Miracle-dz/UniFAR-FTUs huggingface dataset:
The Case of the Missing Ancient Fungal Polyploids

Polyploidy—the increase in the number of whole chromosome sets—is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events. Three hypotheses may explain this finding. First, ancient fungal polyploids are indeed rare, with unique aspects of fungal biology providing similar benefits without genome duplication. Second, fungal polyploids are not successful in the long term, leading to few extant species derived from ancient polyploidy events. Third, ancient fungal polyploids are difficult to detect, causing the real contribution of polyploidy to fungal evolution to be underappreciated. We consider each of these hypotheses in turn and propose that failure to detect ancient events is the most likely reason for the lack of observed ancient fungal polyploids. We examine whether existing data can provide evidence for previously unrecognized ancient fungal polyploidy events but discover that current resources are too limited. We contend that establishing whether unrecognized ancient fungal polyploidy events exist is important to ascertain whether polyploidy has played a key role in the evolution of the extensive complexity and diversity observed in fungi today and, thus, whether polyploidy is a driver of evolutionary diversifications across eukaryotes. Therefore, we conclude by suggesting ways to test the hypothesis that there are unrecognized polyploidy events in the deep evolutionary history of the fungi.
A Comparison of Hypothetical Phone and Mail Contingent Valuation Responses for Green-Pricing Electricity Programs

To date, much of the policy and research debate on contingent valuation mode effects has relied on experiences drawn from other research disciplines. This study provides the first contingent valuation phone-mail comparison that meets current standards for response rates, draws from a general population, is relevant to the valuation of general environmental goods, and allows comparisons with actual sign-ups. Consistent with previous research in other disciplines, social desirability bias is found in responses to subjective questions --thus leading to more environmentally favorable responses on the phone. However, this effect does not carry over to hypothetical participation decisions. Hypothetical bias is found in both modes. Yet, application of calibration methods using debriefing questions provided nearly identical values across modes. As such, neither mode appears to dominate from the perspective of providing more valid estimates of actual participation decisions. The selection of survey mode must be based on other criteria.
Fast image stitching method for handling dynamic object problems in Panoramic Images

The construction of panoramic images on smartphones and low-powered devices is a challenging task. In this paper, we propose a new approach for smoothly stitching images on mobile phones in the presence of moving objects in the scene. Our main contributions include handling moving object problems, reducing processing time, and generating rectangular panoramic images. First, unique and robust feature points are extracted using fast ORB method and a feature matching technique is applied to match the extracted feature points. After obtaining good matched feature points, we employ the non-deterministic RANSAC algorithm to discard wrong matches, and the hommography transformation matrix parameters are estimated with the algorithm. Afterward, we determine precise overlap regions of neighboring images and calculate their absolute differences. Then, thresholding operation and noise removal filtering are applied to create a mask of possible moving object regions. Sequentially, an optimal seam is estimated using dynamic programming algorithm, and a combination of linear blending with the mask information is applied to avoid seam transition and ghosting artifacts. Finally, image-cropping operation is utilized to obtain a rectangular boundary image from the stitched image. Experiments demonstrate that our method is able to produce panoramic images quickly despite the existence of moving objects.
Optimal Allocation Strategy Based on Stackelberg Game for Inspecting Drunk Driving on Traffic Network

As the main means to cope with the stubborn problem of drunk driving, the inspection of drunk driving has already been paid more attention and thus reinforced. In this paper, we model this scenario as a Stackelberg game, where the police department (called defender) allocates resources dynamically in terms of the traffic situation on the traffic network to arrest drink drivers and drivers who drink (called attacker), whether choosing drunk driving or designated driving service, expect to minimize their cost for given travel routes. However, with the number of resources are limited, our goal is to calculate the optimal resource allocation strategy for the defender. Therefore, first, we provide an effective approach (named OISDD) to fulfill our goal, i.e., generate the optimal strategy to inspect drunk driving. Second, we apply OISDD to directed graphs (which are abstracted from Dalian traffic network) to analyze and test its correctness and rationality. The experimental results show that OISDD is feasible and efficient.
Structural Analysis Reveals the Deleterious Effects of Telomerase Mutations in Bone Marrow Failure Syndromes*

Naturally occurring mutations in the ribonucleoprotein reverse transcriptase, telomerase, are associated with the bone marrow failure syndromes dyskeratosis congenita, aplastic anemia, and idiopathic pulmonary fibrosis. However, the mechanism by which these mutations impact telomerase function remains unknown. Here we present the structure of the human telomerase C-terminal extension (or thumb domain) determined by the method of single-wavelength anomalous diffraction to 2.31 Å resolution. We also used direct telomerase activity and nucleic acid binding assays to explain how naturally occurring mutations within this portion of telomerase contribute to human disease. The single mutations localize within three highly conserved regions of the telomerase thumb domain referred to as motifs E-I (thumb loop and helix), E-II, and E-III (the FVYL pocket, comprising the hydrophobic residues Phe-1012, Val-1025, Tyr-1089, and Leu-1092). Biochemical data show that the mutations associated with dyskeratosis congenita, aplastic anemia, and idiopathic pulmonary fibrosis disrupt the binding between the protein subunit reverse transcriptase of the telomerase and its nucleic acid substrates leading to loss of telomerase activity and processivity. Collectively our data show that although these mutations do not alter the overall stability or expression of telomerase reverse transcriptase, these rare genetic disorders are associated with an impaired telomerase holoenzyme that is unable to correctly assemble with its nucleic acid substrates, leading to incomplete telomere extension and telomere attrition, which are hallmarks of these diseases.
SPARQLtoUser: Did the Question Answering System Understand me?

In Question Answering (QA) systems, user questions are automatically converted into SPARQL queries. We present SPARQLtoUser, a simple method to produce a user understandable version of a SPARQL query so that the users can check what the QA system understood. Compared to existing similar methods, SPARQLtoUser is multilingual and is not restricted to one single KB, but easily portable to any KBs. This paper presents our method to generate the representation of SPARQL queries, and compares this method to existing ones. Moreover, we present the results of our user study that show that users have difficulties to understand whether the responses of a QA system are correct or not, with or without SPARQL representations.
Graph Regularized Meta-path Based Transductive Regression in Heterogeneous Information Network

A number of real-world networks are heterogeneous information networks, which are composed of different types of nodes and links. Numerical prediction in heterogeneous information networks is a challenging but significant area because network based information for unlabeled objects is usually limited to make precise estimations. In this paper, we consider a graph regularized meta-path based transductive regression model (Grempt), which combines the principal philosophies of typical graph-based transductive classification methods and transductive regression models designed for homogeneous networks. The computation of our method is time and space efficient and the precision of our model can be verified by numerical experiments.
Using Conversation Topics for Predicting Therapy Outcomes in Schizophrenia

Previous research shows that aspects of doctor-patient communication in therapy can predict patient symptoms, satisfaction and future adherence to treatment (a significant problem with conditions such as schizophrenia). However, automatic prediction has so far shown success only when based on low-level lexical features, and it is unclear how well these can generalize to new data, or whether their effectiveness is due to their capturing aspects of style, structure or content. Here, we examine the use of topic as a higher-level measure of content, more likely to generalize and to have more explanatory power. Investigations show that while topics predict some important factors such as patient satisfaction and ratings of therapy quality, they lack the full predictive power of lower-level features. For some factors, unsupervised methods produce models comparable to manual annotation.
A study of the learning curve for robotic oesophagectomy for oesophageal cancer†

OBJECTIVES Robot-assisted minimally invasive oesophagectomy (RAMIE) enables radical, meticulous dissection of the oesophagus and lymph nodes. Our goal was to identify the effect of the learning curve for RAMIE when performing radical upper mediastinal dissection in patients with oesophageal cancer. METHODS We conducted a retrospective review of a prospectively maintained database of patients who underwent RAMIE for oesophageal cancer between May 2008 and July 2016. The gain in proficiency for each postoperative outcome measure was presented using observed-expected cumulative sum (O-E CUSUM) curves. The change points were defined at the maximal distance from the zero axis. RESULTS A total of 140 patients were included. Squamous cell carcinoma (n = 131, 93.6%) was the dominant type. Thirty-day and 90-day deaths occurred in 1 and 5 patients (0.7% and 3.6%, respectively). The change points of the risk-adjusted O-E CUSUM curves were similar to those of the unadjusted O-E CUSUM curves with the exception of those for thoracic procedure time and vocal cord palsy. The number of harvested lymph nodes increased from 25 to 45 before and after 30 cases. The vocal cord palsy rate decreased from 36% to 17% before and after 60 cases. The total operation time decreased from 496 min to 431 min; the length of the hospital stay decreased from 24 days to 14 days; and the anastomotic leakage rate decreased from 15% to 2% before and after 80 cases. CONCLUSIONS Our study demonstrated a temporal improvement in postoperative outcomes based on accumulated experience with RAMIE. The risk-adjusted O-E CUSUM curves were similar to the unadjusted O-E CUSUM curves, which represents the significant impact of the effect of a learning period on the postoperative outcomes of RAMIE in patients with oesophageal cancer.
Modalities for Detection of LV Dysfunction

Abstract The left ventricular ejection fraction (LVEF) assessed by trans-thoracic Echocardiogram (TTE) remains the most common parameter of LV performance that is used in clinical practice. Three-dimensional / volumetric methods are more accurate, but are cumbersome to be performed in every case. The measures of myocardial contractility are more sensitive, reliable and with lesser inter observer variability but their place in daily practice is limited. Two-dimensional echocardiogram has the advantages of easy availability, low cost, portability, lack of radiation and non-invasive nature. Radionuclide studies, SPECT, cardiac CT and cardiac MRI are available only in a few centers and have more specific indication to be performed. The choice of a modality depends on the information sought by the clinician and the availability of expertise. Additional cost, radiation and limited access are important limitations of these special imaging modalities. The invasive methods which were popular a few decades back are by and large relegated to academic exercise.
Particle swarm optimization for integrity monitoring in BDS/DR based railway train positioning

Satellite navigation system, especially the BeiDou Navigation Satellite System (BDS), has become a significant resource for many transport branches. It is strongly required that BDS is applied in modern railway transportation systems to support the rapid development of Chinese railway infrastructure and services. Currently, the BDS is still in the developing period, and the existing resources are not sufficient to support integrity assurance for many safety-related railway applications. The aim of this paper is therefore to develop a novel integrity monitoring method for the BDS-based train positioning with assistance from the additional dead reckoning system. In this method, the raw measurements of sensors are fused with the Bayesian filtering, and the self-weight adaptive particle swarm optimization with a combined objective function is involved to achieve an effective solution for the horizontal protection level which indicates the integrity capability. Field data are taken to validate effectiveness of the proposed solution and the advantages of the integrated particle fitness strategy. The implementation of this method will be positive for realizing fault detection and isolation for a series of safety-related railway applications based on BDS.
16-831 Final Report : Online Anomaly Detection in Videos

This project address the problem of detecting interesting or anomalous frames in lengthy surveillance videos in an online unsupervised manner. The motivation of this project is based on the fact that long stretches of video are becoming a prevalent data source. It is estimated that there are 210 million cameras in use today, generating over 1 billion gigabytes of data per day [1]. These lengthy videos pose a challenge for anomaly frame detections because first, it is difficult to acquire ground truth labels for the hours long lengthy videos for anomaly detection. Second, labeled anomalous frames may not be beneficial for test-time predictions since new anomalies tend to differ from known scenes. Third, anomaly frames are rare, making training data highly imbalanced. Last, learning with video data is difficult because of the dataset size. To meet these challenges we explore online unsupervised learning methods for anomaly detection. In this work we aim to form models of normality and use them to detect anomalous, or novel, frames.
Measuring Habitual Physical Activity in Neuromuscular Disorders: A Systematic Review

Background: Free-living or habitual physical activity (HPA) refers to someone’s performance in his or her free-living environment. Neuromuscular disorders (NMD) manifest through HPA, and the observation of HPA can be used to identify clinical risks and to quantify outcomes in research. This review summarizes and analyses previous studies reporting the assessment of HPA in NMD, and may serve as the basis for evidence-based decision-making when considering assessing HPA in this population. Methods: A systematic review was performed to identify all studies related to HPA in NMD, followed by a critical appraisal of the assessment methodology and a final review of the identified HPA tools. Results: A total of 22 studies were selected, reporting on eight different direct tools (or activity monitors) and ten structured patient-reported outcomes. Overall, HPA patterns in NMD differ from healthy control populations. There was a noticeable lack of validation studies for these tools and outcome measures in NMD. Very little information regarding feasibility and barriers for the application of these tools in this population have been published. Conclusions: The variety and heterogeneity of tools and methods in the published literature makes the comparison across different studies difficult, and methodological guidelines are warranted. We propose a checklist of considerations for the assessment and reporting of HPA in NMD.
Localized Marked Elongation of the Distal Internal Carotid Artery with or without PHACE Syndrome: Segmental Dolichoectasia of the Distal Internal Carotid Artery

Intracranial dolichoectasia of the distal ICA was identified in 20 patients from 2005–2016 through a review of diagnostic cerebral angiography results. Images were reviewed to determine the vascular morphologic dispositions around the distal ICA, including dysplasia, mural calcification, vessel wall enhancement, lumen narrowing, and aneurysm formation. In this cohort, which had a strong female predominance (male/female ratio2:18), intracranial dolichoectasia had a more ipsilateral vascular morphologic disposition. Mural calcification was detected more frequently in elderly patients, whereas vessel wall enhancement was detected more frequently in younger patients. Follow-up images showed a slow progression of the lesions. The segmental nature of the striking elongation and tortuosity of the distal ICA suggest a type of congenital lesion representing either a sporadic phenomenon or an arterial change associated with PHACE syndrome. BACKGROUND AND PURPOSE: Segmental intracranial dolichoectasia of the distal ICA is a feature of PHACE syndrome or a sporadic phenomenon. We evaluated the relationship between intracranial dolichoectasia of the distal ICA and PHACE syndrome and illustrated the characteristic radiologic findings of the lesions. MATERIALS AND METHODS: Intracranial dolichoectasia of the distal ICA was identified in 20 patients at our institution from 2005 to 2016 through a review of diagnostic cerebral angiography results. All radiologic images were reviewed to determine the vascular morphologic dispositions around the distal ICA, including dysplasia, mural calcification, vessel wall enhancement, lumen narrowing, and aneurysm formation. Medical records were reviewed to determine the symptoms of PHACE syndrome. Subsequently, the correlation between radiologic findings and PHACE syndrome was assessed. RESULTS: In this cohort, which had a strong female predominance (male/female ratio= 2:18), intracranial dolichoectasia had a more ipsilateral vascular morphologic disposition. Mural calcification was detected more frequently in elderly patients, whereas vessel wall enhancement was detected more frequently in younger patients. Follow-up images showed a slow progression of the lesions. However, no significant differences in the vascular morphologic disposition and brain structural changes were observed between patients with (n = 11) and without (n = 9) PHACE syndrome. CONCLUSIONS: The striking elongation and tortuosity of the distal ICA generally appeared to be a type of congenital lesion occurring early in embryogenesis as either a sporadic phenomenon or an arterial change associated with PHACE syndrome. Imaging findings revealed various mural abnormalities with a benign clinical course.
SOLVED AND UNSOLVED PROBLEMS IN ADAPTIVE BLIND EQUALIZATION

This paper presents some results and conjectures dealing with channel equalization. For several possible equalizers, the following question is considered: if the equalizer output sequence has identical statistics to the input signal sequence, has the equalizer correctly converged? 1. THE PROBLEM DOMAIN Many communication signal processing problems envisage a transmitted sequence a0 a1, . drawn from a finite signal alphabet, with passage of that sequence through a linear channel which produces intersymbol interference in the channel output sequence, call it {bk}. There is then possible addition of noise, followed by processing of bk to try to undo the effects of the channel, through a device termed an equalizer. The equalizer output {âk} is supposed to reconstruct the signal alphabet, eg âk=ak-δ for some fixed integer δ and all k. Many equalizers need to be adaptive, and often also blind, ie not even a training sequence of known {ak} is provided to allow equalization. In the blind case, adaptive equalizers rely either on being close to correct to begin with (eg open eye diagram) or computing certain statistics which are used to guide changes in equalizer parameters, such as in Godard blind equalizers [1] and decision directed equalizers [2]. When the parameters or taps in a blind adaptive equalizer settle down, ie cease making gross movements and remain in the neighbourhood of some point, it is reasonable to ask the question: has convergence occurred to a correct point. Such questions can be subtle. For example, for the Godard equalizers, with an infinite number of taps, the existence of incorrect equilibria was demonstrated in [1], but they were shown to be unstable (and thus irrelevant) in [3]. However, with finite equalizer length, stable undesirable equilibria were shown to exist in [4] (and with an 11 year interval from [1] to [4]). In this paper we study the issue of establishing whether convergence for certain equalizers has occurred, given that the equalizer output sequence has the same statistics as the signal sequence. The equalizers are decision directed and decision feedback equalizers, embodying linear system processing together with quantization. 2. DECISION DIRECTED EQUALIZERS The behaviour of decision directed equalizers after adaptation can often be described in the following way. The channel input sequence {ak} is a sequence of independent random variables taking values in an M-ary alphabet, with equal probability. We shall, for convenience, assume M=2, and ak ∈ {±1}. The channel impulse response is {d0, d1. }. In the absence of noise, the channel output is b d a k l l k l = = ∞
TCR-based lineage tracing: no evidence for conversion of conventional into regulatory T cells in response to a natural self-antigen in pancreatic islets

Foxp3-expressing regulatory T (T reg) cells derive primarily from selection in the thymus. Yet conversion of mature conventional CD4+ T (T conv) cell lymphocytes can be achieved in several conditions, such as transforming growth factor β treatment, homeostatic expansion, or chronic exposure to low-dose antigen. Such conversion might provide a means to generate peripheral tolerance by “converting” potentially damaging T cells that react to self-antigens. We tested this hypothesis in mice transgenic for the BDC2.5 T cell receptor (TCR), which is representative of a diabetogenic specificity that is naturally present in NOD mice and reactive against a pancreatic self-antigen. In the thymus, before any exposure to antigen, clonotype-positive T reg and T conv cells express a second TCRα chain derived from endogenous loci. High-throughput single-cell sequencing of secondary TCRs of the Vα2 family showed their joining CDR3α regions to be very different in T reg and T conv cell thymocytes. These specific CDR3α motifs, thus, provided a “tag” with which to test the actual impact of T conv to T reg cell conversion in response to peripheral self-antigen; should the autoreactive clonotypic TCR induce T conv to T reg cell conversion upon encounter of cognate antigen in the pancreas or draining lymph node, one would expect to detect tag CDR3α motifs from T conv cells in the T reg cell populations. Sequencing large numbers of peripheral BDC+Vα2+ cells showed that little to no conversion occurs in response to this pancreatic autoantigen.