Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative study of antiretroviral drug regimens and drug–drug interactions between younger and older HIV-infected patients at a tertiary care teaching hospital in South Korea

Background With the advent of combination antiretroviral therapy (ART), people living with HIV have lived to older age. So they have experienced age-related illnesses and have taken non-antiretroviral (ARV) medications to manage these illnesses. The aims of this study were to investigate the use patterns of ARV agents in HIV-positive patients by age and to evaluate potential or contraindicated drug–drug interactions (DDIs) between ARV and non-ARV. Methods This study was retrospectively conducted with HIV-infected patients receiving ART medications between October 2011 and September 2017 at Chonbuk National University Hospital in South Korea. Data were collected by reviewing patients’ electronic medical charts. Results Among 207 patients diagnosed with HIV infection, 183 (86.9% males; 104 aged <50 years and 79 aged ≥50 years) were selected based on inclusion criteria. In 2017, the most frequently prescribed ART regimen was nucleoside reverse transcriptase inhibitors (NRTIs)/integrase strand transfer inhibitors (INSTIs; total, 66.3%; <50 years, 36.3%; ≥50 years, 30.0%) followed by NRTIs/protease inhibitors (PIs; total, 23.8%; <50 years, 15.0%; ≥50 years, 8.8%). In 2017, the most frequently prescribed NRTI combination was abacavir/lamivudine (total, 34.4%; <50 years, 20.6%; ≥50 years, 13.8%) followed by tenofovir alafenamide/emtricitabine (FTC; total, 31.3%; <50 years, 16.3%; ≥50 years, 15.0%) and tenofovir disoproxil fumarate/FTC (total, 28.1%; <50 years, 16.9%; ≥50 years, 11.3%). In 2017, elvitegravir (EVG)/cobicistat (COBI; total, 57.1%; <50 years, 30.4%; ≥50 years, 26.8%) was most frequently prescribed followed by dolutegravir (total, 32.1%; <50 years, 19.6%; ≥50 years, 12.5%). Potential or contraindicated DDIs between boosted PIs with ritonavir or EVG/COBI and coprescribed drugs occurred most frequently. Conclusion Currently, NRTIs/INSTIs is the most frequently prescribed ARV combination. Abacavir/lamivudine, tenofovir alafenamide/FTC, and tenofovir disoproxil fumarate/FTC are the most used NRTIs, and EVG/COBI followed by dolutegravir is the most prescribed INSTIs. Potential or contraindicated DDIs occur mainly between boosted PIs or EVG/COBI and non-ARV medications.
Molecular serotyping of Haemophilus parasuis isolated from diseased pigs and the relationship between serovars and pathological patterns in Taiwan

Background Haemophilus parasuis is the etiological agent of Glässer’s disease, and causes severe economic losses in the swine industry. Serovar classification is intended as an indicator of virulence and pathotype and is also crucial for vaccination programs and vaccine development. According to a polysaccharide biosynthesis locus analysis, H. parasuis isolates could be classified by a molecular serotyping assay except serovars 5 and 12 detected by the same primer pair. The aim of this study was to identify H. parasuis isolates from diseased pigs in Taiwan by using a molecular serotyping assay and to analyze the relationship between serovars and pathological patterns. Methods From August 2013 to February 2017, a total of 133 isolates from 277 lesions on 155 diseased animals from 124 infected herds serotyped by multiplex PCR and analyzed with pathological data. Results The dominant serovars of H. parasuis in Taiwan were serovars 5/12 (37.6%), 4 (27.8%) and 13 (15%) followed by molecular serotyping non-typable (MSNT) isolates (13.5%). Nevertheless, the serovar-specific amplicons were not precisely the same sizes as previously indicated in the original publication, and MSNT isolates appeared with unexpected amplicons or lacked serovar-specific amplicons. Most H. parasuis isolates were isolated from nursery pigs infected with porcine reproductive and respiratory syndrome virus. The percentage of lung lesions (30.4%) showing H. parasuis infection was significantly higher than that of serosal lesions. Discussion Collectively, the distribution of serovars in Taiwan is similar to that found in other countries, but MSNT isolates remain due to genetic variations. Furthermore, pulmonary lesions may be optimum sites for H. parasuis isolation, the diagnosis of Glässer’s disease, and may also serve as points of origin for systemic H. parasuis infections in hosts.
Combining Bayesian genetic clustering and ecological niche modeling: Insights into wolf intraspecific genetic structure

Abstract The distribution of intraspecific genetic variation and how it relates to environmental factors is of increasing interest to researchers in macroecology and biogeography. Recent studies investigated the relationships between the environment and patterns of intraspecific genetic variation across species ranges but only few rigorously tested the relation between genetic groups and their ecological niches. We quantified the relationship of genetic differentiation (F ST) and the overlap of ecological niches (as measured by n‐dimensional hypervolumes) among genetic groups resulting from spatial Bayesian genetic clustering in the wolf (Canis lupus) in the Italian peninsula. Within the Italian wolf population, four genetic clusters were detected, and these clusters showed different ecological niches. Moreover, different wolf clusters were significantly related to differences in land cover and human disturbance features. Such differences in the ecological niches of genetic clusters should be interpreted in light of neutral processes that hinder movement, dispersal, and gene flow among the genetic clusters, in order to not prematurely assume any selective or adaptive processes. In the present study, we found that both the plasticity of wolves—a habitat generalist—to cope with different environmental conditions and the occurrence of barriers that limit gene flow lead to the formation of genetic intraspecific genetic clusters and their distinct ecological niches.
Radiotherapy in Patients with Mycosis Fungoides and Central Nervous System Involvement

Background: Involvement of the central nervous system (CNS) by mycosis fungoides (MF) is rare; however, it portends a poor prognosis. While aggressive multimodality therapy may improve outcomes, the role of radiation therapy (RT) is not well defined. Objectives: We sought to explore the efficacy of RT in the management of CNS involvement by MF. Method: We retrospectively identified five patients with MF and CNS involvement who received cranial or craniospinal RT at a single institution. Patient characteristics, disease features, radiographic findings, treatments delivered, and outcome data were extracted from the electronic medical record. Results: All 5 patients had neurologic deficits at RT initiation, and 4 experienced at least a partial improvement. Of 4 patients evaluated by MRI after RT completion, 3 had complete resolution of CNS disease within the irradiated field. At the time of last follow-up, all patients had died of MF. The median time to death was 7.4 months (range 1.0–21 months) from their diagnosis with CNS involvement and 1.2 months (range 0.4–7.1 months) from the end of RT treatment. Conclusions: We observed high rates of radiographic response and palliation of neurological symptoms. Nonetheless, all patients succumbed to their disease shortly after treatment, confirming the poor prognosis of this condition. Our findings suggest that RT may play a valuable palliative role for these patients.
Ecology and life history of Meta bourneti (Araneae: Tetragnathidae) from Monte Albo (Sardinia, Italy)

The orb-weaver spider Meta bourneti Simon 1922 (Araneae: Tetragnathidae) is one of the most common cave predators occurring in the Mediterranean basin. Although the congeneric M. menardi represented the model species in several studies, our knowledge of M. bourneti is only founded on observations performed on a handful of populations. In this study M. bourneti spiders were studied in caves of Monte Albo (Sardinia, Italy) over a year. Generalized Linear Mixed Models were used to analyze spider occupancy inside cave environments, as well as spider abundance. Analyses on M. bourneti occupancy and abundance were also repeated for adults and juveniles separately. Generalized Linear Models, were used to weight species absence based on its detection probability. Linear Mixed Models were used to detect possible divergences in subterranean spatial use between adult and juvenile spiders. Although widespread on the mountain, M. bourneti generally showed low density and low detection probability. Most of the individuals observed were juveniles. The spiders generally occupied cave sectors with high ceilings that were deep enough to show particular microclimatic features. Adults tended to occupy less illuminated areas than juveniles, while the latter were more frequently found in sectors showing high humidity. The abundance of M. bourneti was strongly related to high humidity and the presence of two troglophile species, Hydromantes flavus Wake, Salvador & Alonso-Zarazaga, 2005 (Amphibia: Caudata) and Oxychilus oppressus (Shuttleworth, 1877) (Gastropoda: Panpulmonata). The abundance of juveniles was related to sector temperature and humidity, the presence of H. flavus and O. oppressus and to morphological sector features. However, when only adults were considered, no significant relationships were found. Adult and juvenile spiders did not differ in their spatial distribution inside the caves studied, but a seasonal distribution of the species along cave walls was observed. Microclimate was one of the most important features affecting both the presence and abundance of M. bourneti in subterranean environments. Individuals tended to occupy lower heights during hot seasons.
Pose and Expression Invariant Alignment based Multi-View 3D Face Recognition

In this study, a fully automatic pose and expression invariant 3D face alignment algorithm is proposed to handle frontal and profile face images which is based on a two pass course to fine alignment strategy. The first pass of the algorithm coarsely aligns the face images to an intrinsic coordinate system (ICS) through a single 3D rotation and the second pass aligns them at fine level using a minimum nose tip-scanner distance (MNSD) approach. For facial recognition, multi-view faces are synthesized to exploit real 3D information and test the efficacy of the proposed system. Due to optimal separating hyper plane (OSH), Support Vector Machine (SVM) is employed in multi-view face verification (FV) task. In addition, a multi stage unified classifier based face identification (FI) algorithm is employed which combines results from seven base classifiers, two parallel face recognition algorithms and an exponential rank combiner, all in a hierarchical manner. The performance figures of the proposed methodology are corroborated by extensive experiments performed on four benchmark datasets: GavabDB, Bosphorus, UMB-DB and FRGC v2.0. Results show mark improvement in alignment accuracy and recognition rates. Moreover, a computational complexity analysis has been carried out for the proposed algorithm which reveals its superiority in terms of computational efficiency as well.
Treatment of chronic oroantral fistula with platelet-rich fibrin clot and collagen membrane: a case report

An oroantral fistula is a complication of the maxillary posterior teeth that can occur after a tooth extraction that affects the maxillary sinus. Improper management may lead to a persistent fistula, which may become chronic. In this case report, platelet-rich fibrin (PRF) was used with a collagen membrane to close a chronic fistula in a single patient. A flap was raised, the oroantral fistula tract was eliminated, and the opening was closed with a resorbable membrane as a first layer and covered with a PRF clot as a second layer. The flap was closed, and the patient was followed up for suture removal and confirmation of complete soft tissue closure. The postsurgical sign and symptoms of the patient disappeared in the first week; complete tissue healing was detected within 2 weeks, and tissue hypertrophy was observed in the fourth week. The use of PRF may have advantages for soft-tissue healing and for accelerating soft tissue formation by subsequent hypertrophy.
Fine-Grained User Profiling for Personalized Task Matching in Mobile Crowdsensing

In mobile crowdsensing, finding the best match between tasks and users is crucial to ensure both the quality and effectiveness of a crowdsensing system. Existing works usually assume a centralized task assignment by the crowdsensing platform, without addressing the need of fine-grained personalized task matching. In this paper, we argue that it is essential to match tasks to users based on a careful characterization of both the users’ preference and reliability. To that end, we propose a personalized task recommender system for mobile crowdsensing, which recommends tasks to users based on a recommendation score that jointly takes each user’s preference and reliability into consideration. We first present a hybrid preference metric to characterize users’ preference by exploiting their implicit feedback. Then, to profile users’ reliability levels, we formalize the problem as a semi-supervised learning model, and propose an efficient block coordinate descent algorithm to solve the problem. For some tasks that lack users’ historical information, we further propose a matrix factorization method to infer the users’ reliability levels on those tasks. We conduct extensive experiments to evaluate the performance of our system, and the evaluation results demonstrate that our system can achieve superior performance to the benchmarks in both user profiling and personalized task recommendation.
Amnestic Mild Cognitive Impairment Is Associated With Frequency-Specific Brain Network Alterations in Temporal Poles

There is general agreement that the neuropathological processes leading to Alzheimer’s disease (AD) begin decades before the clinical onset. In order to detect early topological changes, we applied functional connectivity and network analysis to magnetoencephalographic (MEG) data obtained from 16 patients with amnestic Mild Cognitive Impairment (aMCI), a prodromal stage of AD, and 16 matched healthy control (HCs). Significant differences between the two groups were found in the theta band, which is associated with memory processes, in both temporal poles (TPs). In aMCI, the degree and betweenness centrality (BC) were lower in the left superior TP, whereas in the right middle TP the BC was higher. A statistically significant negative linear correlation was found between the BC of the left superior TP and a delayed recall score, a sensitive marker of the “hippocampal memory” deficit in early AD. Our results suggest that the TPs, which are involved early in AD pathology and belong to the memory circuitry, have an altered role in the functional network in aMCI.
A Control-Theoretic Approach for Modeling, Classification, and Robust Traffic Density Estimation

Monitoring and control of traffic networks represent alternative, inexpensive strategies to minimize traffic congestion. As the number of traffic sensors is naturally constrained by budgetary requirements, real-time estimation of traffic flow in road segments that are not equipped with sensors is of significant importance---thereby providing situational awareness and guiding feedback-control strategies. To that end, firstly we build a generalized traffic flow model for stretched highways with arbitrary number of ramp flows based on the Lighthill Whitham Richards (LWR) flow model. Secondly, we characterize the function set corresponding to the nonlinearities present in the LWR model, and use this characterization to design real-time and robust state estimators (SE) for stretched highway segments. Specifically, we show that the nonlinearities from the derived models are locally Lipschitz continuous by providing the analytical Lipschitz constants. Thirdly, the analytical derivation is then incorporated through a robust SE method given a limited number of traffic sensors, under the impact of process and measurement disturbances and unknown inputs. Finally, numerical tests are given showcasing the applicability and scalability of the proposed methods for large systems under high magnitude disturbances and unknown inputs.
SSR‐seq: Genotyping of microsatellites using next‐generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring

Abstract Microsatellites (or simple sequence repeats, SSR) are widely used markers in population genetics. Traditionally, genotyping was and still is carried out through recording fragment length. Now, next‐generation sequencing (NGS) makes it easy to obtain also sequence information for the loci of interest. This avoids misinterpretations that otherwise could arise due to size homoplasy. Here, an NGS strategy is described that allows to genotype hundreds of individuals at many custom‐designed SSR loci simultaneously, combining multiplex PCR, barcoding, and Illumina sequencing. We created three different datasets for which alleles were coded according to (a) length of the repetitive region, (b) total fragment length, and (c) sequence identity, in order to evaluate the eventual benefits from having sequence data at hand, not only fragment length data. For each dataset, genetic diversity statistics, as well as F ST and R ST values, were calculated. The number of alleles per locus, as well as observed and expected heterozygosity, was highest in the sequence identity dataset, because of single‐nucleotide polymorphisms and insertions/deletions in the flanking regions of the SSR motif. Size homoplasy was found to be very common, amounting to 44.7%–63.5% (mean over all loci) in the three study species. Thus, the information obtained by next‐generation sequencing offers a better resolution than the traditional way of SSR genotyping and allows for more accurate evolutionary interpretations.
Clinical Effect of Adjuvant Cytokine-Induced Killer Cells Immunotherapy in Patients with Stage II-IVB Nasopharyngeal Carcinoma after Chemoradiotherapy: A propensity score analysis

As an adjuvant immunotherapy, cytokine-induced killer cells (CIKs) infusion has been demonstrated to exert potent effectiveness in several types of cancer patients who received curative treatment. However, controversy exists regarding whether nasopharyngeal carcinoma (NPC) patients can benefit from additional treatment after radical radiotherapy or chemoradiotherapy to improve their distant control and survival. In this retrospective study, we aimed to evaluate the efficacy of adjuvant CIK cells therapy in NPC patients with stage II-IVB after curative treatment. From January 1, 2005 to December 31, 2012, 85 pairs of NPC patients matching by propensity score matching (PSM) method to balance prognostic factors were included in this study: 85 cases underwent radical treatment, 85 cases received radical treatment and sequential CIKs infusion. We found that disease-free survival (DFS) and overall survival (OS) were significantly better in the CIK group than that in the control group (P = 0.009, P < 0.001, respectively). Adjuvant CIK cells immunotherapy was showed to be an independent prognostic factor for survival of the patients in further multivariate analysis. In subgroup analyses, the DFS and OS of patients with T3/4, III and IV A-B TNM (tumor-node-metastasis) stages were significantly enhanced in CIK group compared to control group. Nevertheless, both NPC patients with high and low EBV DNA benefited from adjuvant CIK cells immunotherapy. In conclusion, CIKs infusion is an effective adjuvant immunotherapy for enhancing the prognosis of NPC patients who have received the standard treatment, particularly for those with more aggressive tumor (T3/4) or advanced TNM stage.
How Energy-Efficient Can a Wireless Communication System Become?

The data traffic in wireless networks is steadily growing. The long-term trend follows Cooper’s law, where the traffic is doubled every two-and-a-half year, and it will likely continue for decades to come. The data transmission is tightly connected with the energy consumption in the power amplifiers, transceiver hardware, and baseband processing. The relation is captured by the energy efficiency metric, measured in bit/Joule, which describes how much energy is consumed per correctly received information bit. While the data rate is fundamentally limited by the channel capacity, there is currently no clear understanding of how energy-efficient a communication system can become. Current research papers typically present values on the order of 10Mbit$/$Joule, while previous network generations seem to operate at energy efficiencies on the order of 10 kbit$/$Joule. Is this roughly as energy-efficient future systems $(5G$ and beyond) can become, or are we still far from the physical limits? These questions are answered in this paper. We analyze a different cases representing potential future deployment and hardware characteristics.
Learning Single-View 3D Reconstruction with Adversarial Training

Single-view 3D shape reconstruction is an important but challenging problem, mainly for two reasons. First, as shape annotation is very expensive to acquire, current methods rely on synthetic data, in which ground-truth 3D annotation is easy to obtain. However, this results in domain adaptation problem when applied to natural images. The second challenge is that it exists multiple shapes that can explain a given 2D image. In this paper, we propose a framework to improve over these challenges using adversarial training. On one hand, we impose domain-confusion between natural and synthetic image representations to reduce the distribution gap. On the other hand, we impose the reconstruction to be `realistic' by forcing it to lie on a (learned) manifold of realistic object shapes. Moreover, our experiments show that these constraints improve performance by a large margin over a baseline reconstruction model. We achieve results competitive with the state of the art using only RGB images and with a much simpler architecture.
Fragile X mental retardation protein is a Zika virus restriction factor that is antagonized by subgenomic flaviviral RNA

Subgenomic flaviviral RNA (sfRNA) accumulates during infection due to incomplete degradation of viral genomes and interacts with cellular proteins to promote infection. Here we identify host proteins that bind the Zika virus (ZIKV) sfRNA. We identified fragile X mental retardation protein (FMRP) as a ZIKV sfRNA-binding protein and confirmed this interaction in cultured cells and mouse testes. Depletion of FMRP elevated viral translation and enhanced ZIKV infection, indicating that FMRP is a ZIKV restriction factor. We further observed that an attenuated ZIKV strain compromised for sfRNA production was disproportionately stimulated by FMRP knockdown, suggesting that ZIKV sfRNA antagonizes FMRP activity. Importantly, ZIKV infection and expression of ZIKV sfRNA upregulated endogenous FMRP target genes in cell culture and ZIKV-infected mice. Together, our observations identify FMRP as a ZIKV restriction factor whose activity is antagonized by the sfRNA. Interaction between ZIKV and FMRP has significant implications for the pathogenesis of ZIKV infections.