Miracle-dz/UniFAR-FTUs huggingface dataset:
Achromatopsia caused by novel mutations in both CNGA3 and CNGB3

Complete achromatopsia or rod monochromatism is a stationary cone dystrophy, with an incidence of ~1 in 30 000, in which functional cones are absent from the retina.1,2 Affected individuals usually present in infancy with nystagmus, poor visual acuity (6/60–6/36), photophobia, and complete colour blindness. Fundal examination is normal, but electroretinography reveals absent photopic (cone) responses and normal scotopic (rod) responses. Individuals with incomplete achromatopsia retain some colour vision.3 Achromatopsia is recessively inherited and genetically heterogeneous. To date, three achromatopsia genes have been characterised, the first two described being CNGA3 4–6 and CNGB3 ,7–9 located at chromosome positions 2q11 and 8q21 respectively. CNGA3 and CNGB3 respectively code for the α and β subunits of the cGMP gated cation channel in cone cells. Recently, mutations within a third gene, GNAT2 , which encodes the α subunit of cone transducin, have also been shown to cause achromatopsia.10,11 All these genes encode crucial components of cone specific phototransduction. Studies of patients with achromatopsia have revealed more than 40 disease causing mutations in CNGA3 , the majority being missense mutations.5,6,12 In the patient groups studied, four CNGA3 mutations (Arg277Cys, Arg283Trp, Arg436Trp, and Phe547Leu) accounted for 40% of all mutant CNGA3 alleles. In contrast, only eight different mutations of CNGB3 have been identified to date, with six of these being nonsense mutations.8,9 The most common mutation is a 1 bp frameshift deletion, 1148delC, which accounts for 84% (199/237) of CNGB3 mutations.14 Current estimates suggest that mutations in CNGB3 account for 40–50% of achromatopsia,14 with mutations in CNGA3 contributing a further 20%. 5 There is therefore a significant proportion of patients for whom neither CNGA3 nor CNGB3 mutations can be found (~30%). GNAT2 is the third gene to be implicated in achromatopsia, …
Cytokines as Biomarkers of Pancreatic Ductal Adenocarcinoma: A Systematic Review

Objectives A systematic review of the role of cytokines in clinical medicine as diagnostic, prognostic, or predictive biomarkers in pancreatic ductal adenocarcinoma was undertaken. Materials and Methods A systematic review was conducted according to the 2009 PRISMA guidelines. PubMed database was searched for all original articles on the topic of interest published until June 2015, and this was supplemented with references cited in relevant articles. Studies were evaluated for risk of bias using the Quality in Prognosis Studies tools. Results Forty one cytokines were investigated with relation to pancreatic ductal adenocarcinoma (PDAC) in 65 studies, ten of which were analyzed by more than three studies. Six cytokines (interleukin[IL]-1β, -6, -8, -10, vascular endothelial growth factor, and transforming growth factor) were consistently reported to be increased in PDAC by more than four studies; irrespective of sample type; method of measurement; or statistical analysis model used. When evaluated as part of distinct panels that included CA19-9, IL-1β, -6 and -8 improved the performance of CA19-9 alone in differentiating PDAC from healthy controls. For example, a panel comprising IL-1β, IL-8, and CA 19–9 had a sensitivity of 94.1% vs 85.9%, specificity of 100% vs 96.3%, and area under the curve of 0.984 vs 0.925. The above-mentioned cytokines were associated with the severity of PDAC. IL-2, -6, -10, VEGF, and TGF levels were reported to be altered after patients received therapy or surgery. However, studies did not show any evidence of their ability to predict treatment response. Conclusion Our review demonstrates that there is insufficient evidence to support the role of individual cytokines as diagnostic, predictive or prognostic biomarkers for PDAC. However, emerging evidence indicates that a panel of cytokines may be a better tool for discriminating PDAC from other non-malignant pancreatic diseases or healthy individuals.
On Building Constructive Formal Theories of Computation Noting the Roles of Turing, Church, and Brouwer

In this article I will examine a few key concepts and design decisions that account for the high value of implemented constructive type theories in computer science. I'll stress the historical fact that these theories, and the proof assistants that animate them, were born from a strong partnership linking computer science, logic, and mathematics. I will recall how modern type theory researchers built on deep insights from the earliest pioneers: Turing - the first computer scientist, Church - the patriarch of logic in computer science, and Brouwer - a singular pioneer of intuitionism and constructive mathematics. They created solid intellectual ground on which to build a formal implemented constructive theory of computation whose influence will be felt well beyond computing and information science alone. All generations of constructive type theory researchers since this beginning have had leaders from all three disciplines. Much of the seminal modern work creating these type theories and their proof assistants was presented in LICS proceedings, and LICS could be a natural home for future work in this flourishing area which is the epitome of logic in computer science.
BLIND GENE CLASSIFICATION BASED ON ICA OF MICROARRAY DATA

The present study shows that an ICA-based method can, e®ectively and blindly, classify a vast amount of gene expression data into biologically meaningful groups. Speci cally, we show (1) that genes, whose expression data are sampled at di®erent times, can be classi ed into several groups, based on the correlation of each gene with independent component curves over time, and (2) that these classi ed groups by ICA-based method have a good match with the classi ed groups that are determined by use of domain knowledge and considered to be a benchmark. These results suggest that the ICA-based method can be a powerful approach to discover unknown gene functions.
Hyperbolic dimension of metric spaces

We introduce a new quasi-isometry invariant of metric spaces called the hyperbolic dimension, hypdim, which is a version of the Gromov's asymptotic dimension, asdim. The hyperbolic dimension is at most the asymptotic dimension, however, unlike the asymptotic dimension, the hyperbolic dimension of any Euclidean space R^n is zero (while asdim R^n=n.) This invariant possesses usual properties of dimension like monotonicity and product theorems. Our main result says that the hyperbolic dimension of any Gromov hyperbolic space X (with mild restrictions) is at least the topological dimension of the boundary at infinity plus 1. As an application we obtain that there is no quasi-isometric embedding of the real hyperbolic space H^n into the (n-1)-fold metric product of metric trees stabilized by any Euclidean factor.
Potential alternate smoldering ignition sources: literature review with analysis

Existing and proposed U.S. flammability standards for soft furnishings such as mattresses and upholstered furniture specify a “standard” cigarette as the ignition source in smoldering resistance performance tests. With the introduction of reduced ignition propensity cigarettes into the marketplace, the specific conventional cigarette that has been widely used in testing for ignition resistance is no longer in production. A standard reference cigarette, SRM 1196, has been developed as a short-term replacement. However, to support furnishings manufacturers and testing organizations in product design and evaluation, and to assist regulators in the compliance evaluation process, a feasible and preferably non-agricultural ignition source with long-term availability is desirable. A key first step in establishing such a standard ignition source is examination of prior characterizations of smoldering ignition sources and the cigarette ignition process. This report documents a literature survey on these topics.
Phenomenal regression as a potential metric of veridical perception in virtual environments

It is known that limitations of the visual presentation and sense of presence in a virtual environment (VE) can result in deficits of spatial perception such as the documented depth compression phenomena. Investigating size and distance percepts in a VE is an active area of research, where different groups have measured the deficit by employing skill-based tasks such as walking, throwing or simply judging sizes and distances. A psychological trait called phenomenal regression (PR), first identified in the 1930s by Thouless, offers a measure that does not rely on either judgement or skill. PR describes a systematic error made by subjects when asked to match the perspective projections of two stimuli displayed at different distances. Thouless’ work found that this error is not mediated by a subject’s prior knowledge of its existence, nor can it be consciously manipulated, since it measures an individual’s innate reaction to visual stimuli. Furthermore he demonstrated that, in the real world, PR is affected by the depth cues available for viewing a scene. When applied in a VE, PR therefore potentially offers a direct measure of perceptual veracity that is independent of participants’ skill in judging size or distance. Experimental work has been conducted and a statistically significant correlation of individuals’ measured PR values (their ‘Thouless ratio’, or TR) between virtual and physical stimuli was found. A further experiment manipulated focal depth to mitigate the mismatch that occurs between accommodation and vergence cues in a VE. The resulting statistically significant effect on TR demonstrates that it is sensitive to changes in viewing conditions in a VE. Both experiments demonstrate key properties of PR that contribute to establishing it as a robust indicator of VE quality. The first property is that TR exhibits temporal stability during the period of testing and the second is that it differs between individuals. This is advantageous as it yields empirical values that can be investigated using regression analysis. This work contributes to VE domains in which it is desirable to replicate an accurate perception of space, such as training and telepresence, where PR would be a useful tool for comparing subjective experience between a VE and the real world, or between different VEs.
Differences in perceptual latency estimated from judgments of temporal order, simultaneity and duration are inconsistent

Differences in perceptual latency (ΔL) for two stimuli, such as an auditory and a visual stimulus, can be estimated from temporal order judgments (TOJ) and simultaneity judgments (ΔJ), but previous research has found evidence that ΔL estimated from these tasks do not coincide. Here, using an auditory and a visual stimulus we confirmed this and further show that ΔL as estimated from duration judgments also does not coincide with ΔL estimated from TOJ or SJ. These inconsistencies suggest that each judgment is subject to different processes that bias 4L in different ways: TOJ might be affected by sensory interactions, a bias associated with the method of single stimuli and an order difficulty bias; SJ by sensory interactions and an asymmetrical criterion bias; duration judgments by an order duration bias.
Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana

Pinus lambertiana (sugar pine) is an economically and ecologically important conifer with a 1600‐km latitudinal range extending from Oregon, USA, to northern Baja California, Mexico. Like all North American white pines (subsect. Strobus), sugar pine is highly susceptible to white pine blister rust, a disease caused by the fungus Cronartium ribicola. We conducted a chloroplast DNA (cpDNA) survey of Pinus subsect. Strobus with comprehensive geographical sampling of P. lambertiana. Sequence analysis of 12 sugar pine individuals revealed strong geographical differentiation for two chloroplast haplotypes. A diagnostic restriction site survey of an additional 72 individuals demarcated a narrow 150‐km contact zone in northeastern California. In the contact zone, maternal (megagametophtye) and paternal (embryo) haplotypes were identified in 31 single seeds, demonstrating bidirectional pollen flow extending beyond the range of maternal haplotypes. The frequencies of the Cr1 allele for white pine blister rust major gene resistance, previously determined for 41 seed zones, differ significantly among seed zones that are fixed for the alternate haplotypes, or contain a mixture of both haplotypes. Interspecific phylogenetic analysis reveals that the northern sugar pine haplotype belongs to a clade that includes Pinus albicaulis (whitebark pine) and all of the East Asian white pines. Furthermore, there is little cpDNA divergence between northern sugar pine and whitebark pine (dS = 0.00058). These results are consistent with a Pleistocene migration of whitebark pine into North America and subsequent chloroplast introgression from whitebark pine to sugar pine. This study demonstrates the importance of placing phylogeographical results in a broader phylogenetic context.
Biodiversity effects on productivity and stability of marine macroalgal communities: the role of environmental context

The influence of biodiversity on ecosystem functioning has been the focus of much recent research, but the role of environmental context and the mechanisms by which it may influence diversity effects on production and stability remain poorly understood. We assembled marine macroalgal communities in two mesocosm experiments that varied nutrient supply, and at four field sites that differed naturally in environmental conditions. Concordant with theory, nutrient addition promoted positive species richness effects on algal growth in the first mesocosm experiment; however, it tended to weaken the positive diversity relationship found under ambient conditions in a second experiment the next year. In the field experiments, species richness increased algal biomass production at two of four sites. Together, these experiments indicate that diversity effects on algal biomass production are strongly influenced by environmental conditions that vary over space and time. In decomposing the net biodiversity effect into its component mechanisms, seven of the eight experimental settings showed positive complementarity effects (suggesting facilitation or complementary resource use) countered by negative selection effects (i.e. enhanced growth in mixture of otherwise slow growing species) to varying degrees. Under no conditions, including nutrient enrichment, did we find evidence of positive selection effects commonly thought to drive positive diversity effects. Species richness enhanced stability of algal community biomass across a range of environmental settings in our field experiments. Hence, while species richness can increase production, enhanced stability is also an important functional outcome of maintaining diverse marine macroalgal communities.
Stability Modeling and Comparative Study of Series Vectorial Compensators

Complete stability analyses, including voltage, small perturbation and transient stability studies, and the associated models and controls of a series vectorial compensator (SVeC) are presented in this paper. It is also shown through detailed simulations that the SVeC is a competitive device against series power-flow controllers and it might be a better option for similar purposes where space and costs are at premium. Hence, a full comparative evaluation of this controller with respect to controllers used mainly for oscillation control in transmission corridors, namely, thyristor-controlled series capacitors (TCSC) and series static synchronous compensators (SSSC), is also presented for the first time. The IEEE 14-bus benchmark system and a 190-bus, 46-machine model of the Mexican grid are used for illustrative and comparison purposes. The results obtained show that the SVeC has better oscillation damping characteristics than the TCSC and SSSC, hence making these types of controllers a competitive alternative against existing series flexible ac transmission system (FACTS) controllers for dynamic series compensation of transmission lines.
Risk Factors Associated with Positive QuantiFERON-TB Gold In-Tube and Tuberculin Skin Tests Results in Zambia and South Africa

Introduction The utility of T-cell based interferon-gamma release assays for the diagnosis of latent tuberculosis infection remains unclear in settings with a high burden of tuberculosis. Objectives To determine risk factors associated with positive QuantiFERON-TB Gold In-Tube (QFT-GIT) and tuberculin skin test (TST) results and the level of agreement between the tests; to explore the hypotheses that positivity in QFT-GIT is more related to recent infection and less affected by HIV than the TST. Methods Adult household contacts of tuberculosis patients were invited to participate in a cross-sectional study across 24 communities in Zambia and South Africa. HIV, QFT-GIT and TST tests were done. A questionnaire was used to assess risk factors. Results A total of 2,220 contacts were seen. 1,803 individuals had interpretable results for both tests, 1,147 (63.6%) were QFT-GIT positive while 725 (40.2%) were TST positive. Agreement between the tests was low (kappa = 0.24). QFT-GIT and TST results were associated with increasing age (adjusted OR [aOR] for each 10 year increase for QFT-GIT 1.15; 95% CI: 1.06–1.25, and for TST aOR: 1.10; 95% CI 1.01–1.20). HIV positivity was less common among those with positive results on QFT-GIT (aOR: 0.51; 95% CI: 0.39–0.67) and TST (aOR: 0.61; 95% CI: 0.46–0.82). Smear positivity of the index case was associated with QFT-GIT (aOR: 1.25; 95% CI: 0.90–1.74) and TST (aOR: 1.39; 95% CI: 0.98–1.98) results. We found little evidence in our data to support our hypotheses. Conclusion QFT-GIT may not be more sensitive than the TST to detect risk factors associated with tuberculous infection. We found little evidence to support the hypotheses that positivity in QFT-GIT is more related to recent infection and less affected by HIV than the TST.
Achieving Lower Nitrogen Balance and Higher Nitrogen Recovery Efficiency Reduces Nitrous Oxide Emissions in North America's Maize Cropping Systems

Few studies have assessed the common, yet unproven, hypothesis that an increase of plant nitrogen (N) uptake and/or recovery efficiency (NRE) will reduce nitrous oxide (N2O) emission during crop production. Understanding the relationships between N2O emissions and crop N uptake and use efficiency parameters can help inform crop N management recommendations for both efficiency and environmental goals. Analyses were conducted to determine which of several commonly used crop N uptake-derived parameters related most strongly to growing season N2O emissions under varying N management practices in North American maize systems. Nitrogen uptake-derived variables included total aboveground N uptake (TNU), grain N uptake (GNU), N recovery efficiency (NRE), net N balance (NNB) in relation to GNU [NNB(GNU)] and TNU [NNB(TNU)], and surplus N (SN). The relationship between N2O and N application rate was sigmoidal with relatively small emissions for N rates <130 kg ha−1, and a sharp increase for N rates from 130 to 220 kg ha−1; on average, N2O increased linearly by about 5 g N per kg of N applied for rates up to 220 kg ha−1. Fairly strong and significant negative relationships existed between N2O and NRE when management focused on N application rate (r2 = 0.52) or rate and timing combinations (r2 = 0.65). For every percentage point increase, N2O decreased by 13 g N ha−1 in response to N rates, and by 20 g N ha−1 for NRE changes in response to rate-by-timing treatments. However, more consistent positive relationships (R2 = 0.73–0.77) existed between N2O and NNB(TNU), NNB(GNU), and SN, regardless of rate and timing of N application; on average N2O emission increased by about 5, 7, and 8 g N, respectively, per kg increase of NNB(GNU), NNB(TNU), and SN. Neither N source nor placement influenced the relationship between N2O and NRE. Overall, our analysis indicated that a careful selection of appropriate N rate applied at the right time can both increase NRE and reduce N2O. However, N2O reduction benefits of optimum N rate-by-timing practices were achieved most consistently with management systems that reduced NNB through an increase of grain N removal or total plant N uptake relative to the total fertilizer N applied to maize. Future research assessing crop or N management effects on N2O should include N uptake parameter measurements to better understand N2O emission relationships to plant NRE and N uptake.
Content-Based Image Unequal Error Protection Strategies for an Open Loop MIMO System

The paper deals with strategies for optimizing the transmission of JPEG2000 coded images over a MIMO quasi-static Rayleigh fading channel, by exploiting different available MIMO STBC (Space Time Block Codes), as well as the image content to be transmitted. The aim is to propose a link adaptation scheme based on the variable radio channel’s conditions, by establishing an UEP (Unequal Error Protection) scheme that leads to the best tradeoff between the robustness to errors and the image visual quality. Comparisons are made with the EEP (Equal Error Protection) case, in terms of the PSNR (Peak Signal to Noise Ratio) fidelity metric, as well as the subjective image quality.
Assessing the Adhesive Performance in CLT Exposed to Fire

Cross-laminated timber (CLT) became a popular engineered wood product in recent years for highquality and innovative timber buildings. As for any building product, the fire behaviour of CLT panels requires careful evaluation in the design of such buildings. The adhesive used in the bond lines of CLT plays an important role in the fire design. However, currently, European standards do not provide a test method to assess the adhesive performance in CLT exposed to fire. This paper presents a series of fire tests performed with CLT panels glued with different adhesives. It is shown how the mass loss of the CLT panels in standard fire resistance tests can be used to assess the adhesive performance in CLT exposed to fire.
Face-emotion processing in offspring at risk for panic disorder.

OBJECTIVE Panic disorder (PD) has been linked to perturbed processing of threats. This study tested the hypotheses that offspring of parents with PD and offspring with anxiety disorders display relatively greater sensitivity and attention allocation to fear provocation. METHOD Offspring of adults with PD, major depressive disorder (MDD), or no disorder (ages 9-19) viewed computer-presented face photographs depicting angry, fearful, and happy faces. Offspring rated (1) subjectively experienced fear level, (2) how hostile the face appeared, and (3) nose width. Attention allocation was indexed by latency to perform ratings. RESULTS Compared with offspring of parents without PD (n = 79), offspring of PD parents (n = 65) reported significantly more fear and had slower reaction times to rate fear, controlling for ongoing anxiety disorder in the offspring. Offspring with an anxiety disorder (n = 65) reported significantly more fear than offspring without an anxiety disorder but not when parental PD was controlled. Social phobia but no other anxiety disorder in offspring was associated with slower reaction times for fear ratings (but not greater fear ratings). Parental PD and offspring social phobia independently predicted slower reaction time. CONCLUSIONS Results support an association between parental PD and offspring responses to fear provocation. Social phobia in children may have a specific relationship to allocation of attention to subjective anxiety during face viewing.