Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis of C3b binding by glycoprotein C of herpes simplex virus

Glycoproteins C (gC) from herpes simplex virus type 1 (HSV-1) and HSV-2, gC-1 and gC-2, bind the human complement fragment C3b, although the two glycoproteins differ in their abilities to act as C3b receptors on infected cells and in their effects on the alternative complement pathway. Previously, we identified three regions of gC-2 (I, II, and III) which are important for C3b binding. In this study, our goal was to identify C3b-binding sites on gC-1 and to continue our analysis of gC-2. We constructed a large panel of mutants by using the cloned gC-1 and gC-2 genes. Most of the mutant proteins were transported to the surface of transiently transfected L cells and reacted with one or more monoclonal antibodies to discontinuous epitopes. By using 31 linker insertion mutants spread across the coding region of gC-1, we identified four regions in the ectodomain of gC-1 which are important for C3b binding, three of which are similar in position to C3b-binding regions I, II, and III of gC-2. Region III shares some similarities with the short consensus repeat found in CR1, the human complement receptor. These were, in part, the targets for construction of 20 single amino acid changes in region III of gC-1 and gC-2. These mutants identified similarities and differences in the C3b-binding properties of gC-1 and gC-2 and suggest that the amino half of region III is more important for C3b binding. However, our results do not support the concept of a structural relationship between the short consensus repeat of CR1 and gC, since mutations of some of the conserved residues, including three of four cysteines in region III, had no effect on C3b binding. Finally, we constructed four deletion mutants of gC-1, including one which lacked residues 33 to 123, as well as residues 367 to 449. This severely truncated molecule, lacking four cysteines and five potential N-linked glycosylation sites, was transported to the cell surface and retained its ability to bind monoclonal antibodies as well as C3b. Thus, the four distinct C3b-binding regions of gC-1 and several epitopes within two different antigenic sites are localized within residues 124 to 366.
A Perspective on the Future of Middleware-based Software Engineering

Middleware is a software layer that stands between the networked operating system and the application and provides well known reusable solutions to frequently encountered problems like heterogeneity, interoperability, security, dependability. Further, with networks becoming increasingly pervasive, middleware appears as a major building block for the development of future software systems. Starting with the impact of pervasive networking on computing models, manifested by now common grid and ubiquitous computing, this paper surveys related challenges for the middleware and related impact on the software development. Indeed, future applications will need to cope with advanced non-functional properties such as context- awareness and mobility, for which adequate middleware support must be devised together with accompanying software development notations, methods and tools. This leads us to introduce our view on next generation middleware, considering both technological advances in the networking area but also the need for closer integration with software engineering best practices, to ultimately suggest middleware-based software processes.
Unsupervised cross-lingual speaker adaptation for HMM-based speech synthesis

In the EMIME project, we are developing a mobile device that performs personalized speech-to-speech translation such that a user's spoken input in one language is used to produce spoken output in another language, while continuing to sound like the user's voice. We integrate two techniques, unsupervised adaptation for HMM-based TTS using a word-based large-vocabulary continuous speech recognizer and cross-lingual speaker adaptation for HMM-based TTS, into a single architecture. Thus, an unsupervised cross-lingual speaker adaptation system can be developed. Listening tests show very promising results, demonstrating that adapted voices sound similar to the target speaker and that differences between supervised and unsupervised cross-lingual speaker adaptation are small.
A Propensity-Matched Analysis Between Standard Versus Tapered Oral Vancomycin Courses for the Management of Recurrent Clostridium difficile Infection

Abstract Background This study was conducted to compare clinical outcomes of oral vancomycin courses without taper versus oral vancomycin courses with taper for treatment of recurrent Clostridium difficile infection (CDI). Methods This investigation was a multicenter, retrospective, propensity score-matched analysis study using a Veterans Health Administration national clinical administrative database. Adult patients who were treated for recurrent CDI from any Veterans Affairs Medical Center between June 1, 2011 and October 31, 2016 were included if they were treated with oral vancomycin with or without a tapering regimen. The 2 groups were matched by next-nearest approach from a propensity score formula derived from independent variables associated with the selection of a taper regimen. Results Propensity score matching resulted in 2 well-matched groups consisting of 226 episodes of patients treated with a vancomycin taper regimen and 678 episodes treated by vancomycin regimen without taper. No difference was found for the primary outcome of 180-day recurrence (59 of 226 [26.1%] for taper regimens versus 161 of 678 [23.8%], P = .48). A secondary outcome of 90-day all-cause mortality met statistical significance, favoring a taper regimen (5.31% vs 9.29%, P = .049); however, secondary outcomes of 90-day recurrence and 180-day all-cause mortality were not different. Conclusions Vancomycin taper regimens did not provide benefit over vancomycin regimens without taper in preventing additional CDI recurrence in patients with first or second recurrent episodes in this propensity score-matched analysis.
Disseminated intravascular coagulation in acute leukemia: clinical and laboratory features at presentation

Abstract: Background: Although there are two major scoring systems for the clinical diagnosis of disseminated intravascular coagulation (DIC), the validity of these systems for leukemia‐associated DIC remains to be confirmed. Methods: By analyzing 125 newly diagnosed acute leukemia patients, we investigated clinical and laboratory features of leukemia‐associated DIC, and determined the validity of the two established criteria. Results: A total of 36 patients (29%) were diagnosed with DIC according to expert opinion, a method regarded as the de facto gold standard. Leukemia‐associated DIC is characterized by rare manifestation of organ failure because of thrombosis and no relevance of the platelet count for the diagnosis. The results of receiver operating characteristics analysis favored fibrin degradation product (FDP) rather than D‐dimer as the fibrin‐related marker test. Although prothrombin time, plasma fibrinogen, and serum FDP levels were significantly different for patients with and without DIC, multivariate analysis identified FDP levels to be the only factor associated with DIC diagnosis. The cut‐off level of 15 μg/mL for FDP was found to be the most effective to differentiate DIC from non‐DIC, resulting in diagnostic sensitivity and specificity of 92% and 96%, respectively. The diagnostic results for our patients produced with this FDP‐based system were at least comparable with or superior to those obtained with the two currently available scoring systems. Conclusions: Our findings suggest that an FDP‐based criterion may be applicable for the diagnosis of leukemia‐associated DIC. Although it appears to be simple and practicable enough for clinical use, prospective validation of this criterion is needed.
LDPC Coded Turbo Equalization for MIMO System

—In this paper, MIMO (Multiple-Input-Multiple Output) system based on turbo equalization techniques which LDPC (Low Density Parity Check) codes were outer code and STTC (Space Time Trellis Code) were employed as an inner code are studied. LDPC decoder and STTC decoder are connected through the interleaving and de-interleaving that updates each other's information repeatedly. On the receiver side, in processing the turbo equalization with STTC decoder, in order to feed extrinsic information to STTC decoder, the extrinsic information of LDPC decoder must be two bit processing. However LDPC codes can't be applied to these system because LDPC decoder require just one bit processing. Therefore this paper proposes a turbo equalization model for LDPC codes able to apply MIMO systems combined with STTC codes. Through simulation results, we show that the performance of the proposed turbo equalization model is improved about 2.5 dB than that of turbo codes and about 10.5dB than that of conventional scheme.
Plant Image Segmentation and Annotation with Ontologies in BisQue

Author(s): Preece, Justin; Elser, Justin; Jaiswal, Pankaj; Kvilekval, Kristian; Fedorov, Dmitry; Manjunath, BS; Kitchen, Ryan; Xu, Xu; Trigkakis, Dmitrios; Todorovic, Sinisa; Carbon, Seth | Editor(s): Jaiswal, Pankaj; Hoehndorf, Robert; Arighi, Cecilia N; Meier, Austin
Cardiovascular effects of traffic noise: the role of negative self-statements

Synopsis This study assesses cardiovascular and subjective effects of traffic noise and the mediator role that negative self-statements play. Eighty-four female students underwent a Physiological Reaction Test to two 15 min presentations of high intensity traffic noise (85–95 db) under two noise conditions, with and without negative self-statements. Half of the subjects were given specific instructions to increase the credibility of the self-statements. Dependent variables were heart rate (HR), blood volume pulse amplitude from both temporal arteries and subjective tension. Traffic noise provoked subjective tension and cardiovascular responses that did not habituate either within or between noise presentations. Negative self-statements had the greatest effect on HR. In fact, this response habituated to a second noise presented only when this condition was without negative self-statements. Instructions increased the effect of the self-statements only on the left temporal artery and also increased subjective tension. The implications of this physiological reactivity in psychosomatic problems and the importance of negative self-statements are discussed.
Helicobacter pylori CagA and gastric carcinogenesis.

OBJECTIVES This study aimed to demonstrate the tyrosine phosphorylation motif (TPM) and 3' region structure of the Helicobacter pylori CagA gene as well as its SHP-2 binding activity in AGS cells and relation to gastric carcinogenesis. METHODS Sixteen clinical isolate H. pylori strains from eight duodenal ulcer and eight gastric adenocarcinoma patients were studied for CagA repeat sequence EPIYA motifs, C-terminal structure, and western blot analysis of CagA protein expression, translocation, and SHP-2 binding in AGS cells. RESULTS Except for strain 547, all strains from the gastric adenocarcinoma patients were positive for CagA by PCR and had three EPIYA copy motifs. Western blotting showed that all strains were positive for CagA protein expression (100%), CagA protein translocation (100%), and SHP-2 binding (100%). CagA protein expression was significantly higher in the gastric adenocarcinoma patients than in the duodenal ulcer patients (P=0.0023). CagA protein translocation and SHP-2 binding in the gastric adenocarcinoma patients were higher than those in the duodenal ulcer patients, but no significant differences were found between the two groups (P=0.59, P=0.21, respectively). CONCLUSIONS The TPMs and 3' region structures of the H. pylori CagA gene in the duodenal ulcer and gastric adenocarcinoma patients have no significant differences.
Plant Diversity of The Mid Silurian (Lower Wenlock, Sheinwoodian) Terrestrial Vegetation Preserved in Marine Sediments from The Barrandian Area, The Czech Republic

Abstract Plant mega- and microfossils are described from the middle Sheinwoodian of the Barrandian area. The material comes from the Loděnice locality and the same horizon as the earliest unequivocal land plant, Cooksonia barrandei LIBERTÍN, J.KVAČEK, BEK, ŽÁRSKÝ et ŠTORCH. Its age (432 Myr) is inferred from the associated graptolite fauna, including the zonal index graptolite Monograptus belophorus. Megafossils have clear similarity with Cooksonia, due to their dichotomised axes with slightly widened subtending axes bearing putative sporangia. They document some of the plant diversity that was in place when the first proven representative of the genus Cooksonia appeared, and together with dispersed spores they provide strong and important evidence that a diversified terrestrial ecosystem had developed on the Barrandian volcanic archipelago in the peri-Gondwanan realm by the end of the Sheinwoodian Stage of the Silurian Period.
Low Pathogenic Avian Influenza and Coinfecting Pathogens: A Review of Experimental Infections in Avian Models

SUMMARY Low pathogenic avian influenza virus (LPAIV) usually causes mild disease or asymptomatic infection in poultry. LPAIV has, however, become a great threat to poultry industry due to mixed infections with other pathogens. Coinfections do frequently occur in the field but are not easily detected, and their impact on pathobiology is not clearly defined due to their complicated nature, but it is well known that there is an impact. One way to increase our knowledge of coinfections in poultry is to challenge birds in experimental and controlled conditions. While many articles report in vivo experiments with LPAIV in avian models, only a few have studied coinfections. Moreover, researchers tend to choose different bird types, ages, inoculation routes, and doses for their experiments, making it difficult to compare between studies. This review describes the state of the art for experimental infections with LPAIV alone or associated with coinfecting pathogens in avian models. It also discusses how best to mimic field infections in laboratory settings. In the field of avian diseases, experimental design is obviously directly linked with the research question addressed, but there is a gap between field and experimental data, and further studies are warranted to better understand how to bring laboratory settings closer to field situations.
TISSUE DISTRIBUTION AND ONTOGENY OF ORGANIC CATION TRANSPORTERS IN MICE

Organic cation transporters (Octs) play an important role in transporting cationic xeno- and endobiotics across biological membranes. Little is known about Octs in mice; therefore, the tissue distribution and developmental changes in the mRNA expression of Octs in mice were quantified. Oct1, Oct2, Oct3, Octn1, Octn2, and Octn3 mRNA expression was quantified in 14 tissues from male and female mice using the branched DNA signal amplification assay. Oct1 mRNA expression was highest in kidney, followed by liver. Oct2 mRNA was almost exclusively expressed in kidney, with male mice having twice that in female mice. The higher expression of Oct2 in male mice is due to testosterone. Oct3 mRNA was most highly expressed in placenta, ovary, and uterus, but was expressed at low levels in most tissues. Octn1 and Octn2 mRNA expression was similar, with the highest levels in kidney followed by small intestine. Octn3 mRNA was almost exclusively expressed in testes. The developmental expression of Oct1, Oct2, Octn1, and Octn2 mRNA in kidneys as well as Oct1 in liver was determined in young mice. Ontogenic expression data indicate that each of the Octs approached adult expression levels by about 3 weeks of age. The gender difference in Oct mRNA expression did not become apparent until day 30 after birth. The differences in tissue distribution of the Octs may play an important role in drug disposition to various tissues. Furthermore, low expression of the Octs in young animals may affect the pharmacokinetic behavior of drugs compared with that in adults.
The Association between Parameters of Malnutrition and Diagnostic Measures of Sarcopenia in Geriatric Outpatients

Objectives Diagnostic criteria for sarcopenia include measures of muscle mass, muscle strength and physical performance. Consensus on the definition of sarcopenia has not been reached yet. To improve insight into the most clinically valid definition of sarcopenia, this study aimed to compare the association between parameters of malnutrition, as a risk factor in sarcopenia, and diagnostic measures of sarcopenia in geriatric outpatients. Material and Methods This study is based on data from a cross-sectional study conducted in a geriatric outpatient clinic including 185 geriatric outpatients (mean age 82 years). Parameters of malnutrition included risk of malnutrition (assessed by the Short Nutritional Assessment Questionnaire), loss of appetite, unintentional weight loss and underweight (body mass index <22 kg/m2). Diagnostic measures of sarcopenia included relative muscle mass (lean mass and appendicular lean mass [ALM] as percentages), absolute muscle mass (total lean mass and ALM/height2), handgrip strength and walking speed. All diagnostic measures of sarcopenia were standardized. Associations between parameters of malnutrition (independent variables) and diagnostic measures of sarcopenia (dependent variables) were analysed using multivariate linear regression models adjusted for age, body mass, fat mass and height in separate models. Results None of the parameters of malnutrition was consistently associated with diagnostic measures of sarcopenia. The strongest associations were found for both relative and absolute muscle mass; less stronger associations were found for muscle strength and physical performance. Underweight (p = <0.001) and unintentional weight loss (p = 0.031) were most strongly associated with higher lean mass percentage after adjusting for age. Loss of appetite (p = 0.003) and underweight (p = 0.021) were most strongly associated with lower total lean mass after adjusting for age and fat mass. Conclusion Parameters of malnutrition relate differently to diagnostic measures of sarcopenia in geriatric outpatients. The association between parameters of malnutrition and diagnostic measures of sarcopenia was strongest for both relative and absolute muscle mass, while less strong associations were found with muscle strength and physical performance.
An Evaluation of the Current Land Laws in Solving the Urban Squatter Land Tenure Problem

viii LIST OF ABBREVIATIONS . x LIST OF CASES. xi LIST OF FIGURES . xii LIST OF STATUTES AND INTERNATIONAL INSTRUMENTS . xiii CHAPTER ONE: INTRODUCTION TO THE STUDY . 1 1.1. Background . 1 1.2. Statement of the Problem . 7 1.3. Research Questions . 7 1.4. Objectives of the Study . 8 1.5. Hypotheses . 8 1.6. Justification of the Study . 8 1.7. Literature Review . 8 1.7. 1. Understanding Urban Squatter Settlements/Informal Settlements . 9 1.7. 2. Land Tenure in Kenya . 10 1.7. 3. Land Access and Land Tenure in Squatter/Informal settlements . 12 1.7. 4. Securing tenure in squatter or informal settlements . 14 1.8. Analytical Framework . 18 1.8. 1. Conceptual framework . 19 1.9. Research Methodology . 22 1.9. 1. Research design . 22 1.9. 2. Study Site . 23 1.9. 3 Sampling and data collection . 23 1.9. 4 Data analysis . 23 1.10 Anonymity . 24 1.11 Study Limitations . 24
A weighted flexible naive Bayesian classifier for continuous attributes

In this paper, a weighted flexible naive Bayesian classifier (simply WFNB) is proposed to handle the classification problem with the continuous attributes. In WFNB, every marginal probability density function (p.d.f.) in the class-conditional p.d. f. is assigned a weight by measuring the dependence between the corresponding condition attribute and the class attribute. The dependence is the mutual information between the individual attribute and the class attribute. Then, we compare the classification accuracy of WFNB with the traditional flexible naive Bayesian classifier (FNB) on 10 VCI datasets. The experimental results show that our proposed WFNB can obtain the statistically better classification accuracy and demonstrate that WFNB is feasible and efficient.
Robust -∞ Filtering of Time-Delay Jump Systems with Respect to the Finite-Time Interval

This paper studied the problem of stochastic finite-time boundedness and disturbance attenuation for a class of linear time-delayed systems with Markov jumping parameters. Sufficient conditions are provided to solve this problem. The 𝐿2-𝐿∞ filters are, respectively, designed for time-delayed Markov jump linear systems with/without uncertain parameters such that the resulting filtering error dynamic system is stochastically finite-time bounded and has the finite-time interval disturbance attenuation 𝛾 for all admissible uncertainties, time delays, and unknown disturbances. By using stochastic Lyapunov-Krasovskii functional approach, it is shown that the filter designing problem is in terms of the solutions of a set of coupled linear matrix inequalities. Simulation examples are included to demonstrate the potential of the proposed results.
The elliptical galaxy colour–magnitude relation as a discriminant between the monolithic and merger paradigms

The colour-magnitude relation (CMR) of cluster elliptical galaxies has been widely used to constrain their star formation histories (SFHs) and to discriminate between the monolithic collapse and merger paradigms of elliptical galaxy formation. We use a �CDM hierarchical merger model of galaxy formation to investigate the existence and redshift evolution of the elliptical galaxy CMR in the merger paradigm. We show that the star formation history (SFH) of cluster ellipticals predicted by the model is quasimonolithic, with only � 10 percent of the total stellar mass forming after z � 1. The quasi-monolithic SFH results in a predicted CMR that agrees well with its observed counterpart in the redshift range 0 < z < 1.27. We use our analysis to argue that the elliptical-only CMR can be used to constrain the SFHs of present-day cluster ellipticals only if we believe a priori in the monolithic collapse model. It is not a meaningful tool for constraining the SFH in the merger paradigm, since a progressively larger fraction of the progenitor set of present-day cluster ellipticals is contained in late-type star forming systems at higher redshift, which cannot be ignored when deriving the SFHs. Hence, the elliptical-only CMR is not a useful discriminant between the two competing theories of elliptical galaxy evolution.