Miracle-dz/UniFAR-FTUs huggingface dataset:
Methylation of High-Risk Human Papillomavirus Genomes Are Associated with Cervical Precancer in HIV-Positive Women

Background: HIV-positive women are at substantial risk of HPV-associated cervical neoplasia caused by high-risk (HR) HPVs. Methylation of the HPV genome is associated with cervical intraepithelial neoplasia grade 3 (CIN3) in HIV-negative women, yet it is unknown whether this holds true for HIV-positive women. Methods: We designed a case–control study within the Women's Interagency HIV Study (WIHS) cohort comparing HIV-positive CIN3 cases (N = 72) to HIV-positive controls without detectable CIN2+. The unit of analysis and matching was HPV-type infection. Cases with ≥2 HR-HPV types (N = 23; 32%) had a separate control for each HR-HPV type. We developed and utilized next-generation sequencing (NGS) methylation assays for 12 different HR-HPVs, focusing on CpG sites in the L1/L2 regions. Results: Significant case–control differences in individual CpG site methylation levels were observed for multiple alpha-9 (HPV16/31/35/58) and alpha-7 HPV (HPV18/39/45) types, based on dichotomization of tertile levels (T3 vs. T1 and T2). Analyses combining homologous CpG sites [e.g., HPV16-L1-5608/HPV31-L1-5521/HPV35-L2L1-5570; OR = 7.28; 95% confidence interval (CI): 2.75–19.3], and (e.g., HPV18-L1-7062/HPV45-L1-7066; OR = 6.94; 95% CI: 1.23–39.3) were significant in separate case–control comparisons. In cases with multiple HR-HPVs, we tested and confirmed the hypothesis that one HR-HPV type would have higher methylation than other types detected, consistent with there being a single HR-HPV causally related to a lesion. Conclusions: CIN3 is associated with elevated L1/L2 CpG methylation levels in HIV-positive women. Impact: HPV DNA CpG methylation is a promising triage option in HIV-positive women testing positive for HR-HPV types and provides risk attribution in women with multiple HPV type infections.
Indomethacin increases severity of Clostridium difficile infection in mouse model.

AIM To evaluate the effect on the nonsteroidal anti-inflammatory drug indomethacin on Clostridium difficile infection (CDI) severity. MATERIALS & METHODS Indomethacin was administered in two different mouse models of antibiotic-associated CDI in two different facilities, using a low and high dose of indomethacin. RESULTS Indomethacin administration caused weight loss, increased the signs of severe infection and worsened histopathological damage, leading to 100% mortality during CDI. Indomethacin-treated, antibiotic-exposed mice infected with C. difficile had enhanced intestinal inflammation with increased expression of KC, IL-1β and IL-22 compared with infected mice unexposed to indomethacin. CONCLUSION These results demonstrate a negative impact of nonsteroidal anti-inflammatory drugs on antibiotic-associated CDI in mice and suggest that targeting the synthesis or signaling of prostaglandins might be an approach to ameliorating the severity of CDI.
Baculovirus as a Tool for Gene Delivery and Gene Therapy

Based on its ability to express high levels of protein, baculovirus has been widely used for recombinant protein production in insect cells for more than thirty years with continued technical improvements. In addition, baculovirus has been successfully applied for foreign gene delivery into mammalian cells without any viral replication. However, several CpG motifs are present throughout baculoviral DNA and induce an antiviral response in mammalian cells, resulting in the production of pro-inflammatory cytokines and type I interferon through a Toll-like receptor (TLR)-dependent or -independent signaling pathway, and ultimately limiting the efficiency of transgene expression. On the other hand, by taking advantage of this strong adjuvant activity, recombinant baculoviruses encoding neutralization epitopes can elicit protective immunity in mice. Moreover, immunodeficient cells, such as hepatitis C virus (HCV)- or human immunodeficiency virus (HIV)-infected cells, are more susceptible to baculovirus infection than normal cells and are selectively eliminated by the apoptosis-inducible recombinant baculovirus. Here, we summarize the application of baculovirus as a gene expression vector and the mechanism of the host innate immune response induced by baculovirus in mammalian cells. We also discuss the future prospects of baculovirus vectors.
Is reading automatic? Are the ERP correlates of masked priming really lexical?

Humans have an almost unbounded ability to adapt their behaviour to perform different tasks. In the laboratory, this flexibility is sometimes viewed as a nuisance factor that prevents access to the underlying cognitive mechanisms of interest. For example, in order to study “automatic” lexical processing, psycholinguists have used masked priming or evoked potentials to measure “automatic” lexical processing. However, the pattern of masked priming can be radically altered by changing the task. In lexical decision, priming is observed for words but not for nonwords, yet in a same-different matching task, priming is observed for same responses but not for different responses, regardless of whether the target is a word or a nonword (Norris & Kinoshita, 2008). Here we show that evoked potentials are equally sensitive to the nature of required decision, with the neural activity normally associated with lexical processing being seen for both words and nonwords on same trials, and for neither on different trials. (150)
On the Feasibility of Ultrasound Imaging Enrichment by Medium-Temperature Changes

We describe the concept of a new imaging modality based on the tracking and dynamic modeling of local intensity changes (ICs) observed in conventional ultrasound images collected during a medium-temperature change. We computed the pixel-by-pixel IC from averaged B-mode images that exhibited different behaviors with varying temperature resulting from changes in the speed of sound, which consequently induce changes in the backscattered energy. Moreover, for each pixel, a first-order polynomial model was adjusted to the different temperature-dependent ICs. The representation of the polynomial angular parameter in 2D pixel space was used to obtain a parametric image. The results obtained by simulations and with real B-mode images indicated that this new ultrasound imaging modality was able to enhance the contrast and highlight structures that were poorly visible or even undetected in conventional images. A temperature change of 3°C was found to be sufficient to generate appropriate images with the proposed method. In addition, if a temperature change of 6°C was considered, the thermal dose, measured as the cumulative number of equivalent minutes at 43°C (CEM43°C), was 2.4 CEM43°C, which is a value that is considered safe according to the literature. We provide a proof-of-concept of a new imaging modality that opens new opportunities for the enhancement of ultrasound images and consequently contributes to improvements in ultrasound-based diagnoses. Our approach is based on images returned by commercial ultrasound scanners. Therefore, it can be implemented in any ultrasound system and is independent of specific ultrasound hardware and software data acquisition characteristics.
Successful treatment of acquired hemophilia A associated with immune thrombocytopenia and joint hemarthrosis

Introduction: Acquired hemophilia A (AHA) is a rare bleeding disease caused by autoantibodies against factor VIII (FVIII). Spontaneous bleeding symptoms usually affect the skin, musco, muscle, and internal organs, while joint hemarthrosis in AHA is an extremely rare manifestation. AHA may have an autoimmune cause and is often associated with autoimmune disease, but no demonstrable platelet impairment was found in AHA patients. We report a patient with AHA complicated with a right shoulder joint hemarthrosis and immune thrombocytopenia. The patient was treated with fresh frozen plasma (FFP) and human prothrombin complex concentrate (hPCC) to control the active bleeding. Simultaneously this patient firstly accepted cyclophosphamide combined with prednisone to eradicate the inhibitor, while the treatment effect of cyclophosphamide combined with prednisone was not satisfactory. At last, she was successfully treated through the use of an anti-CD20 monoclonal antibody. Conclusion: AHA is an autoimmune disease and can co-exist with immune cytopenia besides connective tissue disease (CTD). Joint hemarthrosis is not specific to congenital hemophilia and mainly related to the extent of prolonged aPTT and weight loading of joint in AHA. When the first-line therapy of cyclophosphamide combined with prednisone is not enough to eradicate the inhibitor, especially for a higher inhibitor titer, anti-CD20 monoclonal antibody could play an important role.
Disk-Based Indexing of Recent Trajectories

The plethora of location-aware devices has led to countless location-based services in which huge amounts of spatiotemporal data get created every day. Several applications require efficient processing of queries on the locations of moving objects over time, i.e., the moving object trajectories. This calls for efficient trajectory-based indexing methods that capture both the spatial and temporal dimensions of the data in a way that minimizes the number of disk I/Os required for both updating and querying. Most existing spatiotemporal index structures capture either the current locations of the moving objects or the entire history of the moving objects. Historical spatiotemporal indexing methods require multiple disk I/Os to process new updates and use a discrete trajectory representation that may result in incomplete query results. In this article, we introduce the trails-tree, a disk-based data structure for indexing recent trajectories. The trails-tree requires half the number of disk I/Os needed by other historical spatiotemporal indexing methods for the insertion and querying operations. We give a detailed description of the trails-tree, and we mathematically analyze its performance. Moreover, we present a novel query processing algorithm that ensures the completeness of the query result set. We experimentally verify the performance of the trails-tree using various real and synthetic datasets.
Correction: Spreading of bovine TB by hunting hounds

We read with interest last week’s letter discussing Mycobacterium bovis infection in working foxhounds ( VR , 15 September, 2018, vol 183, pp 327-328), and the discussion of our recent paper on the subject.1 However, in addition to our concerns over the over-interpretation of the IGRA (interferon gamma release assay) blood test result in the in-contact person (see above letter), we would also like to clarify a factual inaccuracy. > All …
John E. Gerich: Father of Modern Physiology of Glucose Homeostasis, Counterregulation to Hypoglycemia, and Mechanistic Treatment of Diabetes

John “Jack” E. Gerich as a young child (left panel); at graduation from medical school, age 26 (middle panel); and at present (right panel). Original graph, hand drawn by John and completed by his wife, is a classic teaching example of the insulin dose-response curve. Printed with permission of the American Journal of Physiology (6). Top: Jack writing papers with one of his fellows (author Geremia Bolli) at the Mayo Clinic. Bottom: Jack and the author playing a game of pool in Jack’s basement. Jack, fishing on Beaver Lake (Pennsylvania). When the letter from Diabetes Care arrived inviting me to write a Profile in Progress on John Edward Gerich (Jack, to his friends), I assumed it was because of my long-term research association and friendship with him. I felt, in a way, like a dwarf asked to report on a giant standing in front of me. After initial hesitation, I decided to accept this challenging task to acquaint younger professionals who do not know Jack Gerich with what kind of scientist—and also what kind of man—he is. To ensure that my narrative did not miss any aspect of his extraordinarily large and multifaceted research, I consulted with several of his former fellows who had been associated with him and contributed so much to the golden era of clinical research in metabolism over the last few decades. My interest in Jack’s work started in 1979 when I came across his legendary paper in the Journal of Clinical Investigation on the relative roles of glucagon, catecholamines, and growth hormone responses in glucose counterregulation to acute, insulin-induced hypoglycemia (1). At that time, in my small laboratory in Perugia, Italy, I was able to measure plasma glucagon, catecholamines, and other counterregulatory hormones during hypoglycemia experiments in humans, but I had no idea how …
Unexpected Structure of a Helical N4 -Schiff-Base Zn(II) Complex and Its Demetallation: Experimental and Theoretical Studies.

A new Zn-N4 -Schiff base L=((±)-trans-N,N'-Bis(2-aminobenzylidene)-1,2-diaminocyclohexane) complex was synthesized and fully characterized, showing an unexpected self-assembled double-stranded helicate structure. The X-ray crystal analysis of the Zn2 L2 complex ((C40 H44 N8 Zn2 ,CH2 Cl2 , a=14.2375(3) Å, b=16.7976(4) Å, c=16.1613(4) Å, monoclinic, P21 /n, Z=4) shows a centrosymmetrical structure in which zinc atoms are in distorted tetrahedral environments, revealing an M- (R, R) left-handed helicity in its asymmetric unit. However, it was observed that this dinuclear complex is thermodynamically unstable in the presence of small water amounts and undergoes demetallation into free N4-Schiff base ligand and ZnO nanoparticles. This hydrolysis process was thoroughly identified and monitored through detailed 1 H NMR, DOSY NMR analysis. The reaction mechanism of this demetallation event was elucidated by using the DFT method, involving an activation energy smaller than 13 kcal/mol. Besides, a theoretical mechanism of the demetallation process is given for the first time.
Adaptive work-stealing with parallelism feedback

Multiprocessor scheduling in a shared multiprogramming environment can be structured as two-level scheduling, where a kernel-level job scheduler allots processors to jobs and a user-level thread scheduler schedules the work of a job on its allotted processors. We present a randomized work-stealing thread scheduler for fork-join multithreaded jobs that provides continual parallelism feedback to the job scheduler in the form of requests for processors. Our A-STEAL algorithm is appropriate for large parallel servers where many jobs share a common multiprocessor resource and in which the number of processors available to a particular job may vary during the job's execution. Assuming that the job scheduler never allots a job more processors than requested by the job's thread scheduler, A-STEAL guarantees that the job completes in near-optimal time while utilizing at least a constant fraction of the allotted processors. We model the job scheduler as the thread scheduler's adversary, challenging the thread scheduler to be robust to the operating environment as well as to the job scheduler's administrative policies. For example, the job scheduler might make a large number of processors available exactly when the job has little use for them. To analyze the performance of our adaptive thread scheduler under this stringent adversarial assumption, we introduce a new technique called trim analysis, which allows us to prove that our thread scheduler performs poorly on no more than a small number of time steps, exhibiting near-optimal behavior on the vast majority. More precisely, suppose that a job has work T1 and span T∞. On a machine with P processors, A-STEAL completes the job in an expected duration of O(T1/&Ptilde; + T∞ + L lg P) time steps, where L is the length of a scheduling quantum, and &Ptilde; denotes the O(T∞ + L lg P)-trimmed availability. This quantity is the average of the processor availability over all time steps except the O(T∞ + L lg P) time steps that have the highest processor availability. When the job's parallelism dominates the trimmed availability, that is, &Ptilde; ≪ T1/T∞, the job achieves nearly perfect linear speedup. Conversely, when the trimmed mean dominates the parallelism, the asymptotic running time of the job is nearly the length of its span, which is optimal. We measured the performance of A-STEAL on a simulated multiprocessor system using synthetic workloads. For jobs with sufficient parallelism, our experiments confirm that A-STEAL provides almost perfect linear speedup across a variety of processor availability profiles. We compared A-STEAL with the ABP algorithm, an adaptive work-stealing thread scheduler developed by Arora et al. [1998] which does not employ parallelism feedback. On moderately to heavily loaded machines with large numbers of processors, A-STEAL typically completed jobs more than twice as quickly as ABP, despite being allotted the same number or fewer processors on every step, while wasting only 10% of the processor cycles wasted by ABP.
FleXeen: Visually Manipulating Perceived Fabric Bending Stiffness in Spatial Augmented Reality

The appearance of fabric motion is suggested to affect the human perception of bending stiffness. This study presents a novel spatial augmented reality, or projection mapping, approach that can visually manipulate the perceived bending stiffness of a fabric. Particularly, we proposed a flow enhancement method that can change the apparent fabric motion by using a simple optical flow analysis technique rather than complex physical simulations for interactive applications. Through a psychophysical experiment, we investigated the relationship between the magnification factor of our flow enhancement and the perceived bending stiffness of a fabric. Furthermore, we constructed a prototype application system that allows users to control the stiffness of a fabric without changing the actual physical fabric. By evaluating the prototype, we confirmed that the proposed technique can manipulate the perceived stiffness of various materials (i.e., cotton, polyester, and mixed cotton and linen) at an average accuracy of 90.3 percent.
Distribuição da proteína Fos no lobo temporal medial de ratos Wistar durante o medo condicionado ao contexto, luz e som

3 Lista de Abreviaturas . 5 Lista de Figuras . 6 1. Introdução . 9 1.1. Medo e Ansiedade: Conceito . 9 2. Objetivos . 20 3. Material e Métodos . 22 3.1 Animais . 22 3.2. Medo Condicionado . 22 3.3. Treinamento . 23 3.4. Teste . 24 3.5. Imunohistoquímica para Fos . 24 3.6. Quantificação de células imunorreativas (positivas) para Fos . 25 3.7. Análise Estatística . 26 4. Resultados . 28 4.1. Efeitos Comportamentais . 28 4.2. Expressão da proteína Fos . 29 5. Discussão . 34 6. Referências Bibliográficas . 43
Antifungal Activities of Isoflavonoids from Uromyces striatus Infected Alfalfa

Fungal pathogens constitute a severe yield‐limiting factor for the pasture crop alfalfa (Medicago sativa L.). Eleven phenolic compounds, including a new isoflavane, were isolated from the Uromyces striatus Schroet. infected alfalfa. The effect of infection with U. striatus Schroet. on the phytochemical profile of alfalfa was investigated using ultra‐performance liquid chromatography (UPLC), and the antifungal properties of isolated compounds against a range of pathogens were tested. It was found that the contents of most of the isolated compounds in U. striatus infected alfalfa were higher than those in healthy alfalfa. Compounds 1–5 exhibited a moderate inhibitory activity against Curvularia lunata with 40.14±1.63 %, 48.03±1.22 %, 57.54±1.18 %, 50.10±1.56 %, and 61.54±2.14 % inhibition ratio at the concentration of 50 μg/mL. Compounds 3 and 5 showed a weak inhibitory activity against Fusarium graminearum with the EC50 values of 104.2±2.66 and 123.0±1.23 μg/mL, and a moderate inhibitory activity against Bipolaris sorokinianum with the EC50 values of 39.1±2.05 and 95.0±1.01 μg/mL, respectively. In pot experiments with wheat, compounds 1–5 possessed desirable protective efficacy of over 80 % and curative effectiveness of over 50 % against Puccinia striiformis f. sp. tritici at a concentration of 0.5 mg/mL
Uncertainties of potentials and recent changes in global yields of major crops resulting from census- and satellite-based yield datasets at multiple resolutions

Global agriculture is under pressure to meet increasing demand for food and agricultural products. There are several global assessments of crop yields, but we know little about the uncertainties of their key findings, as the assessments are driven by the single best yield dataset available when each assessment was conducted. Recently, two different spatially explicit, global, historical yield datasets, one based on agricultural census and the other largely based on satellite remote sensing, became available. Using these datasets, we compare the similarities and differences in global yield gaps, trend patterns, growth rates and changes in year-to-year variability. We analyzed maize, rice, wheat and soybean for the period of 1981 to 2008 at four resolutions (0.083°, 0.5°, 1.0° and 2.0°). Although estimates varied by dataset and resolution, the global mean annual growth rates of 1.7–1.8%, 1.5–1.7%, 1.1–1.3% and 1.4–1.6% for maize, rice, wheat and soybean, respectively, are not on track to double crop production by 2050. Potential production increases that can be attributed to closing yield gaps estimated from the satellite-based dataset are almost twice those estimated from the census-based dataset. Detected yield variability changes in rice and wheat are sensitive to the choice of dataset and resolution, but they are relatively robust for maize and soybean. Estimates of yield gaps and variability changes are more uncertain than those of yield trend patterns and growth rates. These tendencies are consistent across crops. Efforts to reduce uncertainties are required to gain a better understanding of historical change and crop production potential to better inform agricultural policies and investments.
Causes of Persistent Positional Vertigo Following Posterior Semicircular Canal Occlusion for Benign Paroxysmal Positional Vertigo.

OBJECTIVE To report causes of persistent recalcitrant positional vertigo (PRPV) after posterior semicircular canal occlusion (PSCO) for benign paroxysmal positional vertigo (BPPV). STUDY DESIGN Retrospective chart review. SETTING Single high-volume otology practice. PATIENTS Patients diagnosed with BPPV from 2007 to 2017. INTERVENTION PSCO and follow-up care including diagnostic and particle repositioning maneuvers for recurrent BPPV. MAIN OUTCOME MEASURES PRPV, defined as recalcitrant positional vertigo for any reason following PSCO. RESULTS Twenty seven PSCO operations were performed in 26 patients. Twenty five patients (96.2%) had resolution of the Dix-Hallpike test in the operated ear. Eleven patients (42.3%) developed BPPV postoperatively, three (11.5%) in the operated ear and eight (30.8%) in the contralateral ear. Five of eight patients (62.5%) who developed contralateral BPPV had unilateral BPPV preoperatively. Eight patients (30.8%) developed BPPV at least twice after surgery or did not resolve, qualifying as PRPV, and all but one of these events occurred in the nonsurgical ear. No instances of cerebrospinal fluid leak, postoperative infection, facial palsy, clinically significant hearing loss, or death occurred. CONCLUSIONS PSCO is a safe and effective option for recalcitrant BPPV. However, 30.8% of patients, including patients with initially unilateral BPPV, had recalcitrant positional vertigo postoperatively, usually due to contralateral BPPV. Patients considering PSCO should be counseled regarding this risk to ensure realistic expectations.