Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of Human Immunodeficiency Virus Type 1 Recombination Ex Vivo Provide Evidence for Coadaptation of Distant Sites, Resulting in Purifying Selection for Intersubtype Recombinants during Replication

ABSTRACT High-frequency recombination is a hallmark of HIV-1 replication. Recombination can occur between two members of the same subtype or between viruses from two different subtypes, generating intra- or intersubtype recombinants, respectively. Many intersubtype recombinants have been shown to circulate in human populations. We hypothesize that sequence diversity affects the emergence of viable recombinants by decreasing recombination events and reducing the ability of the recombinants to replicate. To test our hypothesis, we compared recombination between two viruses containing subtype B pol genes (B/B) and between viruses with pol genes from subtype B or F (B/F). Recombination events generated during a single cycle of infection without selection pressure on pol gene function were analyzed by single-genome sequencing. We found that recombination occurred slightly (∼30%) less frequently in B/F than in B/B viruses, and the overall distribution of crossover junctions in pol was similar for the two classes of recombinants. We then examined the emergence of recombinants in a multiple cycle assay, so that functional pol gene products were selected. We found that the emerging B/B recombinants had complex patterns, and the crossover junctions were distributed throughout the pol gene. In contrast, selected B/F recombinants had limited recombination patterns and restricted crossover junction distribution. These results provide evidence for the evolved coadapted sites in variants from different subtypes; these sites may be segregated by recombination events, causing the newly generated intersubtype recombinants to undergo purifying selection. Therefore, the ability of the recombinants to replicate is the major barrier for many of these viruses.
A Novel Frequency-Domain Implementation of Tomlinson-Harashima Precoding for SC-FDMA

There is considerable interest in the use of Single Carrier Frequency Division Multiple Access (SC-FDMA) as the uplink transmission scheme in the 3GPP Long Term Evolution standard. This interest is justified by the inherent single carrier structure of SC-FDMA, which results in reduced sensitivity to phase noise and a lower Peak-to-Average Power Ratio (PAPR) compared to Orthogonal Frequency Division Multiple Access. This, consequently, makes it more attractive for low cost devices with limited transmit power. In this paper we demonstrate how precoding the uplink transmission is an alternative signal processing technique to equalization in order to combat the frequency selective nature of the propagation channel. The frequency-domain implementation of Tomlinson-Harashima Pre- coding (THP) for uplink SC-FDMA is proposed. We investigate the BER performance and the PAPR characteristics of the precoded SC-FDMA waveform for ZF and MMSE based THP. Results reported here show that the MMSE-THP outperforms the ZF-THP in terms of BER performance and PAPR. Index Terms: 3GPP LTE, SC-FDMA, Tomlinson-Harashima Pre- coding, PAPR, Equalization.
Geometric morphometric analysis as a proxy to evaluate age‐related change in molar shape variation of low‐crowned Notoungulata (Mammalia)

Shape and age variation in dentition of Paleogene extinct native South American ungulates (Notoungulata) has been traditionally described using qualitative and quantitative approaches, and has played a controversial role in the systematics of several groups. Such is the case of the Notopithecidae, a group of notoungulates with low‐crowned teeth, known from the middle Eocene of Patagonia (Argentina). In this group, as well as in other contemporary families, extreme morphological changes associated to increasing dental wear were originally assumed to represent taxonomic differences; thus, dozens of species were erected, clearly reflecting the difficulty of defining discrete characters. In this contribution, a total of 89 upper molars and 91 lower molars were analyzed distributed in two factors, wear and species; three species of notopithecids were considered as study case, Notopithecus adapinus, Antepithecus brachystephanus, and Transpithecus obtentus, based on the large and well‐identified sample of upper and lower molars for each species. We have coupled geometric morphometric analyses with traditional comparative methods to get a better understanding and interpretation of both the changes in tooth shape contour and the link between shape and ontogeny. In addition, we evaluate the utility of this approach to identify which changes are strictly wear‐related and also test the qualitative characteristics used for diagnosing and differentiating notopithecid species. Our study yielded consistent results when applying independent geometric morphometric analyses on complex structures such as brachydont molar teeth. The landmark data is highly congruent with alternative sources of evidence, such as morphological studies using discrete characters. In notopithecid species, wear is the main factor affecting molar shape, followed by species (in lower molars) and allometry; in addition, lower teeth morphology is more definitive in separating species than upper molars, a fact that entails a key point for systematic studies of Paleogene brachydont notoungulates.
A systematic map of data analytics in breast cancer

Data mining or Data Analytics is a set of techniques that allows to analyzing data from different perspectives and summarizing it into useful information. It is the process of finding correlations or patterns in large historical datasets. It can be applied in almost any field ranging from business to education, then to medicine. Data mining has been increasingly used in medicine, especially in oncology. Breast cancer (BC) becomes the most common cancer among females worldwide and the leading cause of death in developed countries. Many studies have attempted to apply Data mining techniques to detect survivability of cancers in human beings. This paper aims to perform a systematic mapping study to analyze and synthesize studies on the application of Data mining techniques in breast cancer. 403 articles published between 2000 and 2016 were therefore selected and analyzed according to five criteria: year and channel of publication, research type, medical task, empirical type and DM techniques. Results show that conferences and journals are the most publication venues, researchers were more interested in applying DM techniques for diagnosis of BC, historical based evaluation was the empirical type of studies most used in the evaluation of DM techniques in BC, and classification was the most investigated task of DM in BC.
Semantic Analysis of Field Sports Video using a Petri-Net of Audio-Visual Concepts

The most common approach to automatic summarization and highlight detection in sports video is to train an automatic classifier to detect semantic highlights based on occurrences of low-level features such as action replays, excited commentators or changes in a scoreboard. We propose an alternative approach based on the detection of perception concepts (PCs) and the construction of Petri-Nets, which can be used for both semantic description and event detection within sports videos. Low-level algorithms to detect PCs using visual, aural and motion characteristics are proposed, and a series of Petri-Nets composed of PCs is formally defined to describe video content. We call this a perception concept network–Petri-Net (PCN–PN) model. Using PCN–PNs, personalized high-level semantic descriptions of video highlights can be facilitated and queries on high-level semantics can be achieved. A particular strength of this framework is that we can easily build semantic detectors based on PCN–PNs to search within sports videos and locate interesting events. Experimental results based on recorded sports video data across three types of sports games (soccer, basketball and rugby), and each from multiple broadcasters, are used to illustrate the potential of this framework.
Risk factors associated with struvite urolithiasis in dogs evaluated at general care veterinary hospitals in the United States.

OBJECTIVE To identify factors associated with development of struvite urolithiasis in dogs evaluated at general care veterinary hospitals in the United States. DESIGN Retrospective case-control study. ANIMALS 508 dogs with a first-time diagnosis of struvite urolithiasis and 7,135 control dogs. PROCEDURES Electronic medical records of all dogs evaluated at 787 general care veterinary hospitals in the United States between October 2007 and December 2010 were reviewed to identify dogs that developed struvite urolithiasis and 2 groups of control dogs with no history of urolithiasis. Information extracted included diet, age, sex, neuter status, breed size category, hospital location, and date of diagnosis. Urinalysis results, urolith composition, and other disease conditions were recorded if applicable. Potential risk factors were assessed with univariable and multivariable regression analysis. RESULTS Toy- or small-sized breeds had significantly greater odds of struvite urolithiasis, compared with medium- or large-sized breeds. Neutering significantly increased the odds of this outcome in females only; sexually intact females were more likely to develop struvite urolithiasis than were sexually intact males, but only up to 5 years of age. Urinary factors significantly associated with the outcome were basic (vs acidic) pH, presence of RBCs or WBCs, protein concentration > 30 mg/dL, and ketone concentration ≥ 5 mg/dL. CONCLUSIONS AND CLINICAL RELEVANCE Evaluation of demographic characteristics and urinalysis results may be useful in the early identification of struvite urolithiasis in dogs. Periodic urinalysis in dogs is recommended because of the potential health impact of a late diagnosis of urolithiasis.
Outsourcing network functionality

This paper presents an architecture for adding functionality to networks via outsourcing. In this model, the enterprise network only forwards data; any additional processing is performed by external Feature Providers (FPs). FPs provide and manage features, scaling and moving them in response to customer demand, and providing automated recovery in case of failure. Benefits to the enterprise include reduced cost and management complexity, improved features through FP specialization, and increased choice in services. Central to the model are a policy component and a Feature API (FAPI). Policy is specified with features not locations, enabling features to be located anywhere. FAPI enables communication between enterprise and FP control planes to share policy and configure features. We have built a prototype implementation of this architecture called Jingling. Our prototype system incorporates a nation-wide backbone network and FPs located in six sites around the United States.
A new model for Cerebellar computation

The standard state space model is widely believed to account for the cerebellar computation in motor adaptation tasks [1]. Here we show that several recent experiments [2-4] where the visual feedback is irrelevant to the motor response challenge the standard model. Furthermore, we propose a new model that accounts for the the results presented in [2-4]. According to this new model, learning and forgetting are coupled and are error size dependent. We also show that under reasonable assumptions, our proposed model is the only model that accounts for both the classical adaptation paradigm as well as the recent experiments [2-4].
The Variegated Landscape of Local Immigration Policies in the United States

Hundreds of municipalities and counties across the United States have proposed or implemented immigration policies at the local level, ranging from "sanctuary" policies to those designed to exclude undocumented immigrants. Data collected on these policies are presented, and statistically analyzed at the municipal level to interrogate existing hypotheses about factors driving these policy decisions. Municipalities experiencing rapid growth of their foreign-born population and with a high percentage of owner-occupied housing are more likely to introduce exclusionary policies, whereas municipalities with better educated populations are more likely to adopt inclusionary policies. The location of municipalities in the U.S. South and outside central cities is also associated with exclusionary policies. Textual analysis of policy documents for selected municipalities provides insight into why similarly located places adopt contrasting policies. Local ordinances reflect contrasting local imaginaries of race, nation, and place.
Interpretable Machine Teaching via Feature Feedback

A student’s ability to learn a new concept can be greatly improved by providing them with clear and easy to understand explanations from a knowledgeable teacher. However, many existing approaches for machine teaching only give a limited amount of feedback to the student. For example, in the case of learning visual categories, this feedback could be the class label of the object present in the image. Instead, we propose a teaching framework that includes both instance-level labels as well as explanations in the form of feature-level feedback to the human learners. For image categorization, our feature-level feedback consists of a highlighted part or region in an image that explains the class label. We perform experiments on real human participants and show that learners that are taught with feature-level feedback perform better at test time compared to existing methods.
Evolution of the Internet and its measures

The Internet has being growing rapidly with the development of technique. Understanding the evolution of Internet is essential to the Internet security. there has been some studies on the evolution of Internet, which only analyze the change of the Internet during a quiet short period. In this paper, we have roughly analyzed the evolution of the Internet for last 20 years and take days as the granularity of time. Some important measures, such as average-distance and average-node-degree, have been analyzed. Our findings show that the growth of Internet is nearly binomial and the evolution of Internet can be divided into 3 different phases. Moreover, these findings can be used to model the evolution of Internet which would help us to better protect network security.
Influence of black carbon and chemical planarity on bioavailability of sediment‐associated contaminants

Black carbon (BC) and chemical properties may play a significant role in defining the bioavailability of hydrophobic organic compounds (HOCs) in sediment. In the current study, bioavailability of four HOCs with differing planarity was determined in sediments amended with two types of BC (soot and charcoal) at different concentrations by matrix solid‐phase microextraction (matrix‐SPME) and bioaccumulation testing using the freshwater oligochaete Lumbriculus variegatus. Furthermore, the applicability of the matrix‐SPME method to bioavailability estimation in BC‐amended sediment was tested. The charcoal treatment significantly reduced the bioaccumulation of the planar compounds (3,3′,4,4′‐tetrachlorobiphenyl and benzo[a]pyrene) in L. variegatus, and the matrix‐SPME method showed a similar trend as contaminant bioaccumulation in L. variegatus. Conversely, manipulation of sediment with soot had no effect or slightly increased bioavailability of the planar compounds in both bioaccumulation and matrix‐SPME tests. Little if any affect was noted in bioavailability of the nonplanar compounds (2,2′,4,4′,5,5′‐hexachlorobiphenyl and permethrin) with the soot and charcoal amendments. Results showed that the role of BC in defining bioavailability of HOCs depends not only on the type and concentrations of BC present, but also the planarity of the HOCs. Environ. Toxicol. Chem. 2010;29:1976–1983. © 2010 SETAC
The Incremental Value of Subjective and Quantitative Assessment of 18F-FDG PET for the Prediction of Pathologic Complete Response to Preoperative Chemoradiotherapy in Esophageal Cancer

A reliable prediction of a pathologic complete response (pathCR) to chemoradiotherapy before surgery for esophageal cancer would enable investigators to study the feasibility and outcome of an organ-preserving strategy after chemoradiotherapy. So far no clinical parameters or diagnostic studies are able to accurately predict which patients will achieve a pathCR. The aim of this study was to determine whether subjective and quantitative assessment of baseline and postchemoradiation 18F-FDG PET can improve the accuracy of predicting pathCR to preoperative chemoradiotherapy in esophageal cancer beyond clinical predictors. Methods: This retrospective study was approved by the institutional review board, and the need for written informed consent was waived. Clinical parameters along with subjective and quantitative parameters from baseline and postchemoradiation 18F-FDG PET were derived from 217 esophageal adenocarcinoma patients who underwent chemoradiotherapy followed by surgery. The associations between these parameters and pathCR were studied in univariable and multivariable logistic regression analysis. Four prediction models were constructed and internally validated using bootstrapping to study the incremental predictive values of subjective assessment of 18F-FDG PET, conventional quantitative metabolic features, and comprehensive 18F-FDG PET texture/geometry features, respectively. The clinical benefit of 18F-FDG PET was determined using decision-curve analysis. Results: A pathCR was found in 59 (27%) patients. A clinical prediction model (corrected c-index, 0.67) was improved by adding 18F-FDG PET–based subjective assessment of response (corrected c-index, 0.72). This latter model was slightly improved by the addition of 1 conventional quantitative metabolic feature only (i.e., postchemoradiation total lesion glycolysis; corrected c-index, 0.73), and even more by subsequently adding 4 comprehensive 18F-FDG PET texture/geometry features (corrected c-index, 0.77). However, at a decision threshold of 0.9 or higher, representing a clinically relevant predictive value for pathCR at which one may be willing to omit surgery, there was no clear incremental value. Conclusion: Subjective and quantitative assessment of 18F-FDG PET provides statistical incremental value for predicting pathCR after preoperative chemoradiotherapy in esophageal cancer. However, the discriminatory improvement beyond clinical predictors does not translate into a clinically relevant benefit that could change decision making.
High-Frequency Illegitimate Strand Transfers of Nascent DNA Fragments During Reverse Transcription Result in Defective Retrovirus Genomes

Background:Two strand transfers of nascent DNA fragments during reverse transcription are required for retrovirus replication. However, whether strand transfers occur at illegitimate sites and how this may affect retrovirus replication are not well understood. Methods:The reverse transcription was carried out with reverse transcriptases (RTs) from HIV-1, HIV-2, and murine leukemia virus. The nascent complementary DNA fragments were directly cloned without polymerase chain reaction amplification. The sequences were compared with the template sequence to determine if new sequences contained mismatched sequences caused by illegitimate strand transfers. Results:Among 1067 nascent reverse transcript sequences, most of them (72%) matched to the template sequences, although they randomly stopped across the RNA templates. The other 28% of them contained mismatched 3′-end sequences because of illegitimate strand transfers. Most of the illegitimate strand transfers (81%) were disassociated from RNA templates and realigned onto opposite complementary DNA strands. Up to 3 strand transfers were detected in a single sequence, whereas most of them (93%) contained 1 strand transfer. Because most of the illegitimate strand-transfer fragments were generated from templates at 2 opposite orientations, they resulted in defective viral genomes and could not be detected by previous methods. Further analysis showed that mutations at pause/disassociation sites resulted in significantly higher strand-transfer rates. Moreover, illegitimate strand-transfer rates were significantly higher for HIV-2 RT (38.2%) and murine leukemia virus RT (44.6%) than for HIV-1 RT (5.1%). Conclusions:Illegitimate strand transfers frequently occur during reverse transcription and can result in a large portion of defective retrovirus genomes.
Selecting attentive frames from visually coherent video chunks for surveillance video summarization

This paper investigates how to extract key-frames from surveillance video while maximizing their diversity and representational ability. We solve this problem by two steps, i.e., video partition and frame selection. The first step is to partition a surveillance video into visually coherent video chunks, which have high intra-chunk similarity and interchunk dissimilarity. In particular, we propose an object-based frame metric to measure the relevance of two frames, and apply the Normalized Cut algorithm to achieve video partition. The second step is to select the attentive frames from the partitioned video chunks. We propose an attention score based on the content completeness and the visual satisfaction for each frame, and select most attentive frame with highest attention score in each chunk. Extensive experiments on both public and our newly created datasets suggest that our approach significantly outperforms other video summarization methods.
Effects of a Short-Term Conditioning Intervention on Knee Flexor Sensorimotor and Neuromuscular Performance in Men.

CONTEXT Long-term conditioning programs for enhanced sensorimotor performance have been causally linked to reduced risk of serious ligamentous injury. However, the efficacy of brief, short-term conditioning interventions has not been established. OBJECTIVE To assess the effects of short-term sensorimotor conditioning on the knee flexors. DESIGN Randomized controlled trial. SETTING University research laboratory. PARTICIPANTS 23 males randomly assigned to conditioning (n = 12; age: 20.5 ± 1.8 y; height: 1.80 ± 0.05 m; body mass: 74.3 ± 6.0 kg [mean ± SD]) and no-conditioning control (n = 11; age: 20.6 ± 1.9 y; height: 1.79 ± 0.05 m; body mass: 73.6 ± 6.3 kg) groups. INTERVENTION Sensorimotor conditioning of the nondominant leg (4 sessions/wk; 3 wk). MAIN OUTCOME MEASURES Sensorimotor (blind force and limb-position-replication errors) and neuromuscular (peak force, electromechanical delay [volitional and magnetically evoked]) performance of the knee flexors of both legs were assessed. The contralateral limb and an antecedent period of no conditioning were controls. RESULTS The conditioned leg showed decreased force error to 3.8% (3.8 ± 6.9% vs 6.3 ± 3.7% [mean ± SD], post- vs preconditioning, respectively; F1,21 = 5.4; P = .04) and a trend toward decreased positional error to 2.0% (2.0 ± 6.9% vs 4.7 ± 7.7%, post- vs preconditioning; F1,21 = 2.7; P = .06). Performances were not altered in the control conditions. Modest improvements were noted for volitional electromechanical delay following conditioning (39.8 ± 4.3 ms vs 42.3 ± 5.2 ms [F1,21 = 7.2; P = .01]), but peak force (overall, 202 ± 78 N) and magnetically evoked electromechanical delay (24.7 ± 4.2 ms) were not influenced. CONCLUSION Short-term conditioning offered improved sensorimotor performance and positively affected neuromuscular determinants of knee flexor performance in men.