKGROUND Bleomycin induces apoptosis in alveolar epithelial cells. The expression of caveolin-1 and -2 in lung epithelial-derived A549 cells was analysed in terms of apoptosis after exposure to bleomycin. MATERIALS AND METHODS Apoptosis was investigated using flow cytometry, ELISA, immunohistochemistry and Western blot analysis. Caveolin-1 and -2 were determined at the protein level (Western blot). Intracellular caveolin-1 distribution was studied with immunofluorescence, as well as sucrose density gradient centrifugation. RESULTS Caveolin-1 and -2 were up-regulated 1 h after exposure to bleomycin and preceding the occurrence of caspase-8, and of caspase-3 and caspase-9 cleavage products. Sucrose density gradient centrifugation revealed that bleomycin exposure led to a partial translocation of caveolin-1 from caveolin-rich membrane fractions to non-raft fractions. Successful inhibition of bleomycin-induced apoptosis by the broad-spectrum caspase inhibitor zVAD-fmk did not influence the amount of caveolin-1 and -2. CONCLUSION The early up-regulation of caveolin-1 and -2 following bleomycin exposure is a rather apoptosis-independent event related to other unknown mechanisms of bleomycin-mediated cell injury.
Exploring Spanish-morphology effects on Chinese – Spanish SMT

This paper presents some statistical machine translation results among English, Spanish and Chinese, and focuses on exploring Spanish-morphology effects on the Chinese to Spanish translation task. Although not strictly comparable, it is observed that by reducing Spanish morphology the accuracy achieved in the Chinese to Spanish translation task becomes comparable to the one achieved in the Chinese to English task. Further experimentation on approaching the problem of generating Spanish morphology as a translation task by itself is also performed, and results discussed. All experiments have been carried out by using a trilingual parallel corpus extracted from the Bible.
Interference aware multipath routing protocol for wireless sensor networks

Using multiple paths to transmit data simultaneously in wireless sensor networks is regarded to reduce end-to-end delay and achieve higher throughput. However, the interference between these multiple paths causes a significant reduction in the overall performance. Previous methods tried to solve this problem either with the aid of special hardware or under unrealistic assumption, such as the interference range is the same as the communication range. In this paper, we propose a novel interference aware multipath routing (IAMR) protocol for wireless sensor networks. Without any special hardware support, IAMR can establish interference minimized paths in a simple and efficient way and is also applied for the realistic situation that the interference range is twice as the communication range. We evaluate IAMR by comparing with AOMDV protocol and extensive simulations show that IAMR achieves good performance in terms of packet delivery ratio, end-to-end delay, throughput and energy usage balancing.
Integrating GermaNet into EuroWordNet, a multilingual lexical-semantic database

On peut trouver actuellement des lexiques de mots sur Internet structures a partir du systeme Princeton WordNet. Ces bases de donnees lexicologiques en version electronique ont pour but de relever les mots les plus communs d'une langue et d'indiquer les relations semantiques de base entre les lexemes (synonymie, hyponymie, antonymie et meronymie). Ces informations semantiques permettent une desambiguisation du sens des mots necessaire a certaines applications linguistiques : recouvrement de l'information, construction d'outils technologiques dans des langues diverses. Dans une perspective comparative, ces bases de donnees permettent une etude comparative translinguistique des modeles de lexicalisation. L'article decrit la base de donnee lexicale et semantique allemande 'GermaNet', son architecture et ses principales proprietes. Il presente le projet d'integration de 'GermaNet' au reseau semantique multilingue 'EuroWordNet' dont les principes seront egalement introduits. Enfin, l'article enumere quelques possibilites d'application et d'exploitation de la base de donnees dans le contexte de recherche en langues naturelles
Exploring prion protein biology in flies

The fruit fly Drosophila melanogaster has been a favored tool for genetic studies for over 100 years and has become an excellent model system to study development, signal transduction, cell biology, immunity, and behavior. The relevance of Drosophila to humans is perhaps best illustrated by the fact that more than 75% of the genes identified in human diseases have counterparts in Drosophila. During the last decade, many fly models of neurodegenerative disorders have contributed to the identification of novel pathways mediating pathogenesis. However, the development of prion disease models in flies has been remarkably challenging. We recently reported a Drosophila model of sporadic prion pathology that shares relevant features with the typical disease in mammals. This new model provides the basis to explore relevant aspects of the biology of the prion protein, such as uncovering the genetic mechanisms regulating prion protein misfolding and prion-induced neurodegeneration, in a dynamic, genetically tractable in vivo system.
Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli

We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.
Bacteriophage Therapy for Bacterial Infections: Rekindling a Memory from the Pre-Antibiotics Era

What was the attitude of man toward these new perils, the nature of which he barely grasped? Danger from the wild beasts was a physical reality which man could face and combat, but infectious diseases confronted him with the unknown. Man’s complete helplessness against sudden epidemics which killed wives, husbands, children and friends made these epidemics seem supernatural, as though sent by Providence. Disease was looked upon as the striking arm of Providence, the punishment of sin and immorality. Even when, with the progress of science, we acquired full knowledge of the disease-producing germs, the fatalistic attitude toward infectious disease still remained.Although modified in some degree this belief was still part of our consciousness until the time of the discovery of penicillin. (Sokoloff 1949, p. 253)
Librarians Flip for Students: Teaching Searching Skills to Medical Students Using a Flipped Classroom Approach

ABSTRACT This article describes the development of a flipped classroom instructional module designed by librarians to teach first- and second-year medical students how to search the literature and find evidence-based articles. The pre-class module consists of an online component that includes reading, videos, and exercises relating to a clinical case. The in-class sessions, designed to reinforce important concepts, include various interactive activities. The specifics of designing both components are included for other health sciences librarians interested in presenting similar instruction. Challenges encountered, particularly in the live sessions, are detailed, as are the results of evaluations submitted by the students, who largely enjoyed the online component. Future plans are contingent on solving technical problems encountered during the in-class sessions.
Why older people do not participate in leisure time physical activity: a survey of activity levels, beliefs and deterrents.

BACKGROUND Regular physical activity has been shown to have many health benefits. However, many older people are physically inactive. OBJECTIVE To investigate why older people are reluctant to participate in leisure time physical activity and to identify strategies to encourage increased activity. DESIGN Cross-sectional survey. SETTING 16 general practices in Dundee, Scotland. METHODS 409 randomly selected older people (65-84 years) who lived independently were interviewed at home. Forty-six percent of those invited to take part were recruited into the study. RESULTS Levels of knowledge about the specific health benefits of physical activity were high. Almost all participants (95%) believed that physical activity was beneficial and 79% believed that they did enough to keep healthy. However, 36% did no leisure time physical activity and a further 17% did less than 2 hours per week. Regression modelling identified 11 factors that exerted significant independent effects on levels of leisure time physical activity. The most powerful deterrent was lack of interest (OR = 7.8). Other factors included lack of daily access to a car, shortness of breath, joint pain, dislike of going out alone or in the evening, perceived lack of fitness, lack of energy, doubting that exercise can lengthen life, not belonging to a group and doubting that meeting new people is beneficial. CONCLUSIONS Increasing leisure time physical activities poses major challenges. Beliefs about desirable levels of activity in older people would need to be changed. Action would be needed to relieve physical symptoms and address fears about perceived ability to undertake physical activity. Finally, easily accessible facilities would be needed to encourage participation in physical activity.
Access Osteotomy in the Maxillofacial Skeleton

Surgical accesses for the facial skeleton are based on the concept of modular osteotomies. Various techniques and combination of osteotomies facilitate access to the most inaccessible tumors of craniomaxillofacial region. Most appropriate surgical access is determined by considering size, location, extension of the tumor, and experience of the surgical team. These are primarily used for tumors in the nasopharynx or the skull base. The aim of this paper is to review surgical accesses that aid in removal of inaccessible tumors of craniomaxillofacial region with series of cases operated in the Department of Oral and Maxillofacial Surgery, Armed Forces Medical College, Pune, India, between July 2008 and June 2010. The surgical approaches constituted of transfacial, transoral, lip-split mandibulotomy and modified osteotomy of the orbital rim in cases of juvenile nasoangiofibroma, squamous cell carcinoma of the base of the tongue, orbital floor tumour respectively. Only 3 cases (33.33%) reported with postoperative paresthesia of the infraorbital region and mandibular symphysis region which resolved in 6 months. None of the patients presented with occlusal discrepancy, neuromotor deficit or sign of recurrence in the follow up period of one year.
A Critical Review of Properties of Darunavir and Analytical Methods for Its Determination

Darunavir is a synthetic non-peptidic protease inhibitor that has been shown to be extremely potent against wild-type HIV, and it is an important component of highly active antiretroviral treatment (HAART), which is considered as one of the most significant advances in the field of HIV therapy. However, there are some concerns about darunavir quality control. Darunavir shows pseudo-polymorphism: in different ambient conditions one pseudo-polymorphic form can change to another. This behavior of darunavir is problematic because the dosage form is exposed to different ambient conditions around the world, since HIV/AIDS is prevalent globally. Issues around differences in the solubility and effects that different forms of darunavir can cause are of concern, and a more stable form is preferable. Important investigations of darunavir such as dissolution behavior, polymorphism, stability and degradation studies, and the impact of that on the quality of the product are being conducted by our working group. A cure for HIV/AIDS remains a long-term commitment, and there is much yet to achieve. This article discusses, by a critical review of the literature, the impact of the use of darunavir in the treatment of HIV-infected patients, its physical-chemical properties, the analytical methods to determine it, and challenges that remain in order to ensure the quality and stability of darunavir.
Temporal pattern analysis and its applicability in sport: an explanation and exemplar data

Quantitative analysis of sports performance has been shown to produce information that coaches can use within the coaching process to enhance performance. Traditional methods for quantifying sport performances are limited in their capacity to describe the complex interactions of events that occur within a performance over time. In this paper, we outline a new approach to the analysis of time-based event records and real-time behaviour records on sport performance known as T-pattern detection. The relevant elements of the T-pattern detection process are explained and exemplar data from the analysis of 13 soccer matches are presented to highlight the potential of this form of analysis. The results from soccer suggest that it is possible to identify new profiles for both individuals and teams based on the analysis of temporal behavioural patterns detected within the performances.
A study of the robustness against SEUs of digital circuits implemented with FPGA DSPs

In this paper we present an experimental validation of the reliability increase of digital circuits implemented in XilinxTMFPGAs when they are implemented using the DSPs (Digital Signal Processors) that are available in the reconfigurable device. For this purpose, we have used a fault-injection platform developed by our research group, NESSY [1]. The presented experiments demonstrate that the probability of occurrence of a SEU effect is similar both in the circuits implemented with and without using embedded DSPs. However, the former are more efficient in terms of area usage, which leads to a decrease in the probability of a SEU occurrence.
Monoclonal Antibodies against Beta-2-Glycoprotein I: Use as Reference Material for Lupus Anticoagulant Tests

Summary The laboratory diagnosis of lupus anticoagulants (LA) remains difficult despite internationally accepted guidelines for its detection. Several interlaboratory surveys have shown poor agreement between laboratories. Further standardization of LA testing will to a large extent depend on better insights on the mechanisms by which LA affect phospholipid-dependent coagulation assays as well as on the availability of well characterized and internationally accepted reference materials and control specimens. We recently raised a series of murine monoclonal antibodies against human β2GPI (anti-β2GPI moabs), a phospholipid-binding protein directly involved in the interaction between certain lupus anticoagulants and phospholipids. In this study we report on the use of LA positive anti-β2GPI moabs as easy to handle reference and control material. The relative LA responsiveness of various phospholipid-dependent clotting assays was determined on plasmas spiked with such moabs and compared well with that determined on LA positive plasma samples. Plasmas spiked with LA positive anti-β2GPI moabs were also used as control specimens to study the interlaboratory precision of LA testing. With these control specimens, low interassay coefficients of variation were obtained. Our results indicate that LA positive anti-β2GPI moabs have potential for the production of control specimens that could be made available to routine hemostasis laboratories to assess intra-laboratory precision of LA testing and to manufacturers to control batch-to-batch variability of their reagents.
R & D Accounting and the Tradeoff between Exclusivity and Uncertainty †

Research and development (R&D) expenditures are an important part of many firms’ investment portfolios, with R&D as a percent of assets exceeding capital expenditures on average across publicly traded firms in recent years. U.S. GAAP requires immediate expensing of these investments, which involves several conceptual and practical tradeoffs. We re-examine the continued applicability of this accounting treatment in light of changes in the properties of R&D expenditures and other reporting events in recent years. Using data since 2000, we find that there are benefits to R&D expenditures and these benefits are no more uncertain than those associated with capital expenditures. We find evidence, however, that peer firms’ R&D investments correlate with a firm’s own future benefits, providing evidence of non-exclusive benefits to R&D expenditures, which is distinct from capital expenditures. Thus, although firms benefit from their R&D investments, they may not hold exclusive rights to the R&D-related economic resources. Our results provide recent evidence to the FASB as they deliberate the treatment of intangible assets, including R&D.
Myelodysplastic features and cellular senescence in autoimmune disorders: a pilot study on patients with collagen tissue disorders and immune thrombocytopenic purpura.

Lale OLCAY*, Deniz BILLUR, Esra ERDEMLI, Sidika Esra BASKIN, Havva Fatma BALCI, Sevgi YETGIN Unit of Pediatric Hematology, Dr Abdurrahman Yurtaslan Ankara Oncology Research and Training Hospital, Ankara, Turkey Department of Histology and Embryology, Faculty of Medicine, Ankara University, Ankara, Turkey Unit of Pediatric Nephrology, Department of Pediatrics, Faculty of Medicine, Baskent University, Ankara, Turkey Unit of Pediatric Hematology, Ihsan Dogramaci Children’s Hospital, Faculty of Medicine, Hacettepe University Ankara, Turkey