Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Type–Specific Quantification of Telomere Length and DNA Double-strand Breaks in Individual Lung Cells by Fluorescence In Situ Hybridization and Fluorescent Immunohistochemistry

Telomeres are small repetitive DNA sequences at the ends of chromosomes which act as a buffer in age-dependent DNA shortening. Insufficient telomere repeats will be recognized as double-strand breaks. Presently, it is becoming more evident that telomere attrition, whether or not caused by mutations in telomere maintenance genes, plays an important role in many inflammatory and age-associated diseases. In this report, a method to (semi)quantitatively assess telomere length and DNA double-strand breaks in formalin-fixed paraffin-embedded (FFPE) tissue is described. Therefore, a novel combination of quantitative fluorescence in situ hybridization, tissue elution, and immunofluorescence staining techniques was developed. Caveolin-1 (type 1 pneumocytes), pro-surfactant protein C (type 2 pneumocytes), club cell-10 (club cells), and alpha smooth muscle actin (smooth muscle cells) markers were used to identify cell types. To visualize all the different probes, restaining the tissue by heat-mediated slide elution is essential. Fluorescent signals of telomeres and DNA double-strand breaks were quantified using the Telometer plugin of ImageJ. As example, we analyzed lung tissue from a familial pulmonary fibrosis patient with a mutation in the telomere-associated gene poly(A)-specific ribonuclease (PARN). The protocol displays a novel opportunity to directly quantitatively link DNA double-strand breaks to telomere length in specific FFPE cells.
A New Rate Control Algorithm based on Statistical Analysis for MVC

Rate control is one of important tools in multi-view video coding (MVC). This paper presents a new rate control algorithm for MVC by analyzing the rate allocation proportion among different types of views. The proposed algorithm is performed on three levels, that is, view level, group-of-pictures (GOP) level and frame level. Firstly, we reasonably allocate bit-rate among views based on the statistical analysis in the view level. Then, in the GOP level, the initial quantization parameter (QP) of each GOP is set according to the QP values of B frames. Finally, the frame complexity is used to regulate the target bit for each frame. Experimental results show that the proposed algorithm can accurately control bit-rate to satisfy the requirements of multi-view video systems.
Assessing Dispersal Patterns of Fish Propagules from an Effective Mediterranean Marine Protected Area

Successfully enforced marine protected areas (MPAs) have been widely demonstrated to allow, within their boundaries, the recovery of exploited species and beyond their boundaries, the spillover of juvenile and adult fish. Little evidence is available about the so-called ‘recruitment subsidy’, the augmented production of propagules (i.e. eggs and larvae) due to the increased abundance of large-sized spawners hosted within effective MPAs. Once emitted, propagules can be locally retained and/or exported elsewhere. Patterns of propagule retention and/or export from MPAs have been little investigated, especially in the Mediterranean. This study investigated the potential for propagule production and retention/export from a Mediterranean MPA (Torre Guaceto, SW Adriatic Sea) using the white sea bream, Diplodus sargus sargus, as a model species. A multidisciplinary approach was used combining 1) spatial distribution patterns of individuals (post-settlers and adults) assessed through visual census within Torre Guaceto MPA and in northern and southern unprotected areas, 2) Lagrangian simulations of dispersal based on an oceanographic model of the region and data on early life-history traits of the species (spawning date, pelagic larval duration) and 3) a preliminary genetic study using microsatellite loci. Results show that the MPA hosts higher densities of larger-sized spawners than outside areas, potentially guaranteeing higher propagule production. Model simulations and field observation suggest that larval retention within and long-distance dispersal across MPA boundaries allow the replenishment of the MPA and of exploited populations up to 100 km down-current (southward) from the MPA. This pattern partially agrees with the high genetic homogeneity found in the entire study area (no differences in genetic composition and diversity indices), suggesting a high gene flow. By contributing to a better understanding of propagule dispersal patterns, these findings provide crucial information for the design of MPAs and MPA networks effective to replenish fish stocks and enhance fisheries in unprotected areas.
Sex-Differential Herbivory in Androdioecious Mercurialis annua

Males of plants with separate sexes are often more prone to attack by herbivores than females. A common explanation for this pattern is that individuals with a greater male function suffer more from herbivory because they grow more quickly, drawing more heavily on resources for growth that might otherwise be allocated to defence. Here, we test this ‘faster-sex’ hypothesis in a species in which males in fact grow more slowly than hermaphrodites, the wind-pollinated annual herb Mercurialis annua. We expected greater herbivory in the faster-growing hermaphrodites. In contrast, we found that males, the slower sex, were significantly more heavily eaten by snails than hermaphrodites. Our results thus reject the faster-sex hypothesis and point to the importance of a trade-off between defence and reproduction rather than growth.
A session type provider: compile-time API generation of distributed protocols with refinements in F#

We present a library for the specification and implementation of distributed protocols in native F# (and other .NET languages) based on multiparty session types (MPST). There are two main contributions. Our library is the first practical development of MPST to support what we refer to as interaction refinements: a collection of features related to the refinement of protocols, such as message-type refinements (value constraints) and message value dependent control flow. A well-typed endpoint program using our library is guaranteed to perform only compliant session I/O actions w.r. t. to the refined protocol, up to premature termination. Second, our library is developed as a session type provider, that performs on-demand compile-time protocol validation and generation of protocol-specific . NET types for users writing the distributed endpoint programs. It is implemented by extending and integrating Scribble (a toolchain for MPST) with an SMT solver into the type providers framework. The safety guarantees are achieved by a combination of static type checking of the generated types for messages and I/O operations, correctness by construction from code generation, and automated inlining of assertions.
The Value of Monitoring Clinical Decision Support Interventions

Abstract Background Well-functioning clinical decision support (CDS) can facilitate provider workflow, improve patient care, promote better outcomes, and reduce costs. However, poorly functioning CDS may lead to alert fatigue, cause providers to ignore important CDS interventions, and increase provider dissatisfaction. Objective The purpose of this article is to describe one institution's experience in implementing a program to create and maintain properly functioning CDS by systematically monitoring CDS firing rates and patterns. Methods Four types of CDS monitoring activities were implemented as part of the CDS lifecycle. One type of monitoring occurs prior to releasing active CDS, while the other types occur at different points after CDS activation. Results Two hundred and forty-eight CDS interventions were monitored over a 2-year period. The rate of detecting a malfunction or significant opportunity for improvement was 37% during preactivation and 18% during immediate postactivation monitoring. Monitoring also informed the process of responding to user feedback about alerts. Finally, an automated alert detection tool identified 128 instances of alert pattern change over the same period. A subset of cases was evaluated by knowledge engineers to identify true and false positives, the results of which were used to optimize the tool's pattern detection algorithms. Conclusion CDS monitoring can identify malfunctions and/or significant improvement opportunities even after careful design and robust testing. CDS monitoring provides information when responding to user feedback. Ongoing, continuous, and automated monitoring can detect malfunctions in real time, before users report problems. Therefore, CDS monitoring should be part of any systematic program of implementing and maintaining CDS.
Error recovery for robust language understanding in spoken dialogue systems

In this paper, we proposed an example-based approach aiming at recover ing ill-formed inputs to improve robustness of spoken dialogue systems. In this approach, a treebank, which contains example sentences and their correct parse trees, is used to provide clues for fixing theerrors of ill-formed inputs. Particularly, t he proposed error recovery method is suitable for spoken dialogue application because of computationally efficiency . In addition, when evaluated in a Mandarine spoken dialogue system, the proposed method has shown to improve the system's understaning rate very significantly. Keywords: robust parsing, error recovery, spoken
Efficient BVH‐based Collision Detection Scheme with Ordering and Restructuring

Bounding volume hierarchy (BVH) has been widely adopted as the acceleration structure in broad‐phase collision detection. Previous state‐of‐the‐art BVH‐based collision detection approaches exploited the spatio‐temporal coherence of simulations by maintaining a bounding volume test tree (BVTT) front. A major drawback of these algorithms is that large deformations in the scenes decrease culling efficiency and slow down collision queries. Moreover, for front‐based methods, the inefficient caching on GPU caused by the arbitrary layout of BVH and BVTT front nodes becomes a critical performance issue. We present a fast and robust BVH‐based collision detection scheme on GPU that addresses the above problems by ordering and restructuring BVHs and BVTT fronts. Our techniques are based on the use of histogram sort and an auxiliary structure BVTT front log, through which we analyze the dynamic status of BVTT front and BVH quality. Our approach efficiently handles inter‐ and intra‐object collisions and performs especially well in simulations where there is considerable spatio‐temporal coherence. The benchmark results demonstrate that our approach is significantly faster than the previous BVH‐based method, and also outperforms other state‐of‐the‐art spatial subdivision schemes in terms of speed.
Translocation and protein complex co‐localization of mTOR is associated with postprandial myofibrillar protein synthesis at rest and after endurance exercise

Translocation and colocalization of mechanistic target of rapamycin complex 1 (mTORC1) with regulatory proteins represents a critical step in translation initiation of protein synthesis in vitro. However, mechanistic insight into the control of postprandial skeletal muscle protein synthesis rates at rest and after an acute bout of endurance exercise in humans is lacking. In crossover trials, eight endurance‐trained men received primed‐continuous infusions of L‐[ring‐2H5]phenylalanine and consumed a mixed‐macronutrient meal (18 g protein, 60 g carbohydrates, 17 g fat) at rest (REST) and after 60 min of treadmill running at 70% VO2peak (EX). Skeletal muscle biopsies were collected to measure changes in phosphorylation and colocalization in the mTORC1‐pathway, in addition to rates of myofibrillar (MyoPS) and mitochondrial (MitoPS) protein synthesis. MyoPS increased (P < 0.05) above fasted in REST (~2.1‐fold) and EX (~twofold) during the 300 min postprandial period, with no corresponding changes in MitoPS (P > 0.05). TSC2/Rheb colocalization decreased below fasted at 60 and 300 min after feeding in REST and EX (P < 0.01). mTOR colocalization with Rheb increased above fasted at 60 and 300 min after feeding in REST and EX (P < 0.01), which was consistent with an increased phosphorylation 4E‐BP1Thr37/46 and rpS6ser240/244 at 60 min. Our data suggest that MyoPS, but not MitoPS, is primarily nutrient responsive in trained young men at rest and after endurance exercise. The postprandial increase in MyoPS is associated with an increase in mTOR/Rheb colocalization and a reciprocal decrease in TSC2/Rheb colocalization and thus likely represent important regulatory events for in vivo skeletal muscle myofibrillar mRNA translation in humans.
Ring based wavelet transform with arbitrary supports in wireless sensor networks

In this paper, we propose a general transform for wavelet based data compression in wireless sensor networks. By employing a ring topology, our transform is capable of supporting a broad scope of wavelets rather than specified ones. At the same time, the scheme is capable of simultaneously exploring the spatial and temporal correlations among the sensory data. Furthermore, the ring based topology is in particular effective in eliminating the “border effect” generally encountered by wavelet based schemes. Theoretically and experimentally, we show the proposed wavelet transform can effectively explore the spatial and temporal correlation in the sensory data and provide significant reduction in energy consumption compared to other schemes.
Phylogenetic Distribution of Intron Positions in Alpha-Amylase Genes of Bilateria Suggests Numerous Gains and Losses

Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that “resets” of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures.
Influence of Weight on Shared Core Symptoms in Eating Disorders

In terms of the transdiagnostic model of eating disorders, Anorexia Nervosa (AN), Bulimia Nervosa (BN), and Binge Eating Disorder (BED) share the same distinctive psychopathology. However, empirical evidence showing similarities between these eating disorder diagnoses for core symptoms is scarce, and the role of weight status is unclear. Data from a total of 168 female participants were collected between April 2004 and April 2008, at an outpatient unit specialized in eating disorder treatment. Core symptoms of eating disorders were measured via self-report questionnaires. In particular, women with BED and BN showed similar patterns of core symptomatology compared with AN. However, when body mass index (BMI) was considered in the analyses, there were no differences between the three diagnostic groups in relation to body image. Differences in eating behavior are not solely triggered by weight differences, whereas body image disturbances are a transdiagnostic phenomenon among EDs and should also be considered in the treatment of BED.
Kernel Self-Adaptive Learning-Based Satellite Telemetry Data Classification

Telemetry data, containing the data of multiple subsystems such as power system, implies the on-orbit operation status information of the satellite. We can obtain performance characteristics and fault symptom of the satellite subsystems through analyzing these data. Using classification algorithm we can provide normal data for anomaly detection and find the data from various subsystems which have the same category labels. Then we will get potential knowledge of the satellite and rich expert experience. Because of the importance to national defense and people's livelihood fields, we have higher requirements about the accuracy and stability of satellite data processing. We proposed a kernel self-adaptive method based on Fisher Discriminant Analysis (FDA). Firstly map the data to high-dimensional space by kernel function. Then perform PCA in high-dimensional space. Finally classify data by Fisher Discriminant Analysis method. The selection of the kernel function and its parameters realized by self-adaptive method are based on the data. This method can achieve ideal classification accuracy toward satellite telemetry data according to our experiments. And the accuracy is stable when process data of same type. The performance of this method proved that it is reliable.
An Unsupervised Model with Attention Autoencoders for Question Retrieval

Question retrieval is a crucial subtask for community question answering. Previous research focus on supervised models which depend heavily on training data and manual feature engineering. In this paper, we propose a novel unsupervised framework, namely reduced attentive matching network (RAMN), to compute semantic matching between two questions. Our RAMN integrates together the deep semantic representations, the shallow lexical mismatching information and the initial rank produced by an external search engine. For the first time, we propose attention autoencoders to generate semantic representations of questions. In addition, we employ lexical mismatching to capture surface matching between two questions, which is derived from the importance of each word in a question. We conduct experiments on the open CQA datasets of SemEval-2016 and SemEval-2017. The experimental results show that our unsupervised model obtains comparable performance with the state-of-the-art supervised methods in SemEval-2016 Task 3, and outperforms the best system in SemEval-2017 Task 3 by a wide margin.
Expected and unexpected bond excess returns: Macroeconomic and market microstructure effects

This paper shows that order flow determines future bond excess returns. This effect cannot be captured by macroeconomic or forward rate information. To understand how these variables influence future bond excess returns, we decompose excess returns into expected and unexpected excess returns. Expected returns crucially depend on the available information set which is spanned by order flow, forward rates and macroeconomic variables. Thus, the predictability of bond excess returns stems from the strong linkage of expected excess returns to available economic information and order flow. The analysis of unexpected excess returns reveals contemporaneous order flow and changes of the economic environment as main drivers.
Severe osmotic compression triggers a slowdown of intracellular signaling, which can be explained by molecular crowding

Regulation of the cellular volume is fundamental for cell survival and function. Deviations from equilibrium trigger dedicated signaling and transcriptional responses that mediate water homeostasis and volume recovery. Cells are densely packed with proteins, and molecular crowding may play an important role in cellular processes. Indeed, increasing molecular crowding has been shown to modify the kinetics of biochemical reactions in vitro; however, the effects of molecular crowding in living cells are mostly unexplored. Here, we report that, in yeast, a sudden reduction in cellular volume, induced by severe osmotic stress, slows down the dynamics of several signaling cascades, including the stress-response pathways required for osmotic adaptation. We show that increasing osmotic compression decreases protein mobility and can eventually lead to a dramatic stalling of several unrelated signaling and cellular processes. The rate of these cellular processes decreased exponentially with protein density when approaching stalling osmotic compression. This suggests that, under compression, the cytoplasm behaves as a soft colloid undergoing a glass transition. Our results shed light on the physical mechanisms that force cells to cope with volume fluctuations to maintain an optimal protein density compatible with cellular functions.
An Experiment on the Sterilization Effects of Bamboo Vinegar

采用卫生部 有关条文进行试验,研究竹醋液的杀菌作用. 结果显示:在19～21℃下,1:4稀释液作用10 min,对大肠杆菌杀灭率为99. 98%;对金黄色葡萄球菌杀灭率为99. 98%;1:2稀释液作用20min,对白色念珠菌杀灭率为99. 96%. 说明竹醋液具杀菌作用.
Helical 3D‐Printed Metal Electrodes as Custom‐Shaped 3D Platform for Electrochemical Devices

3D‐printing represents an emerging technology that can revolutionize the way object and functional devices are fabricated. Here the use of metal 3D printing is demonstrated to fabricate bespoke electrochemical stainless steel electrodes that can be used as platform for different electrochemical applications ranging from electrochemical capacitors, oxygen evolution catalyst, and pH sensor by means of an effective and controlled deposition of IrO2 films. The electrodes have been characterized by scanning electrode microscopy and energy dispersive X‐ray spectroscopy before the electrochemical testing. Excellent pseudocapacitive as well as catalytic properties have been achieved with these 3D printed steel‐IrO2 electrodes in alkaline solutions. These electrodes also demonstrate Nernstian behavior as pH sensor. This work represents a breakthrough in on‐site prototyping and fabrication of highly tailored electrochemical devices with complex 3D shapes which facilitate specific functions and properties.
OCR Post-Processing Text Correction using Simulated Annealing (OPTeCA)

This paper describes the system details and results of team “EOF” from the University of Melbourne for the shared task of ALTA 2017, which addresses the problem of text correction for post-processed Optical Character Recognition (OCR) based systems. We developed a two stage sys-tem which ﬁrst detects errors in the given OCR post-processed text with the help of a support vector machine trained using given training dataset, followed by rectifying the errors by employing a conﬁdence-based mechanism using simulated annealing to obtain an optimal correction from a pool of candidate corrections. Our system achieved a F 1 -score of 32.98% on the private leaderboard 1 , which is the best score among all the participating systems.