Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein P200 Is Dispensable for Mycoplasma pneumoniae Hemadsorption but Not Gliding Motility or Colonization of Differentiated Bronchial Epithelium

ABSTRACT Mycoplasma pneumoniae protein P200 was localized to the terminal organelle, which functions in cytadherence and gliding motility. The loss of P200 had no impact on binding to erythrocytes and A549 cells but resulted in impaired gliding motility and colonization of differentiated bronchial epithelium. Thus, gliding may be necessary to overcome mucociliary clearance.
Widely Linear Complex-Valued Kernel Methods for Regression

In this paper, we propose a widely linear reproducing kernel Hilbert space (WL-RKHS) for nonlinear regression with complex-valued signals. Our approach is a nonlinear extension of WL signal processing that has been proven to be more versatile than linear systems for dealing with complex-value signals. To be able to use the WL concept in kernel methods, we need to introduce a pseudo-kernel to complement the standard kernel in RKHS, which is not defined in previous RKHS approaches in the existing literature. In this paper, we present WL-RKHS, its properties, and the kernel and pseudo-kernel designs. We illustrate the need of the pseudo-kernel with simply verifiable examples that allow understanding the intuitions behind this kernel. We conclude this paper, showing that in the all-relevant nonlinear equalization problem the pseudo-kernel plays a significant role and previous approaches that do not rely on this kernel clearly underperform.
Region specific optimization of continuous linear attenuation coefficients based on UTE (RESOLUTE): application to PET/MR brain imaging

The reconstruction of PET brain data in a PET/MR hybrid scanner is challenging in the absence of transmission sources, where MR images are used for MR-based attenuation correction (MR-AC). The main challenge of MR-AC is to separate bone and air, as neither have a signal in traditional MR images, and to assign the correct linear attenuation coefficient to bone. The ultra-short echo time (UTE) MR sequence was proposed as a basis for MR-AC as this sequence shows a small signal in bone. The purpose of this study was to develop a new clinically feasible MR-AC method with patient specific continuous-valued linear attenuation coefficients in bone that provides accurate reconstructed PET image data. A total of 164 [18F]FDG PET/MR patients were included in this study, of which 10 were used for training. MR-AC was based on either standard CT (reference), UTE or our method (RESOLUTE). The reconstructed PET images were evaluated in the whole brain, as well as regionally in the brain using a ROI-based analysis. Our method segments air, brain, cerebral spinal fluid, and soft tissue voxels on the unprocessed UTE TE images, and uses a mapping of R2* ? > values to CT Hounsfield Units (HU) to measure the density in bone voxels. The average error of our method in the brain was 0.1% and less than 1.2% in any region of the brain. On average 95% of the brain was within ±10% of PETCT, compared to 72% when using UTE. The proposed method is clinically feasible, reducing both the global and local errors on the reconstructed PET images, as well as limiting the number and extent of the outliers.
Practicability confirmation by meta-analysis of intravitreal ranibizumab compared to photodynamic therapy to treat polypoidal choroidal vasculopathy

Purpose The literatures show that photodynamic therapy (PDT) and intravitreal ranibizumab (IVR) have their own specific advantages in treating polypoidal choroidal vasculopathy (PCV). Using a meta-analysis, we want to provide some suggestions for the clinical application of the two treatments to PCV patients through a comparison of the functional outcomes in a follow-up period after administration. Methods A comprehensive literature search was performed using several databases to assemble the controlled trials of IVR and PDT. The program of RevMan version 5.0 was used to analyze the data. The effects of two treatments on PCV were evaluated by comparing weighted mean differences (WMDs) in the change of LogMar visual acuity, central retinal thickness (CRT), and the deterioration ratio for the proportions of patients with visual reductions from the baseline. Data with homogeneity among studies were analyzed using a fixed-effect meta-analysis model; otherwise, a random-effect model was applied to data with heterogeneity. Results: Five studies are included covering 260 cases in total in this study. The outcomes of IVR treatment compared to PDT appear to significantly improve vision, decrease the central retinal thickness (CRT), and reduce the invalidation rate. The LogMar visual acuity shifts from 0.6 to 0.3 in the following 24 months and the improvement rate of visual acuity ranges from 60–70% in IVR treated patients. However, the visual acuity improvement is moderate in the PDT group. These analyses indicate that IVR is an applicable treatment in PCV patients, although PDT is able to yield about a 35% visual acuity improvement in a short-term follow-up. Our 3-D mesh modal also confirms that IVR is able to yield better effects to treat PCV than PDT. Conclusions: The analysis in this study suggests that IVR has a significant effect on the improvement of visual acuity when treating patients with PCV. Our findings clearly document that IVR can be used as a more effective therapy for long-term administration in PCV.
Reducing Data Transfer Energy by Exploiting Similarity within a Data Transaction

Modern highly parallel GPU systems require highbandwidth DRAM I/O interfaces that can consume a significant amount of energy. This energy increases in proportion to the number of 1 values in the data transactions due to the asymmetric energy consumption of Pseudo Open Drain (POD) I/O interface in contemporary Graphics DDR SDRAMs. In this work, we describe a technique to save energy by reducing the energy-expensive 1 values in the DRAM interface. We observe that multiple data elements within a single cache line/sector are often similar to one another. We exploit this characteristic to encode each transfer to the DRAM such that there is one reference copy of the data, with remaining similar data items being encoded predominantly as 0 values. Our proposed low energy data transfer mechanism, Base+XOR Transfer, encodes the data-similar portion by performing XOR operations between data elements within a single DRAM transaction. We address two challenges that influence the efficiency of our mechanism, i) the frequent appearance of zero data elements in transactions, and ii) the diversity in the underlying size of data types within a transaction. We describe two techniques, Zero Data Remapping and Universal Base+XOR Transfer, to efficiently address these issues. Our proposed encoding scheme requires no additional metadata or changes to existing DRAM devices. We evaluate our mechanism on a modern high performance GPU system with a variety of graphics and compute workloads. We show that our mechanism reduces energy-expensive 1 values by 35.3% with minimal overheads, and combining our mechanism with Dynamic Bus Inversion (DBI) reduces 1 values by 48.2% on average. These 1 value reductions lead to 5.8% and 7.1% DRAM energy savings, respectively.
Evaluating non-invasive sampling as a monitoring tool for the Ethiopian wolf in northern Ethiopia

With an estimated global population of less than 450 individuals, the Ethiopian wolf Canis simensis is the world’s rarest canid. Its distribution is restricted to a few remote and isolated mountain ranges of the Ethiopian highlands where the populations are threatened by habitat destruction and fragmentation, disease outbreaks and persecution. Wolf populations of the northern highlands are under enormous pressure from high altitude agriculture and there is an urgent need to establish efficient methods for monitoring these populations. To this end we conducted a pilot-study evaluating the use of faecal DNA as a tool for individual identification of wolves and population genetic analysis. Faecal samples were collected from Menz in central Ethiopia, the main factors affecting amplification and genotyping success were determined, and additional samples were collected. We experienced a significant increase in the amplification rate between the first and second sampling event. The method improvement was mainly attributed to factors such as sampling strategy and storage method. A set of eight microsatellite markers was analysed for total of 42 samples, resulting in 23 unique multilocus genotypes. We conclude that by following the methodological suggestions proposed here, non-invasive sampling is an efficient way of obtaining population data for the small, elusive Ethiopian wolf populations of northern Ethiopia.
TIL as Hyperintensional Logic for Natural Language Analysis

In the paper, we introduce the main ideas of a new scientific project devoted to new methods of computer-aided linguistic and logical analysis of natural language, in particular English and Czech. The presented project started in 2015 and its main aims lead to the research of the Transparent Intensional Logic (TIL) as a framework for analysis of natural language communication and reasoning. The project follows up the previous successful cooperation between the teams involved and builds new findings on both developed linguistic and logical resources and tools as well as new methods of analysis regarding phenomena such as individual attitudes, dynamic discourse, or tenses and events.
The water footprint of bioenergy

All energy scenarios show a shift toward an increased percentage of renewable energy sources, including biomass. This study gives an overview of water footprints (WFs) of bioenergy from 12 crops that currently contribute the most to global agricultural production: barley, cassava, maize, potato, rapeseed, rice, rye, sorghum, soybean, sugar beet, sugar cane, and wheat. In addition, this study includes jatropha, a suitable energy crop. Since climate and production circumstances differ among regions, calculations have been performed by country. The WF of bioelectricity is smaller than that of biofuels because it is more efficient to use total biomass (e.g., for electricity or heat) than a fraction of the crop (its sugar, starch, or oil content) for biofuel. The WF of bioethanol appears to be smaller than that of biodiesel. For electricity, sugar beet, maize, and sugar cane are the most favorable crops [50 m3/gigajoule (GJ)]. Rapeseed and jatropha, typical energy crops, are disadvantageous (400 m3/GJ). For ethanol, sugar beet, and potato (60 and 100 m3/GJ) are the most advantageous, followed by sugar cane (110 m3/GJ); sorghum (400 m3/GJ) is the most unfavorable. For biodiesel, soybean and rapeseed show to be the most favorable WF (400 m3/GJ); jatropha has an adverse WF (600 m3/GJ). When expressed per L, the WF ranges from 1,400 to 20,000 L of water per L of biofuel. If a shift toward a greater contribution of bioenergy to energy supply takes place, the results of this study can be used to select the crops and countries that produce bioenergy in the most water-efficient way.
Well-Differentiated Papillary Mesothelioma of the Tunica Vaginalis: A Case Study and Review of the Literature

Well-differentiated papillary mesothelioma is an uncommon tumor of the testes that usually presents as a hydrocele. Here, we present the case of one patient who did not have a history of asbestos exposure. The tumor was localized in the tunica vaginalis and was composed of three pedunculated masses macroscopically. Microscopically, branching papillary structures with focal coagulative necrosis were present. In addition to immunohistochemistry, simian virus 40 DNA was also tested by polymerase chain reaction. This report presents one case of this rare entity, its clinical and macroscopic features, and follow-up results.
In vitro Cytotoxicity and Apoptotic Assay in HT-29 Cell Line Using Ficus hispida Linn: Leaves Extract

Background: Ficus hispida Linn. (Family Moraceae), well-known beneficial medicinal shrub, has been traditionally used for the treatment of various diseases such as leukoderma. Objective: The aim of the present study is to investigate the efficacy of F. hispida ethanolic leaves extract for antiproliferative, apoptotic, cell cycle blockade, and wound healing. Materials and Methods: F. hispida leaves extract was treated with colorectal adenocarcinoma cancer cell line HT29 for 24 h with control. The cells were treated at varying concentration ranges of 15, 31, 62, 125, and 250 μg/ml each The cytotoxicity effect of leaves extract was studied by 3-[4, 5-dimethylthiazol-2-yl]-2, 5 diphenyltetrazolium bromide assay and their anticancer activity was further evaluated using cell cycle analysis and wound scratch assay. Results: The end antiproliferative result showed that HT-29 cell viability decreases in a concentration-dependent manner and the growth inhibitory effect (IC50) values are obtained at a concentration of 125 μg. The increase in number of apoptotic cell was observed after treating HT-29 cells with the sample in double-staining methods. G0/G1 phase of the cell cycle was significantly blocked by the test sample followed by the G2/M phase in a negligible manner. In vitro cell wound closure or contracture was not significant when compared the sample against control group. Conclusion: F. hispida Linn. ethanolic leaves extract had shown to possess excellent cytotoxic effect through inducing apoptosis, especially causing cell cycle arrest at the G0/G1 phase. Abbreviations used: HT 29: Human adenocarcinoma colorectal cell line; PBS: Phosphate Buffered Saline; FBS: Fetal Bovine Serum; DMEM: Dulbecco's Modified Eagles Medium; MTT: 3 [4, 5 dimethylthiazol 2 yl] 2, 5 diphenyltetrazolium bromide; NCCS: National Centre for Cell Sciences; DMSO: DiMethyl SulfOxide; PI: Propidium Iodide; AO: Acridine Orange;EB: Ethidium Bromide; IC: Inhibitory Concentration.
Fecal Immunochemical Test and Fecal Calprotectin Results Show Different Profiles in Disease Monitoring for Ulcerative Colitis

Background/Aims Both fecal immunochemical test (FIT) and fecal calprotectin (Fcal) results are useful biomarkers for ulcerative colitis (UC). However, the situations in which each marker should be used are largely unknown. Methods A total of 110 colonoscopy intervals of UC patients were assessed, and correlations between changes in colonoscopic findings and changes in the two aforementioned fecal markers were examined. Results Among patients with mucosal healing (MH) and negative FIT or Fcal results at the initial colonoscopy, FIT and Fcal findings exhibited accuracies of 93% (38/41) and 79% (26/33), respectively, for predicting the results of the subsequent examination. Among the 24 patients who showed endoscopic activity at the precedent colonoscopy and MH at the subsequent examination, positive-to-negative conversion of FIT and Fcal findings at the subsequent examination was observed in 92% (12/13) and 62% (8/13) of patients, respectively. Among the 43 patients who showed endoscopic activity at both the precedent and subsequent examinations, Fcal findings reflected the change in endoscopic activity better than FIT results (r=0.59, p<0.0001 vs r=0.30, p=0.054). Conclusions The FIT is useful for confirming MH and the occurrence of relapse. In contrast, Fcal is useful for monitoring the mucosal status of patients with active inflammation.
Predictors of Adherent Use of Diaphragms and Microbicide Gel in a Four-Arm, Randomized Pilot Study Among Female Sex Workers in Madagascar

Background: Participants' protocol adherence may influence assessments of the effectiveness of new female-controlled methods for sexually transmitted infection prevention. Methods: In 2005 we conducted a randomized pilot study among female sex workers (FSWs) in Madagascar in preparation for sexually transmitted infection prevention trial of diaphragms and a vaginal microbicide. Participants (n = 192) were randomized into 4 arms: diaphragm plus microbicide (Acidform), diaphragm plus placebo gel hydroxyethyl cellulose (HEC), Acidform alone, or HEC alone. FSWs were seen weekly for 4 weeks. Using multivariable regression with generalized estimating equations, we assessed predictors of adherent product use during all sex acts in the last week. We collapsed the gel-diaphragm arms together and the gel-only arms together for this analysis. Results: Between 43% and 67% of gel-diaphragm users (varying by visit) reported using study products during all sex acts in the last week, compared with 20% to 45% of gel-only users. Adherence increased with follow-up [visit 4 vs. visit 1 risk ratio (RR) for gel-diaphragm users: 1.55, P <0.01; for gel-only users, RR: 1.58, P = 0.01]. Gel-diaphragm users whose casual partners were never aware of products (RR: 2.02, P = 0.03) and who had experienced partner violence after requesting condom use (RR: 1.45, P <0.01) were more adherent. Gel-only users reporting lower sexual frequency (1–9 weekly acts vs. ≥19 acts, RR: 1.98, P <0.01) and no sex with primary partners in the past week (RR: 1.54, P = 0.02) were more adherent. Conclusions: Gel-diaphragm users had better adherence than gel-only users, and predictors of adherence differed between groups. Addressing modifiable factors during counseling sessions may improve adherence.
Neonatal Sleep–Wake Analyses Predict 18-month Neurodevelopmental Outcomes

Objectives The neurological examination of critically ill neonates is largely limited to reflexive behavior. The exam often ignores sleep-wake physiology that may reflect brain integrity and influence long-term outcomes. We assessed whether polysomnography and concurrent cerebral near-infrared spectroscopy (NIRS) might improve prediction of 18-month neurodevelopmental outcomes. Methods Term newborns with suspected seizures underwent standardized neurologic examinations to generate Thompson scores and had 12-hour bedside polysomnography with concurrent cerebral NIRS. For each infant, the distribution of sleep-wake stages and electroencephalogram delta power were computed. NIRS-derived fractional tissue oxygen extraction (FTOE) was calculated across sleep-wake stages. At age 18-22 months, surviving participants were evaluated with Bayley Scales of Infant Development (Bayley-III), 3rd edition. Results Twenty-nine participants completed Bayley-III. Increased newborn time in quiet sleep predicted worse 18-month cognitive and motor scores (robust regression models, adjusted r2 = 0.22, p = .007, and 0.27, .004, respectively). Decreased 0.5-2 Hz electroencephalograph (EEG) power during quiet sleep predicted worse 18-month language and motor scores (adjusted r2 = 0.25, p = .0005, and 0.33, .001, respectively). Predictive values remained significant after adjustment for neonatal Thompson scores or exposure to phenobarbital. Similarly, an attenuated difference in FTOE, between neonatal wakefulness and quiet sleep, predicted worse 18-month cognitive, language, and motor scores in adjusted analyses (each p < .05). Conclusions These prospective, longitudinal data suggest that inefficient neonatal sleep-as quantified by increased time in quiet sleep, lower electroencephalogram delta power during that stage, and muted differences in FTOE between quiet sleep and wakefulness-may improve prediction of adverse long-term outcomes for newborns with neurological dysfunction.
Diagnostic Value of D-Dimer in Acute Myocardial Infarction Among Patients With Suspected Acute Coronary Syndrome

Background The role of D-dimer as a diagnostic marker in myocardial infarction (MI) and acute coronary syndrome (ACS) is still a question. The aim of this study was to evaluate the diagnostic value of D-dimer in the diagnosis of AMI in patients suspected with ACS. Methods This cross-sectional study was conducted on patients suspected with ACS. Serial standard 12-lead electrocardiogram (ECG), D-dimer, and troponin tests were done for all the patients. According to the examinations, ECG changes, and troponin, patients were allocated into two groups of MI and unstable angina (UA). Chi-square, independent t-test, and Pearson correlation test were used by SPSS ver, 17. Cut-off point of D-dimer for MI diagnosis was evaluated by receiver operating characteristic (ROC) curve analysis. Results Seventy-five patients with a mean age of 63.1 ± 9.75 years were studied in two groups of MI (n = 34) and UA (n = 41). Patients were homogeneous based on age, gender, and risk factors for diabetes and dyslipidemia. D-dimer in patients with MI patients was higher than in patients with UA (P = 0.001). The optimal cut-off point of D-dimer for diagnosis of MI was 548 mEq/L with sensitivity and specifity of 63.4% and 91.2%, respectively. Conclusions Based on the results of this study, it seems that the measurement of D-dimer serum level can be appropriate as a marker with high sensitivity and relatively high specificity for differentiating MI from UA in patients with suspected ACS.
Piecewise hysteresis-type control of a single phase active three-level rectifier with low THD

This paper is focused on the analysis and design of a switching control strategy to correct power factor, to regulate output voltage of a single-phase active three-level rectifier (SPATR) and to guarantee low harmonic distortion using a type of hysteresis current-mode control. The switching criterion is designed analyzing the stability of the switched linear system, to avoid information loss from sinusoidal signals during the whole period of operation. The main advantage of the proposed control is that it is capable of controlling the input current ripple and maintaining a low harmonic distortion. The approach uses switched linear models instead of average models, therefore its applicability is not restricted in a local set about the operating point. Simulations were carried out to demonstrate the advantages of the control as well as to compare its performance with other existing in the literature. Simulations of the SPATR and control algorithm were performed using the Matlab / Simulink environment.
Impact of HPV infection on oral squamous cell carcinoma

Background Head and neck squamous cell carcinomas (HNSCC) are often divided by their aetiology. Noxae associated collectives are compared with the human papilloma virus (HPV)-associated group, whereas different localisations of oral (OSCC) and oropharyngeal (OPSCC) squamous cell carcinomas are mostly discussed as one single group. Our aim was to show that classification by aetiology is not appropriate for OSCC. Results HPV DNA was detected by PCR in 7 (3.47%) patients, and we identified 12 (5.94%) positive (+) cases by p16INK4a immunostaining. Only 4 (1.98%) of the p16INK4a+ cases were + for HPV using PCR. Our homogenous collective of OSCC allowed us to compare HPV+ and HPV negative (−) patients without creating bias for tumour localisation, age, gender or tumour stage. Materials and methods After testing OSCC samples for HPV positivity, we compared the results of two commonly used HPV detection methods, p16INK4a immunostaining and HPV DNA-related PCR, on 202 OSCC patients. HPV subtypes were determined with an HPV LCD Array Kit. Clinicopathological features of the patients were analysed, and the disease specific survival rates (DSS) for HPV+ and HPV− patients were obtained. Conclusions p16INK4a immunostaining is a not a reliable HPV detection method for OSCC. Positive p16INK4a immunostaining did not agree with + results from PCR of HPV DNA. Furthermore, the influence of HPV-related oncogenic transformation in OSCC is overestimated. The significance of HPV infection remains clinically unclear, and its influence on survival rates is not relevant to OSCC cases.