Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of cholesterol on conformational disorder in dipalmitoylphosphatidylcholine bilayers. A quantitative IR study of the depth dependence.

A method originally proposed by Snyder and Poore [(1973) Macromolecules 6, 708-715] as a specific probe of trans-gauche isomerization in hydrocarbon chains and recently applied [Mendelsohn et al. (1989) Biochemistry 28, 8934-8939] to the quantitative determination of phospholipid acyl chain conformational order is utilized to monitor the effects of cholesterol at various depths in dipalmitoylphosphatidylcholine (DPPC) bilayers. The method is based on the observation that the CD2 rocking modes from the acyl chains of specifically deuterated phospholipids occur at frequencies in the Fourier transform infrared spectrum which depend upon the local geometry (trans or gauche) of the C-C-C skeleton surrounding a central CD2 group. Three specifically deuterated derivatives of DPPC, namely, 4,4,4',4'-d4 DPPC (4-d4 DPPC), 6,6,6',6'-d4 DPPC (6-d4 DPPC), and 12,12,12',12'-d4 DPPC (12-d4 DPPC), have been synthesized, and the effects of cholesterol addition at 2:1 DPPC/cholesterol (mol:mol) on acyl chain order at various temperatures have been determined. At 48 degrees C, cholesterol inhibits gauche rotamer formation by factors of approximately 9 and approximately 6 at positions 6 and 4, respectively, of the acyl chains, thus demonstrating a strong ordering effect in regions of the bilayer where the sterol rings are presumed to insert parallel to the DPPC acyl chains. In contrast, the ability of the sterol to order the acyl chains is much reduced at the 12-position. The sterol demonstrates only a slight disordering of phospholipid gel phases. Finally, the contributions of different classes of gauche conformers to the spectra have been determined. (ABSTRACT TRUNCATED AT 250 WORDS)
N-fold Templated Piped Correction

We describe a broadly-applicable conservative error correcting model,N-fold Templated Piped Correction (NTPC), that consistently improves the accuracy of existing high-accuracy base models. Under circumstances where most obvious approaches actually reduce accuracy more than they improve it, NTPC nevertheless comes with little risk of accidentally degrading performance. NTPC is particularly well suited for natural language applications involving high-dimensional feature spaces, such as bracketing and disambiguation tasks, since its easily customizable templatedriven learner allows efficient search over the kind of complex feature combinations that have typically eluded the base models. We show empirically that NTPC yields small but consistent accuracy gains on top of even high-performing models like boosting. We also give evidence that the various extreme design parameters in NTPC are indeed necessary for the intended operating range, even though they diverge from usual practice.
Inpatient rehabilitation outcome: a matter of diagnosis?

Background Patients with comorbidities are becoming more and more common in Italian rehabilitative wards. These comorbidities are considered a major problem for inpatient rehabilitation, due to the fact that they cause longer lengths of stay, higher costs, and lower functional results. Methods To investigate the possible relationships between comorbidity, functional impairment, age, and type of discharge in patients hospitalized in postacute rehabilitation facilities, we planned an observational study. A total of 178 consecutive inpatients (average age: 78 years [range: 39–99]) from postacute rehabilitation facilities were recruited. Primary diagnosis, comorbidity rating (Cumulative Illness Rating Scale – Geriatric version, CIRS-G) and functional impairment score (Functional Independence Measure, FIM™) were evaluated at admission. The FIM™ rating was also assessed at hospital discharge. Results A total of 178 of the 199 enrolled patients completed the rehabilitation treatment (89.4%). The average length of stay was 46 ± 24 days. CIRS-G showed an average comorbidity score for each patient of 4.45 ± 1.69. The average FIM™ rating was 79 ± 24.88 at admission, and 91.9 ± 25.7 at discharge. Diagnosis at admission (grouped according to the International Classification of Diseases 9-CM) seemed to correlate with functional results, since lower rehabilitative efficiency was obtained for patients who had a history of stroke. Conclusion The number and type of comorbidities (CIRS-G) in rehabilitation inpatients do not seem to affect functional outcomes of treatment. The determining factor for a lower level of functional recovery seems to be the diagnosis at admission.
Boosting the Detection of Malicious Documents Using Designated Active Learning Methods

Most organizations usually create, send and receive huge amounts of documents daily, Attackers increasingly take advantage of innocent users who tend to casually open email massages assumed to be benign, carrying malicious documents. Recent targeted attacks aimed at organizations, utilize the new Microsoft Word documents (*.docx). Anti-virus software fails to detect new unknown malicious files, including malicious docx files. In this study, we present SFEM feature extraction methodology and designated Active Learning (AL) methods, aimed at accurate detection of new unknown malicious docx files that also efficiently enhances the detection's model capabilities over time. Our AL methods identify and acquire only small set of new docx files that are most likely malicious, as well as informative benign files, these files are used for enhancing the knowledge stores of both the detection model and the anti-virus software. Results show that our active learning methods used only 14% of the labeled docx files within organization which led to a reduction of 95.5% in labeling efforts compared to passive learning and SVM-Margin (existing active learning method). Our AL methods also showed a significant improvement of 91% in unknown docx malware acquisition compared to passive learning and SVM-Margin, thus providing an improved updating solution for detection model, as well as the anti-virus software widely used within organizations.
Targeting of a Short Peptide Derived from the Cytoplasmic Tail of the G1 Membrane Glycoprotein of Uukuniemi Virus (Bunyaviridae) to the Golgi Complex

ABSTRACT Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi. We recently mapped the retention signal for Golgi localization in oneBunyaviridae member (Uukuniemi virus) to the cytoplasmic tail of G1. We now show that a myc-tagged 81-residue G1 tail peptide expressed in BHK21 cells is efficiently targeted to the Golgi complex and retained there during a 3-h chase. Green-fluorescence protein tagged at either end with this peptide or with a C-terminally truncated 60-residue G1 tail peptide was also efficiently targeted to the Golgi. The 81-residue peptide colocalized with mannosidase II (a medial Golgi marker) and partially with p58 (an intermediate compartment marker) and TGN38 (a trans-Golgi marker). In addition, the 81-residue tail peptide induced the formation of brefeldin A-resistant vacuoles that did not costain with markers for other membrane compartments. Removal of the first 10 N-terminal residues had no effect on the Golgi localization but abolished the vacuolar staining. The shortest peptide still able to become targeted to the Golgi encompassed residues 10 to 40. Subcellular fractionation showed that the 81-residue tail peptide was associated with microsomal membranes. Removal of the two palmitylation sites from the tail peptide did not affect Golgi localization and had only a minor effect on the association with microsomal membranes. Taken together, the results provide strong evidence that Golgi retention of the heterodimeric G1-G2 spike protein complex of Uukuniemi virus is mediated by a short region in the cytoplasmic tail of the G1 glycoprotein.
Notice of RetractionEducation background of Top Management Teams and the organizational performance of Small and Medium-sized Enterprises: Based on upper echolons theory

Taking 200 Small and Medium-sized Enterprises (SMEs) listed in Shenzhen Securities Exchanges as samples, this paper analyzed the situation of education backgroud of Top Management Teams (TMTs) by using statistical techniques. Analysis found that most of the TMTs member is in higher diploma, at least associoated degree, while the proportion of TMTs' members who with the educational background of MBA or related courses is relatively low. The results of study also show: (1) the most chief menber's education background of TMTs are relevant to company's industry; (2) the relevance that the MBA backgroud of TMTs to the organizational performance is not significant.
Synthesizing Complementary Circuits Automatically

One of the most difficult jobs in designing communication and multimedia chips is to design and verify the complex complementary circuit pair (E, E-1), in which circuit E transforms information into a format suitable for transmission and storage, and its complementary circuit E-1 recovers this information. In order to facilitate this job, we proposed a novel two-step approach to synthesize the complementary circuit E-1 from E automatically. First, a SAT solver was used to check whether the input sequence of E can be uniquely determined by its output sequence. Second, the complementary circuit E-1 was built by characterizing its Boolean function, with an efficient all-solution SAT solver based on discovering XOR gates and extracting unsatisfiable cores. To illustrate its usefulness and efficiency, we ran our algorithm on several complex encoders from industrial projects, including PCIE and 10 G Ethernet, and successfully built correct complementary circuits for them.
Information Quality Improvement as a Measure of Business Intelligence System Benefits

Since business intelligence systems' impact on performance is first of all long-termed and indirect, most measures of business value are not sufficiently close to immediate influence of such systems and therefore not suitable to justify investments into business intelligence systems in real business environments. Thus, measures related to increased information quality as a result of business intelligence systems introduction are commonly used. The purpose of this study is to test how much does implementation of business intelligence systems actually contribute to solving the major issues regarding information quality. Empirical data were collected through a survey of Slovenian medium and large size organizations. Quantitative analysis was carried out on the data, which related to 181 medium and large size organizations. The results of the analysis show that business intelligence systems actually have a positive impact on both segments of information quality, namely content quality and media quality. However, the impact of business intelligence systems on media quality is stronger, while the quality of content is more important for making better business decisions and providing higher business value of business intelligence systems. Thus, there is still a gap between available information quality and knowledge workers' needs, in other words - key information quality problems still exist.
Cited2 is required both for heart morphogenesis and establishment of the left-right axis in mouse development

Establishment of the left-right axis is a fundamental process of vertebrate embryogenesis. Failure to develop left-right asymmetry leads to incorrect positioning and morphogenesis of numerous internal organs, and is proposed to underlie the etiology of several common cardiac malformations. The transcriptional modulator Cited2 is essential for embryonic development: Cited2-null embryos die during gestation with profound developmental abnormalities, including cardiac malformations, exencephaly and adrenal agenesis. Cited2 is also required for normal establishment of the left-right axis; we demonstrate that abnormal heart looping and right atrial and pulmonary isomerism are consistent features of the left-right-patterning defect. We show by gene expression analysis that Cited2 acts upstream of Nodal, Lefty2 and Pitx2 in the lateral mesoderm, and of Lefty1 in the presumptive floor plate. Although abnormal left-right patterning has a major impact on the cardiac phenotype in Cited2-null embryos, laterality defects are only observed in a proportion of these embryos. We have therefore used a combination of high-resolution imaging and three-dimensional (3D) modeling to systematically document the full spectrum of Cited2-associated cardiac defects. Previous studies have focused on the role of Cited2 in cardiac neural crest cell development, as Cited2 can bind the transcription factor Tfap2, and thus affect the expression of Erbb3 in neural crest cells. However, we have identified Cited2-associated cardiac defects that cannot be explained by laterality or neural crest abnormalities. In particular, muscular ventricular septal defects and reduced cell density in the atrioventricular (AV) endocardial cushions are evident in Cited2-null embryos. As we found that Cited2 expression tightly correlated with these sites, we believe that Cited2 plays a direct role in development of the AV canal and cardiac septa. We therefore propose that, in addition to the previously described reduction of cardiac neural crest cells, two other distinct mechanisms contribute to the spectrum of complex cardiac defects in Cited2-null mice; disruption of normal left-right patterning and direct loss of Cited2 expression in cardiac tissues.
Performance Analysis of Convex Data Detection in MIMO

We study the performance of a convex data detection method in large multiple-input multiple-output (MIMO) systems. The goal is to recover an n-dimensional complex signal whose entries are from an arbitrary constellation $\mathcal{D} \subset \mathbb{C}$, using m noisy linear measurements. Since the Maximum Likelihood (ML) estimation involves minimizing a loss function over the discrete set ${\mathcal{D}^n}$, it becomes computationally intractable for large n. One approach is to relax to a $\mathcal{D}$ convex set and to utilize convex programing to solve the problem precise and then to map the answer to the closest point in the set $\mathcal{D}$. We assume an i.i. d. complex Gaussian channel matrix and derive expressions for the symbol error probability of the proposed convex method in the limit of m, n → ∞. Prior work was only able to do so for real valued constellations such as BPSK and PAM. The main contribution of this paper is to extend the results to complex valued constellations. In particular, we use our main theorem to calculate the performance of the complex algorithm for PSK and QAM constellations. In addition, we introduce a closed-form formula for the symbol error probability in the high-SNR regime and determine the minimum number of measurements m required for consistent signal recovery.
Deep-Syntactic Parsing

“Deep-syntactic” dependency structures that capture the argumentative, attributive and coordinative relations between full words of a sentence have a great potential for a number of NLPapplications. The abstraction degree of these structures is in-between the output of a syntactic dependency parser (connected trees defined over all words of a sentence and language-specific grammatical functions) and the output of a semantic parser (forests of trees defined over individual lexemes or phrasal chunks and abstract semantic role labels which capture the argument structure of predicative elements, dropping all attributive and coordinative dependencies). We propose a parser that delivers deep syntactic structures as output.
Bioinformatics of Genome Evolution : from Ancestral to Modern Metabolism : Phylogenomics and Comparative Genomics to Understand Microbial Evolution

Bioinformatics, that is the interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences, is expected to gain a central role in next feature. Indeed, it has now affected several fields of biology, providing crucial hints for the understanding of biological systems and also allowing a more accurate design of wet lab experiments. In this work, the analysis of sequence data has be used in different fields, such as evolution (e.g. the assembly and evolution of metabolism), infections control (e.g. the horizontal flow of antibiotic resistance), ecology (bacterial bioremediation).
Sola schola et sanitate: human capital as the root cause and priority for international development?

This paper summarizes new scientific evidence supporting the hypothesis that among the many factors contributing to international development, the combination of education and health stands out as a root cause on which other dimensions of development depend. Much of this recent analysis is based on new reconstructions and projections of populations by age, sex and four levels of educational attainment for more than 120 countries using the demographic method of multi-state population dynamics. It also refers to a series of systems analytical population–development–environment case studies that comprehensively assess the role of population and education factors relative to other factors in the struggle for sustainable development. The paper also claims that most concerns about the consequences of population trends are in fact concerns about human capital, and that only by adding the ‘quality’ dimension of education to the traditionally narrow focus on size and age structure can some of the long-standing population controversies be resolved.
Development of a Click Beetle Luciferase Reporter System for Enhanced Bioluminescence Imaging of Listeria monocytogenes: Analysis in Cell Culture and Murine Infection Models

Listeria monocytogenes is a Gram-positive facultative intracellular pathogen that is widely used as a model organism for the analysis of infection biology. In this context, there is a current need to develop improved reporters for enhanced bioluminescence imaging (BLI) of the pathogen in infection models. We have developed a click beetle red luciferase (CBR-luc) based vector (pPL2CBRopt) expressing codon optimized CBR-luc under the control of a highly expressed Listerial promoter (PHELP) for L. monocytogenes and have compared this to a lux-based system expressing bacterial luciferase for BLI of the pathogen using in vitro growth experiments and in vivo models. The CBR-luc plasmid stably integrates into the L. monocytogenes chromosome and can be used to label field isolates and laboratory strains of the pathogen. Growth experiments revealed that CBR-luc labeled L. monocytogenes emits a bright signal in exponential phase that is maintained during stationary phase. In contrast, lux-labeled bacteria produced a light signal that peaked during exponential phase and was significantly reduced during stationary phase. Light from CBR-luc labeled bacteria was more efficient than the signal from lux-labeled bacteria in penetrating an artificial tissue depth assay system. A cell invasion assay using C2Bbe1 cells and a systemic murine infection model revealed that CBR-luc is suited to BLI approaches and demonstrated enhanced sensitivity relative to lux in the context of Listeria infection models. Overall, we demonstrate that this novel CBR reporter system provides efficient, red-shifted light production relative to lux and may have significant applications in the analysis of L. monocytogenes pathogenesis.
Relay Based Cooperative Spectrum Sensing Technique Using Energy Detector in Cognitive Radio Network

The cognitive node which are far away from primary user (PU) which may not be able to detect the Primary User due to severe fading in the channel. To improve the efficiency of spectral sensing channel, we propose here a cooperative communication method this is based on cognitive relaying. Cognitive relay, which node that sense the activity of primary user and forward received data to the cognitive radio (CR) which is far away from primary user. In this condition the probability of detection can be increases, which in turn reduces the bit error rate. Using this number of a relay nodes can reduce the sensing time and increases the throughput of the system.
Azole Resistance by Loss of Function of the Sterol Δ5,6-Desaturase Gene (ERG3) in Candida albicans Does Not Necessarily Decrease Virulence

ABSTRACT The inactivation of ERG3, a gene encoding sterol Δ5,6-desaturase (essential for ergosterol biosynthesis), is a known mechanism of in vitro resistance to azole antifungal drugs in the human pathogen Candida albicans. ERG3 inactivation typically results in loss of filamentation and attenuated virulence in animal models of disseminated candidiasis. In this work, we identified a C. albicans clinical isolate (VSY2) with high-level resistance to azole drugs in vitro and an absence of ergosterol but normal filamentation. Sequencing of ERG3 in VSY2 revealed a double base deletion leading to a premature stop codon and thus a nonfunctional enzyme. The reversion of the double base deletion in the mutant allele (erg3-1) restored ergosterol biosynthesis and full fluconazole susceptibility in VSY2, confirming that ERG3 inactivation was the mechanism of azole resistance. Additionally, the replacement of both ERG3 alleles by erg3-1 in the wild-type strain SC5314 led to the absence of ergosterol and to fluconazole resistance without affecting filamentation. In a mouse model of disseminated candidiasis, the clinical ERG3 mutant VSY2 produced kidney fungal burdens and mouse survival comparable to those obtained with the wild-type control. Interestingly, while VSY2 was resistant to fluconazole both in vitro and in vivo, the ERG3-derived mutant of SC5314 was resistant only in vitro and was less virulent than the wild type. This suggests that VSY2 compensated for the in vivo fitness defect of ERG3 inactivation by a still unknown mechanism(s). Taken together, our results provide evidence that contrary to previous reports inactivation of ERG3 does not necessarily affect filamentation and virulence.
ECOLOGY OF Staphylococcus aureus AND ITS ANTIBIOTIC RE-SISTANCE GENES IN DAIRY FARMS: CONTRIBUTING FACTORS AND PUBLIC HEALTH IMPLICATIONS

Dairy farms are major sources for zoonotic Staphylococcus aureus pathogens and their antibiotic resistance genes. This study was conducted to assess critical sources and factors related to dissemination of S. aureus and its resistance genes within dairy farms in Egypt. In addition, workers' knowledge, attitudes and practices (KAPs) was evaluated. A total of 102 pooled samples were collected from 3 medium-scale dairy farms in Egypt. S. aureus was detected in 72.5% of the examined samples: lactating cows (72.9%), workers (81.5%), barns environment (88.9%), milking equipment (40%), and bulk tank milk (100%). Cows (udder milk and nostril), workers (hand skin and nostril), barns, open-sides parlor, and lack of acid rinse were associated with S. aureus contamination of milking equipment ( P = 0.004 - 0.04). Methicillin resistant S. aureus (MRSA, mecA +), vancomycin-resistant S. aureus (VRSA, vanA +) and methicillin-vancomycin-resistant S. aureus (MVRSA, mecA +- vanA +) represented 27.5%, 5% and 12.5% of S. aureus isolates, respectively. This is the first report of MVRSA in dairy farms in Egypt. For workers KAPs, 48.7% didn't know milk-borne zoonoses, while their high risk practices included consumption of raw milk (52.2%), lack of hand wash (48.7%), and willing to work with sore throat (82.6%). This study highlights the critical sources of S. aureus pathogens and their antibiotic resistance genes in dairy farms. This will help in reforming biosecurity plans in dairy farms; an urgent demand for consumers safety in Egypt. Key words: Staphylococcus aureus ecology; dairy farms; antibiotic resistance genes; public health implications