Miracle-dz/UniFAR-FTUs huggingface dataset:
Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea

ABSTRACT Biomass samples from the Black Sea collected in 1988 were analyzed for SSU genes from Bacteria and Archaea after 10 years of storage at −80°C. Both clonal libraries and direct fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analyses were used to assess the microbial community. Uniform and discrete depth distributions of different SSU phylotypes were observed. However, most recombinant clones were not restricted to a specific depth in the water column, and many of the major T-RFLP peaks remain uncharacterized. Of the clones obtained, an ε-Proteobacteria and a Pseudoalteromonas-like clone accounted for major peaks in the fingerprint, while deeply branching lineages of α- and γ-Proteobacteria were associated with smaller peaks. Additionally, members were found among both the δ-Proteobacteria related to sulfate reducers and the Archaea related to phylotypes from the ANME groups that anaerobically oxidize methane.
Valuing Risky Projects using Mixed Asset Portfolio Selection Models

We examine the valuation of projects in a setting where an investor can invest in a portfolio of private projects as well as in securities in financial markets, but where exact replication of project cash flows in financial markets is not necessarily possible. We consider both single-period and multi-period models, and develop an inverse optimization procedure for valuing projects in this setting. We show that the valuation procedure exhibits several important analytical properties, for example, that project values for a mean-variance investor converge towards prices given by the capital asset pricing model. We also conduct several numerical experiments.
The respiratory-chain NADH dehydrogenase (complex I) of mitochondria.

In mitochondria, electrons are transferred from NADH to O2 through a chain of three large enzyme complexes, namely NADH: ubiquinone oxidoreductase (NADH dehydrogenase or complex I), ubiquinol: ferricytochrome c oxidoreductase (cytochrome reductase or complex III), and ferrocytochrome c:O2 oxidoreductase (cytochrome oxidase or complex IV). The function of these enzyme complexes is to link electron transfer with proton translocation out of the mitochondrion. In doing so, they generate a transmembraneous proton motive force which subsequently drives ATP synthesis by the H+-ATPase (complex V, for a review see [1]).
Structural distortions due to missense mutations in human formylglycine-generating enzyme leading to multiple sulfatase deficiency

The major candidate for multiple sulfatase deficiency is a defective formylglycine-generating enzyme (FGE). Though adequately produced, mutations in FGE stall the activation of sulfatases and prevent their activity. Missense mutations, viz. E130D, S155P, A177P, W179S, C218Y, R224W, N259I, P266L, A279V, C336R, R345C, A348P, R349Q and R349W associated with multiple sulfatase deficiency are yet to be computationally studied. Aforementioned mutants were initially screened through ws-SNPs&GO3D program. Mutant R345C acquired the highest score, and hence was studied in detail. Discrete molecular dynamics explored structural distortions due to amino acid substitution. Therein, comparative analyses of wild type and mutant were carried out. Changes in structural contours were observed between wild type and mutant. Mutant had low conformational fluctuation, high atomic mobility and more compactness than wild type. Moreover, free energy landscape showed mutant to vary in terms of its conformational space as compared to wild type. Subsequently, wild type and mutant were subjected to single-model analyses. Mutant had lesser intra molecular interactions than wild type suggesting variations pertaining to its secondary structure. Furthermore, simulated thermal denaturation showed dissimilar pattern of hydrogen bond dilution. Effects of these variations were observed as changes in elements of secondary structure. Docking studies of mutant revealed less favourable binding energy towards its substrate as compared to wild type. Therefore, theoretical explanations for structural distortions of mutant R345C leading to multiple sulfatase deficiency were revealed. The protocol of the study could be useful to examine the effectiveness of pharmacological chaperones prior to experimental studies.
Resident Enteric Bacteria Are Necessary for Development of Spontaneous Colitis and Immune System Activation in Interleukin-10-Deficient Mice

ABSTRACT Mice with targeted deletion of the gene for interleukin-10 (IL-10) spontaneously develop enterocolitis when maintained in conventional conditions but develop only colitis when kept in specific-pathogen-free (SPF) environments. This study tested the hypothesis that enteric bacteria are necessary for the development of spontaneous colitis and immune system activation in IL-10-deficient mice. IL-10-deficient mice were maintained in either SPF conditions or germfree conditions or were populated with bacteria known to cause colitis in other rodent models. IL-10-deficient mice kept in SPF conditions developed colitis in all segments of the colon (cecum and proximal and distal colon). These mice exhibited immune system activation as evidenced by increased expression of CD44 on CD4+ T cells; increased mesenteric lymph node cell numbers; and increased production of immunoglobulin A (IgA), IgG1, and IL-12 p40 from colon fragment cultures. Mice populated with bacterial strains, including Bacteroides vulgatus, known to induce colitis in other rodent models had minimal colitis. Germfree IL-10-deficient mice had no evidence of colitis or immune system activation. We conclude therefore that resident enteric bacteria are necessary for the development of spontaneous colitis and immune system activation in IL-10-deficient mice.
Linear- and Geiger-Mode Characteristics of Al0.8Ga0.2As Avalanche Photodiodes

We report Al0.8Ga0. 2As avalanche photodiodes with low dark current and low excess noise. In linear mode when biased to a photocurrent gain of 200, a 150-μm diameter device exhibits dark current of 32 pA (180 nA/cm2). The external quantum efficiency is 31% at 490 nm and the excess noise factor corresponds to k ~ 0.15. In Geiger mode operation, low dark count probability of 10-5 at room temperature is reported.
Multi-agent framework for social CRM: Extracting and analyzing opinions

Numerous studies have discussed the benefits of using social networks, even companies started to exploit the usefulness of this valuable information sources. Collecting social data then integrating them into a CRM (Customer Relationship Management) has led companies to understand the customer needs and therefore to improve the development process of their products or their services quality. In this work, we propose a multi-agent framework for analyzing extracted opinions from social media. In the development process, we were brought to consider the huge volumes of data (Big Data) and the response time. To do so, an architecture based on Map/Reduce analysis using Hadoop was made in order to perform the data refinement (classify or remove special words or delete the unvaluable reviews) and sentiment analysis (Sentigem). Finally, a study case using Twitter (Twitter4J API) as a data source, was made to verify the effectiveness of the proposed framework.
Fragments of prochymosin produced in Escherichia coli form insoluble inclusion bodies

Bovine prochymosin produced in Escherichia coli has been used as a model system to investigate factors which may cause a recombinant protein to accumulate as insoluble inclusion bodies. A series of plasmids was constructed to investigate the effect of deletions within the prochymosin-coding sequence on protein inclusion body formation. The results demonstrated that as much as 70% of the prochymosin-coding sequence could be deleted with no significant reduction in the accumulation of insoluble protein. The smallest deletion product identified (11,000 molecular weight) retained only one cysteine, yet this product still accumulated as an insoluble product in E. coli.
Cornering stability improvement for 4 wheel drive hybrid electric vehicle

Cornering stability of 4 wheel drive hybrid electric vehicle has been analyzed and improved, where the front motor and the rear motors are used to drive the vehicle. For the control of the motors, a model reference sliding mode controller is designed to generate the additional yaw moment for the vehicle. The algorithms for the motor driving and the yaw rate control for the 4 wheel drive hybrid electric vehicle have been developed considering the cornering stability based on the reference model for the vehicle. The reference model is described by the two degree of freedom vehicle dynamic state equations. Performance of the vehicle stability control algorithm is evaluated using ADAMS and MATLAB Simulink programs.
Taverna: a tool for building and running workflows of services

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from .
A Survey on Fake Entities as a Method to Detect and Monitor Malicious Activity

This paper surveys research concentrating on fake entities as a method to detect and monitor malware. A fake entity is a digital entity (such as a file) no one except a malicious attacker should access. When the entity is accessed, the defender immediately knows there is unwanted activity in the system and can start to monitor it. We discuss both faking different entities on one machine and in a network using virtual groups of fake hosts.
Local feature descriptor based rapid 3D ear recognition

This paper presents a local feature descriptor based rapid 3D ear recognition method. A coarse-to-fine pose alignment method is proposed to alleviate local extremum problem of ICP algorithm. At first, the LSP descriptors of 3D ear feature points are used to perform coarse pose alignment. Then the improved ICP algorithm (MICP algorithm) is used for fine pose alignment. Three kinds of descriptors, including LBP descriptor, 3D LBP descriptor and 3D CS-LBP descriptor, are used for feature extraction and matching. Experimental results show that 3D CS-LBP descriptor based method has better recognition performance and computational efficiency than the other two descriptors based methods.
Chemometric tools for analysing Terahertz fingerprints in a postscanner

Concerning several attacks using letter bombs within Europe in the last couple of years and the highly rising number of new drugs, there is a need for new kinds of detection devices for explosives and drugs. We present a postscanner on basis of Terahertz (THz) spectroscopy using novel chemometric methods for the evaluation of detected THz fingerprints.
New Quasi-Deadbeat FIR Smoother for Discrete-Time State-Space Signal Models: An LMI Approach

In this letter, we propose a new H2 smoother (H2S) with a finite impulse response (FIR) structure for discrete-time state-space signal models. This smoother is called an H2 FIR smoother (H2FS). Constraints such as linearity, quasi-deadbeat property, FIR structure, and independence of the initial state information are required in advance to design H2FS that is optimal in the sense of H2 performance criterion. It is shown that H2FS design problem can be converted into the convex programming problem written in terms of a linear matrix inequality (LMI) with a linear equality constraint. Simulation study illustrates that the proposed H2FS is more robust against uncertainties and faster in convergence than the conventional H2S.
Binding activity and immunogenic characterization of recombinant C-terminal quarter and half of the heavy chain of botulinum neurotoxin serotype A

In the present study, we explored and compared the binding activity and immunogenic characterization of the most effective part corresponding to C-terminal quarter of heavy chain of botulinum neurotoxin serotype A (AHc-C) with C-terminal half of heavy chain of botulinum neurotoxin serotype A (AHc). Firstly, the fully soluble AHc-C protein successfully expressed in Escherichia coli by co-expression with thioredoxin (Trx) was shown to bind with ganglioside as the AHc, indicating that the recombinant AHc-C protein retains a functionally active conformation. Furthermore, a solid-phase assay showed that the anti-AHc-C sera effectively inhibited the binding of AHc or AHc-C to the ganglioside GT1b, the first step in BoNT/A intoxication of neurons, as good as the anti-AHc sera. Finally, although the recombinant AHc-C protein still induced a high serum antibody titers and afforded protection level as the mice challenged with active botulinum neurotoxin serotype A, the immunization with AHc protein induced stronger protective potency than the AHc-C protein. The data presented in the report shows that there are the same ganglioside binding activity and different immunogenic characterization between the C-terminal quarter and half of heavy chain of botulinum neurotoxin serotype A. Therefore, the recombinant AHc-C protein can not only be developed into a minimal subunit candidate vaccine for prophylaxis against botulinum neurotoxin serotype A but also be used as a promising tool in the search for binding inhibitors and chimeric vaccines.
Non-invasive cardiac output monitoring in pharmacology: A plethysmographie solution in rats

Cardiovascular monitoring is of great importance in pharmacology but there is a lack of convenient non-invasive alternatives. Hence, we aim to evaluate the relevance of inductive plethysmography (IP) in preclinical cardiac studies. An IP system was specifically designed for rat. Its evaluation carried out using a mechanical test bench has shown appropriate instrumental performances for cardiac monitoring in rats. Measurements were also performed during a volume overload hemodynamic challenge in vivo in rats. The cardiac output variation has similar kinetic and amplitude when compared to results of previous studies. This suggests that our system is suitable for cardiac output monitoring in rat.
Senna alata leaves are a good source of propelargonidins

Abstract Proanthocyanidins (PA) in Senna alata leaves were investigated by thiolysis with benzyl mercaptan, LC–MS and NMR and consisted of almost pure propelargonidins with <6% procyanidins, had B-type linkages and a mean degree of polymerisation of three. Epiafzelechin was the major flavan-3-ol subunit (>94%) and epicatechin a minor constituent (6.4%) in residual PA and mainly detected as an extension unit.
Comparison of Perioperative Outcomes between the Supraclavicular Artery Island Flap and Fasciocutaneous Free Flap

Objective Outcomes of the supraclavicular artery island flap (SCAIF) have not been extensively studied in comparison with free tissue transfer (FTT) flaps for head and neck reconstruction. We hypothesize that the pedicled SCAIF has decreased operating room time, length of stay, time to wound healing of recipient site, complications, and hospital charges as compared with FTT. Study Design Case series with chart review. Setting Tertiary care teaching hospital. Subjects and Methods Medical records were reviewed for patients who underwent SCAIF (n = 45) or FTT (n = 28) reconstruction between 2011 and 2013. Results Total operating room time was significantly lower for the SCAIF group vs the FTT group (6.7 vs 8.1 hours, P = .002). Procedural time was 5.7 hours for the SCAIF group, as compared with 7.2 hours for FTT group (P = .0015). Mean area for SCAIF donor site was 63.89 cm2 vs 81.8 cm2 for the radial forearm free flap group (P = .015). There was no significant difference in mean length of stay between SCAIF (8.8 days) and FTT (11 days, P = .12). Mean length of time to wound healing of the recipient site was similar in the SCAIF group vs the FTT group (17.3 vs 22.1 days, P = .071). Ratio of total hospital charges for SCAIF were 32% lower than that of FTT (P = .0001). Conclusion This is among the first studies to compare SCAIF with FTT in a large cohort analysis. We find decreased operating room times for SCAIF vs FTT, with similar length of stay and wound healing. Other outcomes between SCAIF and FTT were also comparable.
Diagnostic utility of polysomnography in children less than 2 years of age?

1. It must have an established normal range, where values outside that range indicate a clinically significant abnormality. To do this, however, requires both a. Standardized methodology: we have to agree upon exactly what we measure and how. b. Standardized criteria: what do we use (both respiratory pattern as well as duration) to define obstructive, central, and mixed apneas? What about severity of associated desaturation? The criteria need to be age appropriate: what is normal for an 18 month old is not normal for an 18 week old (below). Different centers using differing criteria will perforce report different “normal” ranges. 2. To be clinically relevant, “abnormal” also needs to be indicative of disease: specific, but also ideally a sensitive indicator of current or future ill health. 3. Where there is a spectrum of disease, the degree of divergence from normal should correlate with severity of disease.
Managing Locality Sets: The Model and Fixed-Size Buffers

A memory-management model based on describing reference behavior in terms of locality-set sequences is proposed. Specialized for fixed-size buffers, this model is used to define the PSETMIN and SETMIN strategies which are proven to minimize the number of page faults in the presence and absence of prepaging, respectively. In contrast to MIN, they are also realizable for certain computations. The methodology for obtaining the locality-set sequence of a computation in advance is illustrated for relational database management systems with multiattribute-index catalogs, and the concomitant performance gains are discussed. In general, for applications that maintain their own organized collections of data, optimal locality-set management of individual computations provides an alternative to the widely used general-purpose strategies based on heuristics. >
Urinary interleukin-18 and urinary neutrophil gelatinase-associated lipocalin predict acute kidney injury following pulmonary valve replacement prior to serum creatinine.

BACKGROUND It is becoming increasingly recognized that manifestations of congenital heart disease (CHD) extend beyond the cardiovascular system. The factors contributing to renal dysfunction in patients with CHD are multifactorial, with acute kidney injury (AKI) at time of cardiac surgery playing a major role. AKI is often diagnosed based on changes in serum creatinine and estimated glomerular filtration rate (eGFR). Such measurements are often late and imprecise. Recent data indicate that urinary biomarkers interleukin-18 (IL-18) and neutrophil gelatinase-associated lipocalin (NGAL) are earlier markers of AKI. We sought to determine the efficacy of urinary IL-18 and NGAL for detecting early AKI in patients undergoing surgical pulmonary valve replacement (PVR). METHODS Twenty patients presenting for surgical PVR with a history of previous repair of a conotruncal anomaly were enrolled. Preoperative clinical data were measured and urine samples and serum creatinine were collected at 6, 12, 24, and 72 hours post bypass. Urine was evaluated for NGAL and IL-18. AKI was determined using the Risk, Injury, Failure, Loss and End Stage Renal Disease (RIFLE) classification system. RESULTS Using the RIFLE classification system, seven patients (35%) were found to have AKI defined as a drop in the eGFR or an increase in serum creatinine. All seven patients with AKI had marked increase from preoperative baseline in urine IL-18 (sixfold) and NGAL (26-fold). Using NGAL and IL-18, AKI was detected at 6 hours postoperatively, resulting in AKI being identified 12-36 hours prior to detection by conventional methods. No preoperative predictors for AKI were identified. CONCLUSION Both NGAL and IL-18 are early predictive biomarkers of AKI, and both increase in tandem after surgical PVR. Importantly, both rise before an increase in creatinine or a decrease in eGFR is present. Monitoring both biomarkers may allow for earlier detection and subsequent interventions to prevent AKI at time of surgery for CHD.
Finnegans Wake and the Character of the Letter: 644

In the early twentieth-century vanguard milieu, Filippo Marinetti's "parole in liberta" inaugurated a general trend toward the eman cipation of primary units of signification.1 Set forth in dada sound poems and Russian futurist "zaum," these impulses culminated in Eugene Jolas's call for a "revolution of the word. "2 His journal transi tion became the focal point for this revolution from 1927 to 1938, con sistently accommodating Gertrude Stein as well as Joyce, and under Jolas's guidance the magazine maintained rigorous connections with nearly the whole spectrum of avant-garde movements. Undoubtedly transition was the best edited, most widely informed, and most in structively eclectic journal of its time. Its locomotive center was Finnegans Wake? not simply because Jolas became a patron of the text by insuring space for continual installments,3 nor because of the un precedented amount of expository and hortatory material devoted to Joyce's work, but because transition was edited as though this "work in progress" summoned the world around it, like Wallace Stevens's anecdote of the jar on a hill in Tennessee.4 Transition was not just the magazine that happened to print the bulk of Finnegans Wake as it was written but also a laboratory for initiating readers into the nuevo mundo that Joyce prescribed. Jolas recognized in Joyce's work a poly mathic solution to the problem that language had represented for lit erature since the first dissident gestures of dada and futurism (if not Arthur Rimbaud and Stephane Mallarm? ). "By publishing and de fending Work in Progress," Jolas wrote, "transition established a basis for a literary insurrection that included a radically new conception of the processes of consciousness and of the development of language. "5 Joyce provided Jolas with a practical foundation on which he could erect his own mythico-anthropological quest for an "Atlantic or cru cible language. "6 If transition made it appear at the time that Joyce was in collusion with Stein and the dadaists and surrealists in perpetrat ing a cult of the unintelligible, the demonstrable and pertinent links between them have been all but ignored since then.7
Operational criteria for senile dementia of Lewy body type (SDLT)

Synopsis Recent reports have suggested that brain stem and cortical Lewy body formation may identify a neurodegenerative disorder in elderly demented individuals which accounts for up to 20% of cases of senile dementia coming to autopsy. Retrospective analysis of case notes of 21 autopsy patients with neuropathologically proven senile dementia of Lewy body type (SDLT) and 37 cases with neuropathologically proven Alzheimer's disease (AD) identified a characteristic clinical syndrome in SDLT. Fluctuating cognitive impairment; psychotic features including visual and auditory hallucinations, and paranoid delusions; depressive symptoms; falling and unexplained losses of consciousness were all seen significantly more often than in AD. Over half of the SDLT patients in this series who were given neuroleptics in standard dose showed acute and often irreversible adverse reactions indicative of a neuroleptic sensitivity syndrome. The survival time of drug treated patients was reduced by 50%. Operational criteria to aid in the clinical distinction between SDLT and AD patients are proposed and hypotheses regarding possible aetiology and treatment discussed.