Miracle-dz/UniFAR-FTUs huggingface dataset:
An integrated methodology for separating closure and residual stress effects from fatigue crack growth rate data

To properly interpret the results of standard fatigue crack growth tests it is often necessary to incorporate corrective techniques to the ΔK applied data. This is especially true in the near-threshold regime where long crack data need to be closure corrected to predict small crack behaviour. It is also an issue in the presence of residual stress. A methodology to separate the influence of sample size, geometry, crack length and residual stress from the standard crack growth test data to obtain a true material response is presented. Stress ratio and residual stress contributions from known combinations of assumed crack size, applied stress and residual stress are also addressed and incorporated in the fatigue crack growth behaviour.
Protein evolution with an expanded genetic code

We have devised a phage display system in which an expanded genetic code is available for directed evolution. This system allows selection to yield proteins containing unnatural amino acids should such sequences functionally outperform ones containing only the 20 canonical amino acids. We have optimized this system for use with several unnatural amino acids and provide a demonstration of its utility through the selection of anti-gp120 antibodies. One such phage-displayed antibody, selected from a naïve germline scFv antibody library in which six residues in VH CDR3 were randomized, contains sulfotyrosine and binds gp120 more effectively than a similarly displayed known sulfated antibody isolated from human serum. These experiments suggest that an expanded “synthetic” genetic code can confer a selective advantage in the directed evolution of proteins with specific properties.
Type inference with simple subtypes

Abstract Subtyping appears in a variety of programming languages, in the form of the ‘automatic coercion’ of integers to reals, Pascal subranges, and subtypes arising from class hierarchies in languages with inheritance. A general framework based on untyped lambda calculus provides a simple semantic model of subtyping and is used to demonstrate that an extension of Curry's type inference rules are semantically complete. An algorithm G for computing the most general typing associated with any given expression, and a restricted, optimized algorithm GA using only atomic subtyping hypotheses are developed. Both algorithms may be extended to insert type conversion functions at compile time or allow polymorphic function declarations as in ML.
Explorer Cellular and molecular investigations into the development of the pectoral girdle

Cellular and molecular investigations into the development of the pectoral girdle General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact openaccess@ed.ac. uk providing details, and we will remove access to the work immediately and investigate your claim. a b s t r a c t a r t i c l e i n f o The forelimbs of higher vertebrates are composed of two portions: the appendicular region (stylopod, zeugopod and autopod) and the less prominent proximal girdle elements (scapula and clavicle) that brace the limb to the main trunk axis. We show that the formation of the muscles of the proximal limb occurs through two distinct mechanisms. The more superficial girdle muscles (pectoral and latissimus dorsi) develop by the " In–Out " mechanism whereby migration of myogenic cells from the somites into the limb bud is followed by their extension from the proximal limb bud out onto the thorax. In contrast, the deeper girdle muscles (e.g. rhomboideus profundus and serratus anterior) are induced by the forelimb field which promotes myotomal extension directly from the somites. Tbx5 inactivation demonstrated its requirement for the development of all forelimb elements which include the skeletal elements, proximal and distal muscles as well as the sternum in mammals and the cleithrum of fish. Intriguingly, the formation of the diaphragm musculature is also dependent on the Tbx5 programme. These observations challenge our classical views of the boundary between limb and trunk tissues. We suggest that significant structures located in the body should be considered as components of the forelimb. Introduction The limbs of higher vertebrates need to fulfil two quite distinct roles in order to function as a single unit; the appendicular portion distal to the shoulder joint is required to generate skeletal muscle contraction needed to mediate propulsion whereas the proximal (girdle) region is required to brace the limb to the axial skeleton in order to transmit propulsion to the body. The proximal limb (girdle) of the vertebrates underwent considerable …
Does the Duration of Symptoms in Patients With Spinal Stenosis and Degenerative Spondylolisthesis Affect Outcomes?: Analysis of the Spine Outcomes Research Trial

Study Design. Retrospective subgroup analysis of prospectively collected data according to treatment received. Objective. The purpose of this study is to determine whether the duration of symptoms affects outcomes after the treatment of spinal stenosis (SS) or degenerative spondylolisthesis (DS). Summary of Background Data. The Spine Outcomes Research Trial (SPORT) study was designed to provide scientific evidence on the effectiveness of spinal surgery versus a variety of nonoperative treatments. Methods. An as-treated analysis was performed on the patients enrolled in SPORT for the treatment of SS or DS. A comparison was made between patients with SS with 12 or fewer months' (n = 405) and those with more than 12 months' (n = 227) duration of symptoms. A comparison was also made between patients with DS with 12 or fewer months' (n = 397) and those with more than 12 months' (n = 204) duration of symptoms. Baseline patient characteristics were documented. Primary and secondary outcomes were measured at baseline and at regular follow-up time intervals up to 4 years. The difference in improvement among patients whose surgical or nonsurgical treatment began less than or greater than 12 months after the onset of symptoms was measured. In addition, the difference in improvement with surgical versus nonsurgical treatment (treatment effect) was determined at each follow-up period for each group. Results. At final follow-up, there was significantly less improvement in primary outcome measures in SS patients with more than 12 months' symptom duration. Primary and secondary outcome measures within the DS group did not differ according to symptom duration. There were no statistically significant differences in the treatment effect of surgery in SS or DS patients. Conclusion. Patients with SS with fewer than 12 months of symptoms experienced significantly better outcomes with surgical and nonsurgical treatment relative to those with symptom duration greater than 12 months. There was no difference in the outcome of patients with degenerative spondylolisthesis according to symptom duration.
Non-alcoholic fatty liver disease: a practical approach to diagnosis and staging

Non-alcoholic fatty liver disease (NAFLD) is now the commonest cause of abnormal liver function tests (LFTs) in the UK with approximately a third of the population being affected. The exact prevalence is not known, but population studies from the USA and China using magnetic resonance spectroscopy estimate that approximately 30% of the general population have steatosis. It is a spectrum of disease ranging from simple steatosis, to non-alcoholic steatohepatitis (NASH), through to advanced fibrosis and cirrhosis. The majority have simple steatosis, but approximately 10–30% develop NASH and the development of NASH cirrhosis is associated with a poor long-term prognosis. Patients with NASH have increased liver-related and cardiovascular mortality. Many patients with NAFLD remain undiagnosed, and recognising those at risk is the first step. Clinicians overly rely on abnormal liver enzymes to identify patients with NAFLD, so patients with significant liver disease can be overlooked, potentially missing opportunities for intervention. Although liver biopsy is the gold standard method for diagnosing and staging NAFLD, the majority of patients can be effectively diagnosed non-invasively with tests that are routinely available in the clinic today. This review discusses a pragmatic approach to diagnosis and staging of NAFLD so that patients at the highest risk of liver-related complications can be identified.
Exponential Asymptotics and Capillary Waves

Recently developed techniques in exponential asymptotics beyond all orders are employed on the problem of potential flows with a free surface and small surface tension, in the absence of gravity. Exponentially small capillary waves are found to be generated on the free surface where the equipotentials from singularities in the flow (for example, stagnation points and corners) meet it. The amplitude of these waves is determined, and the implications are considered for many quite general flows. The asymptotic results are compared to numerical simulations of the full problem for flow over a polygonal plough and for flow round a right-angled corner, and they show remarkably good agreement, even for quite large values of the surface tension parameter.
Dysmenorrhea in adolescents and young adults: a review in different countries

Background: Dysmenorrhea is still an important public health problem which may have a negative impact on female health, social relationships, school or work activities and psychological status. Methods: The aim of this review is a better understanding of the epidemiology of dysmenorrhoea and its effect on public health. Published studies in English providing relevant information on dysmenorrhea were identified by searching PubMed, Embase and Google; restricting the population to adolescents and young adult women and the year of publishing from 2010 to August 2015, based on the keywords ‘dysmenorrhea’, ‘adolescents’ and ‘epidemiology’. In addition, the reference lists of the selected articles were examined. Results: We found 50 studies that met our inclusion criteria. The majority were cross-sectional studies on 41,140 adolescents and young women published from 2010 onward. The prevalence of dysmenorrhea varied from 34 % (Egypt) to 94% (Oman) and the number of participants, reporting very severe pain varied from 0.9 % (Korea) to 59.8% (Bangladesh). Adolescents who missed school due to dysmenorrhoea ranged from 7.7% to 57.8% and 21.5% missed social activities. About 50% of students (53.7%-47.4%) reported a family history of dysmenorrhea. Incidence of dysmenorrhea was 0.97 times lower as age increased (p <0.006). Despite the high prevalence of dysmenorrhea in adolescents, many girls did not receive professional help or treatment. Mothers were the most important persons the girls turned to for answers regarding menstruation, followed by peers (52.9%) and school nurse. From 21% to 96% practised self-medication either by pharmacological or non pharmacological interventions. The limitation of these studies was that they did not distinguish between primary dysmenorrhea and secondary dysmenorrhea. Conclusions: The main gynecological complaint of adolescents is dysmenorrhea. Morbidity due to dysmenorrhea represents a substantial public health burden. It is one of the leading causes of absenteeism from school and work and is responsible for significant diminished quality of life. Despite its high prevalence and associated negative effects, many adolescents do not seek medical care for this condition. Appropriate counselling and management should be instituted among female students to help them cope with the challenges of dysmenorrhea. Information, education and support should also be extended to parents, school peer leaders, and hostel administrators in order to address the reproductive health needs of the female students(www.actabiomedica.it)
CHARACTERIZATION OF A PEARLESCENT BIAXIALLY ORIENTED MULTILAYER POLYPROPYLENE FILM

Abstract. The morphology, composition, optical, thermal and mechanical properties of acommercial pearlescent and multilayer BOPP film were determined in the present study.Thefilm was polypropylene and it was biaxially oriented as shown by FTIR spectroscopy andX-ray diffraction. FTIR spectroscopy indicated carbonate ions, EDX analysis indicated thepresence of Ca element, X-ray diffraction showed the presence of calcite and thermalgravimetric analysis indicated that 11.2 % calcite was present in the film. The 30 µm filmconsisted of a core layer filled with calcite and 4 µm thick upper and lower layers without anyfiller and from different polymers. There were long air cavities in the core layer with aspectratios of 23 and 19 in machine and transverse directions making the film pearlescent.Thesurfaces of the film were very smooth and had surface roughness in the range of 3.052nmand 11.261 nm as determined by AFM. The film melted at 163.6 o C had 51% crystallinity andhad 6.3 nm polymer crystals when heated at 10
Prion species barrier between the closely related yeast proteins is detected despite coaggregation

Prions are self-perpetuating and, in most cases, aggregation-prone protein isoforms that transmit neurodegenerative diseases in mammals and control heritable traits in yeast. Prion conversion requires a very high level of identity of the interacting protein sequences. Decreased transmission of the prion state between divergent proteins is termed “species barrier” and was thought to occur because of the inability of divergent prion proteins to coaggregate. Species barrier can be overcome in cross-species infections, e.g., from “mad cows” to humans. We studied the counterparts of yeast prion protein Sup35, originated from three different species of the Saccharomyces sensu stricto group and exhibiting the range of prion domain divergence that overlaps with the range of divergence observed among distant mammalian species. All three proteins were capable of forming a prion in Saccharomyces cerevisiae, although prions formed by heterologous proteins were usually less stable than the endogenous S. cerevisiae prion. Heterologous Sup35 proteins coaggregated in the S. cerevisiae cells. However, in vivo cross-species prion conversion was decreased and in vitro polymerization was cross-inhibited in at least some heterologous combinations, thus demonstrating the existence of prion species barrier. Moreover, the barrier between the S. cerevisiae protein and its Saccharomyces paradoxus and Saccharomyces bayanus counterparts was asymmetric both in vivo and in vitro. Our data show that a decreased cross-species prion transmission does not necessarily correlate with a lack of cross-species coaggregation, suggesting that species-specificity of prion transmission is controlled at the level of conformational transition rather than coaggregation.
Efficient Access Control for Wireless Sensor Data

Although very developed in many sectors (databases, filesystems), access control schemes are still somewhat elusive when it comes to wireless sensor networks. However, it is clear that many WSN systems—such as healthcare and automotive ones—need a controlled access to data that sensor nodes produce, given its high sensitivity. Enforcing access control in wireless sensor networks is a particularly difficult task due to the limited computational capacity of wireless sensor nodes. In this paper we present a full-fledged access control scheme for wireless sensor data. We enforce access control through data encryption, thus embedding access control in sensor data units. We also propose a lightweight key generation mechanism, based on cryptographic hash functions, that allows for hierarchical key derivation. The suggested protocol only relies on simple operations, does not require interactions between nodes and data consumers and has minimal storage requirements.
Evaluation of Cytomegalovirus Infection after Six Months of Liver Transplantation in Children in Shiraz, Southern Iran

Background: Liver transplantation (LT) is a life-saving treatment for end-stage liver diseases (ESLD). Cytomegalovirus (CMV) infection is one of the important causes of morbidity after LT. Objective: To evaluate the incidence of late-onset (after 6 months of LT) CMV infection in pediatric recipients. Methods: A retrospective analysis was conducted to evaluate 50 pediatric patients who underwent LT for 8 years at the LT Unit of Nemazee Hospital affiliated to Shiraz University of Medical Sciences, Shiraz, Iran. We retrospectively investigated episodes of CMV infection after 6 months of LT proven by CMV antigenemia test. Results: Three recipients (6%) developed late-onset CMV infection. These patients finally responded to ganciclovir. Conclusion: CMV infection is one of the most common post-LT viral infections that usually occurs in the first six months of LT. Our study shows that the incidence of late-onset CMV infection is relatively low, but it still remains a significant problem. Therefore, monitoring and management is crucial for improving the survival of children.
The Complexity of General-Valued CSPs

An instance of the Valued Constraint Satisfaction Problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P ≠ NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one deals only with the feasibility issue and there is no optimization. This case is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which constraint languages CSPs are tractable (i.e. solvable in polynomial time) and for which NP-hard. The case when all allowed functions take only finite values corresponds to finite-valued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Zivny. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e. the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.
Self and informant reports of mental health difficulties among adults with autism findings from a long-term follow-up study

Data on psychiatric problems in adults with autism are inconsistent, with estimated rates ranging from around 25% to over 75%. We assessed difficulties related to mental health in 58 adults with autism (10 females, 48 males; mean age 44 years) whom we have followed over four decades. All were of average non-verbal intelligence quotient when diagnosed as children. Overall ratings of mental health problems were based on data from the Family History Schedule (Bolton et al., 1994). Informant reports indicated that many of the cohort (44%) had experienced no mental health problems in adulthood; 28% had experienced mild to moderate difficulties, 23% had severe and 5% very severe problems. Depression was the most commonly reported problem. Among those adults (n = 22) able to report on their own mental state, again many (45%) reported no mental health problems, although 27% reported very severe mental health problems related to anxiety, depression and/or obsessive–compulsive symptoms. Informant ratings of poor mental health were not associated with gender, severity of autism in childhood, or child or adult intelligence quotient, but there were small correlations with overall social functioning (rho = 0.34) and current autism severity (rho = 0.37). The findings highlight the difficulties of assessing mental health problems in adults with autism and the need for appropriately validated measures.
Are low but statistically significant levels of genetic differentiation in marine fishes ‘biologically meaningful’? A case study of coastal Atlantic cod

A key question in many genetic studies on marine organisms is how to interpret a low but statistically significant level of genetic differentiation. Do such observations reflect a real phenomenon, or are they caused by confounding factors such as unrepresentative sampling or selective forces acting on the marker loci? Further, are low levels of differentiation biologically trivial, or can they represent a meaningful and perhaps important finding? We explored these issues in an empirical study on coastal Atlantic cod, combining temporally replicated genetic samples over a 10‐year period with an extensive capture–mark–recapture study of individual mobility and population size. The genetic analyses revealed a pattern of differentiation between the inner part of the fjord and the open skerries area at the fjord entrance. Overall, genetic differentiation was weak (average FST = 0.0037), but nevertheless highly statistical significant and did not depend on particular loci that could be subject to selection. This spatial component dominated over temporal change, and temporal replicates clustered together throughout the 10‐year period. Consistent with genetic results, the majority of the recaptured fish were found close to the point of release, with <1% of recaptured individuals dispersing between the inner fjord and outer skerries. We conclude that low levels of genetic differentiation in this marine fish can indeed be biologically meaningful, corresponding to separate, temporally persistent, local populations. We estimated the genetically effective sizes (Ne) of the two coastal cod populations to 198 and 542 and found a Ne/N (spawner) ratio of 0.14.
Strong CD4 Th1 responses to HIV and hepatitis C virus in HIV-infected long-term non-progressors co-infected with hepatitis C virus

Objectives To compare the T-cell responses to hepatitis C virus (HCV) and HIV in HIV-infected long-term non-progressors (LT-NP) and HIV-positive progressors co-infected with HCV and in HIV-negative HCV-infected patients. Methods Three groups were studied: 10 HCV/HIV-infected LT-NP, 26 HCV/HIV-infected progressors and 13 HCV-infected/HIV-negative patients. Virus-specific CD4 and CD8 T-cell responses in peripheral blood were assessed by interferon (IFN)-γ Elispot assays using recombinant proteins (HIV-p24 and three HCV antigens) and 16 HIV or HCV HLA A3- and/or HLA A2-restricted cytotoxic T lymphocytes peptides. Statistical analysis was performed with non-parametric tests. Results In addition to high T helper 1 (Th1) cell frequencies directed against HIV-p24, LT-NP had significantly (P < 0.05) higher frequencies of Th1 cells against HCV than the two other groups. No difference was observed between HIV-infected progressors and HIV-negative controls. Furthermore , HCV-specific CD4 and CD8 T cells were correlated in LT-NP (P = 0.006). Conclusion Thus, independently of the HIV-related immune alterations, LT-NP of the HIV-infection might have an intrinsic capacity to develop strong Th1 cell responses to viruses, particularly HIV and HCV.