Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Systems Biology Peer Review Process File Engineering Microbes to Sense and Eradicate Pseudomonas Aeruginosa, a Human Pathogen Transaction Report

(Note: With the exception of the correction of typographical or spelling errors that could be a source of ambiguity, letters and reports are not edited. The original formatting of letters and referee reports may not be reflected in this compilation.) Thank you again for submitting your work to Molecular Systems Biology. We have now heard back from the two referees whom we asked to evaluate your manuscript. As you will see from the reports below, the referees raise substantial concerns on your work, which, I am afraid to say, preclude its publication. The referees acknowledged that your work describes a functional synthetic circuit that can program E. coli to kill P. aeruginosa under laboratory conditions, however, they had substantial concerns regarding the therapeutic relevance of this technology. Both reviewers felt that is was not clear whether the culture results can be generalized to a disease-relevant state, with specific concerns regarding the density of P. aeruginosa needed to activate the E. coli, the outcomes of long-term culture (including resistance development), and the effects of biofilm formation. Reviewer #1 indicated clearly that, given these concerns and his/her feeling that the conceptual advance demonstrated by the the synthetic genetic system was somewhat modest, they could not support publication of this work in Molecular Systems Biology. The reviewers also felt that the system required additional characterization, in part to clearly demonstrate that both the lysis and the toxin modules are strictly required for P. aeruginosa killing. Both reviewers suggest potentially helpful experiments in this regard (e.g. testing on pyocin-resistant P. aeruginosa, and mutation of the lysis protein). For the reasons stated above, we feel we have no choice but to return this manuscript with the message that we cannot offer to publish it. Nevertheless, given the more encouraging comments from the second reviewer, and the possibility that these concerns could potentially be addressed with additional experiments, we may be willing to reconsider a new, substantially expanded, submission based on this work. Such a work would need
Semi-infinite induction and Wakimoto modules

The purpose of this paper is to suggest the construction and study properties of semi-infinite induction, which relates to semi-infinite cohomology the same way induction relates to homology and coinduction to cohomology. We prove a version of the Shapiro Lemma, showing that the semi-infinite cohomology of a module is isomorphic to that of the semi-infinitely induced module. A practical outcome of our construction is a simple construction of the Wakimoto modules, highest-weight modules used in double-sided BGG resolutions of irreducible modules.
NORTH WEST REGION

The Northwest Region Quality Assurance Unit is comprised of five Operations Review Specialists, a Quality Assurance Manager and is under the direction of the Family Safety Program Manager. Within the past year, the region has had the opportunity, to the extent possible, of co-locating each member of the team in the Department Service Centers of their home County. This has ensured that each Circuit has at least one identified QA Specialist available for consultation.
Nanosize Control on Porous β-MnO2 and Their Catalytic Activity in CO Oxidation and N2O Decomposition

A major challenge in the synthesis of porous metal oxides is the control of pore size and/or wall thickness that may affect the performance of these materials. Herein, nanoporous β-MnO2 samples were prepared using different hard templates, e.g., ordered mesoporous silica SBA-15 and KIT-6, disordered mesoporous silica, and colloidal silica. These samples were characterized by Powder X-Ray Diffraction (PXRD), Transmission Electron Microscopy (TEM), and N2 adsorption-desorption. The pore size distribution of β-MnO2 was tuned by the different hard templates and their preparation details. Catalytic activities in CO oxidation and N2O decomposition were tested and the mesoporous β-MnO2 samples demonstrated superior catalytic activities compared with their bulk counterpart.
Optimal Replenishment and Rework with Multiple Unreliable Supply Sources

We study a production-inventory system with multiple unreliable supply sources. Through inspection and rework, the system can improve the quality of the units received from the supply sources. There are two interleaved decisions: the replenishment quantities from the sources and the inspection-rework quantities among the units received. We show the optimal solution to the replenishment decision can be efficiently derived from a greedy algorithm, and inspection-rework is optimally applied to a single source identified by the algorithm. Furthermore, in the case of linear cost functions, it is optimal to place orders from two supply sources, i.e., dual sourcing. The results extend to the infinite-horizon case, where an order-up-to policy is optimal. The model also readily adapts to situations in which the supply imperfection takes the form of a reduced delivery quantity (yield loss).
Genetic and environmental influences on sodium intake determined by using half-day urine samples: the Healthy Twin Study.

BACKGROUND Salt is essential in our diet, but excess intake is a well-established risk factor for hypertension. The presence and importance of genetic contributions to salt intake, however, are not well understood. OBJECTIVE The aim of this study was to examine whether a genetic predisposition and an environmental influence exist for sodium intake and salt habit. DESIGN In a twin-family cohort, half-day urine samples from 1204 individuals (133 pairs of monozygotic twins, 29 pairs of dizygotic twins, and 880 singletons) were collected to assess 24-h sodium intakes. Daily total sodium intake, sodium density per calorie (Na-D), and salt habit questions were analyzed with adjustment for other epidemiologic characteristics. We calculated heritability (h2) and intraclass correlations to examine the genetic and shared environmental contributions to total sodium intake traits. RESULTS The average sodium intake was 208.4 ± 107.0 mmol/d. Men had a higher absolute sodium intake (242.6 ± 117.4 mmol/d), but Na-D did not differ by sex. Moderate genetic influences existed (h2 = 0.31-0.34) for sodium intake and Na-D. We also found that sharing current residence rather than being a family member explained 22% of the variance in Na-D. CONCLUSION Our findings suggest that both genetic predisposition and shared environment contribute to sodium intakes and salt habits alike.
Protograph LDPC Codes With Block Thresholds: Extension to Degree-One and Generalized Nodes

Protograph low-density-parity-check (LDPC) codes are considered to design near-capacity low-rate codes over the binary erasure channel and the binary additive white Gaussian noise channel. For protographs with degree-one variable nodes and doubly-generalized LDPC (DGLDPC) codes, conditions are derived to ensure the equality of bit-error threshold and block-error threshold. Using this condition, low-rate codes with block-error threshold close to capacity are designed and shown to have better error rate performance than other existing codes.
Generation of test sequences from formal specifications: GSM 11‐11 standard case study

This paper presents the results of a case study on generating test cases for a fragment of the smart card GSM 11‐11 standard. The generation method is based on an original approach using the B notation and techniques of constraint logic programming with sets. The GSM 11‐11 technical specifications were formalized with the B notation. From this B specification, a system of constraints was derived, equivalent to this formal model. Using a set constraint solver, boundary states were computed and test cases were obtained by traversing the constrained reachability graph of the specifications. The purpose of this project was to evaluate the contribution of this testing environment, called B‐TESTING‐TOOLS, in an industrial process on a real life‐size application, by comparing the generated test sequences with the already used and high‐quality manually‐designed tests. This comparison enabled us to validate our approach and showed its effectiveness in the validation process of critical applications: the case study gives a wide coverage (about 85%) of the generated tests compared to the pre‐existing tests and a saving of 30% in test design time. Copyright © 2004 John Wiley & Sons, Ltd.
Information-theoretic limits of matrix completion

We propose an information-theoretic framework for matrix completion. The theory goes beyond the low-rank structure and applies to general matrices of “low description complexity”. Specifically, we consider random matrices X ∈ ℝ<sup>m×n</sup> of arbitrary distribution (continuous, discrete, discrete-continuous mixture, or even singular). With S ⊆ ℝ<sup>m×n</sup> an ε-support set of X, i.e., P[X ∈ S] ≥ 1 - ε, and equation denoting the lower Minkowski dimension of S, we show that equation measurements of the form 〈A<sub>i</sub>,X〉, with A<sub>i</sub> denoting the measurement matrices, suffice to recover X with probability of error at most ε. The result holds for Lebesgue a.a. A<sub>i</sub> and does not need incoherence between the A<sub>i</sub> and the unknown matrix X. We furthermore show that equation measurements also suffice to recover the unknown matrix X from measurements taken with rank-one A<sub>i</sub>, again this applies to a.a. rank-one A<sub>i</sub>. Rank-one measurement matrices are attractive as they require less storage space than general measurement matrices and can be applied faster. Particularizing our results to the recovery of low-rank matrices, we find that k > (m+n-r)r measurements are sufficient to recover matrices of rank at most r. Finally, we construct a class of rank-r matrices that can be recovered with arbitrarily small probability of error from k <; (m + n - r)r measurements.
Comparing Similarity Combination Methods for Schema Matching

A recurring manual task in data integration or ontology alignment is finding mappings between complex schemas. In order to reduce the manual effort, many matching algorithms for semi-automatically computing mappings were introduced. In the last decade it turned out that a combination of matching algorithms often improves mapping quality. Many possible combination methods can be found in literature, each promising good result quality for a specific domain of schemas. We introduce the rationale of each strategy shortly. Then we evaluate the most commonly used methods on a number of mapping tasks and try to find the most robust strategy that behaves well across all given tasks.
Amphetamines, Atomoxetine and the Risk of Serious Cardiovascular Events in Adults

Main Objective To compare the incidence rates of serious cardiovascular events in adult initiators of amphetamines or atomoxetine to rates in non-users. Methods This was a retrospective cohort study of new amphetamines (n = 38,586) or atomoxetine (n = 20,995) users. Each medication user was matched to up to four non-users on age, gender, data source, and state (n = 238,183). The following events were primary outcomes of interest 1) sudden death or ventricular arrhythmia, 2) stroke, 3) myocardial infarction, 4) a composite endpoint of stroke or myocardial infarction. Cox proportional hazard regression was used to calculate propensity-adjusted hazard ratios for amphetamines versus matched non-users and atomoxetine versus matched non-users, with intracluster dependence within matched sets accounted for using a robust sandwich estimator. Results The propensity-score adjusted hazard ratio for amphetamines use versus non-use was 1.18 (95% CI: 0.55–2.54) for sudden death/ventricular arrhythmia, 0.80 (95% CI: 0.44–1.47) for stroke, 0.75 (95% CI: 0.42–1.35) for myocardial infarction, and 0.78 (95% CI: 0.51–1.19) for stroke/myocardial infarction. The propensity-score adjusted hazard ratio for atomoxetine use versus non-use was 0.41 (95% CI: 0.10–1.75) for sudden death/ventricular arrhythmia, 1.30 (95% CI: 0.52–3.29) for stroke, 0.56 (95% CI: 0.16–2.00) for myocardial infarction, and 0.92 (95% CI: 0.44–1.92) for stroke/myocardial infarction. Conclusions Initiation of amphetamines or atomoxetine was not associated with an elevated risk of serious cardiovascular events. However, some of the confidence intervals do not exclude modest elevated risks, e.g. for sudden death/ventricular arrhythmia.
MIMO-OFDM Channel Estimation Using Pilot Carries

A multiple-input multiple-output (MIMO) communication system combined with the orthogonal frequency division multiplexing (OFDM) modulation technique can achieve reliable high data rate transmission over broadband wireless channels. Channel state information for both single-input single-output (SISO) and MIMO systems based on pilot aided arrangement is investigated in this paper. The estimation of channel at pilot frequencies with conventional Least Square (LS) and Minimum Mean Square (MMSE) estimation algorithms is carried out through Matlab simulation. The performance of MIMO OFDM and SISO OFDM are evaluated on the basis of Bit Error Rate (BER) and Mean Square Error (MSE) level. Further enhancement of performance can be achieved through maximum diversity Space Time Block Coding (STBC) and Maximum Likelihood Detection at transmission and reception ends respectively. MMSE estimation has been shown to perform much better than LS but is more complex than LS for the MIMO system using pilot carriers.
Oncopharmacological Perspectives of a Plant Lectin (Viscum album Agglutinin-I): Overview of Recent Results from In vitro Experiments and In vivo Animal Models, and Their Possible Relevance for Clinical Applications

An old goal of natural complementary medical therapy has been to aim at a long-term stimulation of natural resistance in order to restrain cancer progression or improve defective immunological conditions without toxic side effects. Mistletoe extracts were applied to a large number of cancer patients because of their modulatory effect on the natural immune system. By carefully removing lectins, an essential group of components, from mistletoe extracts, a significant reduction of their effectiveness on several cellular immune parameters could be observed in vivo (1). That is the reason why, for the last 14 years, biological research of mistletoe extracts has focused on lectins. Meanwhile, the quantitatively dominant lectin, Viscum album agglutinin (VAA)-I has become available in a recombinant form (rVAA). Other constitiuents of plant extracts such as viscotoxins (2,3), poly- and oligosaccharides (4), flavonoids (5,6), chitin-binding mistletoe lectin (7) and arginine have also been investigated in connection with the effects of mistletoe extracts on the host defense. However, little evidence has been found that these substances contribute to the effects of mistletoe in vivo (8).
THERAPEUTIC DRUG MONITORING OF VALPROIC ACID IN PEDIATRIC EPILEPTIC PATIENTS

Therapeutic drug monitoring (TDM) or the measurement of drug concentrations in plasma, serum or blood, aims to improve clinical activity, avoid toxicity, and reduce the costs of drug treatment. Specific conditions for TDM to be reasonably applied include the availability of a validated assay, a considerable inter-individual pharmacokinetic variability, a high correlation between drug concentration and toxicity, and a narrow therapeutic index. Our aim of study is to investigate that, therapeutic drug monitoring of valproic acid in pediatric epileptic patients at tertiary care government hospital. The study was carried out prospectively during course of research activity in MGMH between March 2009 – October 2010. The study was approved by hospital ethical committee, Warangal. The patient group was selected from epileptic pediatrics patients who visited tertiary care hospital. All of the patients fulfilled the inclusion criteria and exclusion criteria. Informed consent was taken from the patients and guardian. Blood samples were collected from patients after morning dose at peak level. In our study total 30 pediatric epileptic patients are included in which 17 were males and 13 were females with mean age in years (7.93±3.38), mean BMI kg/m2 (12.14±4.61) & mean total VPA serum concentration of 53.39±4.18 μg/ml . Serum levels within the therapeutic range were found in 46. 33% of epileptic patient. Serum levels were below the therapeutic range in 56.66% of study population achieved partial control . Our article suggests that there was Poor correlation between daily dose and therapeutic level. There was a need for individual monitoring of liver function tests and blood urea nitrogen. In addition to that, a clinician has to check the therapeutic level or and despite daily dose being prescribed as per the guidelines. In future, clinician should step forward in the effort to ensure a more optimal and individual valproic acid therapy.
Thermoplastic polyurethane microcellular fibers via supercritical carbon dioxide based extrusion foaming

This study aims to develop, for the first time, thermoplastic polyurethane (TPU) microcellular composite fibers via an extrusion foaming process using supercritical CO2 as a blowing agent. Results showed that by employing organically modified montmorillonite clay nanoparticles (Cloisite TR 20A) in the matrix at an optimal concentration of about 1.0 wt%, the nucleation rate of foaming was enhanced, thus resulting in the formation of small bubbles in the extruded fibers. Cell sizes as low as several microns or even submicron and fiber diameters less than 30 lm were obtained in the present study. When processed with 0.5 wt% of a slip agent (Oleamide TR121), the extruded TPU fiber foams exhibited fewer cells near the fiber surface. Mechanical studies showed that the tensile modulus per mass based on the initial slope of the stress‐strain curve remained almost the same for both unstretched and stretched fibers with or without foaming. However, the yield stress and the maximum tensile load at an equal mass basis were lower for fibers with foaming. POLYM. ENG. SCI., 53:2360‐2369, 2013. a 2013 Society of Plastics Engineers
Characterization of the oxysterol‐binding protein gene family in the yellow fever mosquito, Aedes aegypti

The oxysterol‐binding protein (OSBP) and OSBP‐related proteins (ORPs) are sterol‐binding proteins that may be involved in cellular sterol transportation, sterol metabolism and signal transduction pathways. Four ORP genes were cloned from Aedes aegypti. Based on amino acid sequence homology to human proteins, they are AeOSBP, AeORP1, AeORP8 and AeORP9. Splicing variants of AeOSBP and AeORP8 were identified. The temporal and spatial transcription patterns of members of the AeOSBP gene family through developmental stages and the gonotrophic cycle were profiled. AeORP1 transcription seemed to be head tissue‐specific, whereas AeOSBP and AeORP9 expression was induced by a bloodmeal. Furthermore, over‐expression of AeORPs facilitated [3H]‐cholesterol uptake in Ae. aegypti cultured Aag ‐2 cells.
Prevention in primary care: facilitators and barriers to transform prevention from a random coincidence to a systematic approach.

RATIONALE, AIMS AND OBJECTIVES The Dutch general practitioner (GP) plays a substantial role in prevention. At the same time, many GPs hesitate to incorporate large-scale cardiovascular risk management (CVRM) programmes into their daily practice. By exploring facilitators and barriers occurring during the past three decades, we wish to find clues on how to motivate professionals to adopt and implement prevention programmes. METHODS A witness seminar was organized in September 2011, inviting key figures to discuss the decision-making process of the implementation of systematic prevention programmes in the Netherlands in the past, thereby adding new perspectives on past events. The extensive discussion was fully audiotaped. The transcript was content-analysed. RESULTS We came across four different transitional stages: (1) the conversion from GPs disputing prevention to the implementation of systematic influenza vaccination; (2) the transition from systematic influenza vaccination to planning CVRM programmes; (3) the transition from planning and piloting CVRM programmes to cancelling the large-scale implementation of the CVRM programme; and (4) the reinforcement of prevention. CONCLUSIONS The GPs' fear to lose the domain of prevention to other health care professionals and financial and logistical support are the main facilitators for implementing prevention programmes in primary care. The main barriers for implementing prevention are the combination of insecurity about reimbursement and lack of scientific evidence. It appears that the ethical view of GPs that everyone should have the same right to obtain preventive care gradually takes over the inclination to hold on to evidence-based prevention.
Canonical and Cross-reactive Binding of NK Cell Inhibitory Receptors to HLA-C Allotypes Is Dictated by Peptides Bound to HLA-C

Background Human natural killer (NK) cell activity is regulated by a family of killer-cell Ig-like receptors (KIR) that bind human leucocyte antigen (HLA) class I. Combinations of KIR and HLA genotypes are associated with disease, including susceptibility to viral infection and disorders of pregnancy. KIR2DL1 binds HLA-C alleles of group C2 (Lys80) and KIR2DL2 and KIR2DL3 bind HLA-C alleles of group C1 (Asn80). However, this model does not capture allelic diversity in HLA-C or the impact of HLA-bound peptides. The goal of this study was to determine the extent to which the endogenous HLA-C peptide repertoire can influence the specific binding of inhibitory KIR to HLA-C allotypes. Results The impact of HLA-C bound peptide on inhibitory KIR binding was investigated taking advantage of the fact that HLA-C*05:01 (HLA-C group 2, C2) and HLA-C*08:02 (HLA-C group 1, C1) have identical sequences apart from the key KIR specificity determining epitope at residues 77 and 80. Endogenous peptides were eluted from HLA-C*05:01 and used to test the peptide dependence of KIR2DL1 and KIR2DL2/3 binding to HLA-C*05:01 and HLA-C*08:02 and subsequent impact on NK cell function. Specific binding of KIR2DL1 to the C2 allotype occurred with the majority of peptides tested. In contrast, KIR2DL2/3 binding to the C1 allotype occurred with only a subset of peptides. Cross-reactive binding of KIR2DL2/3 with the C2 allotype was restricted to even fewer peptides. Unexpectedly, two peptides promoted binding of the C2 allotype-specific KIR2DL1 to the C1 allotype. We showed that presentation of endogenous peptides, or predicted HIV Gag peptides, by HLA-C can promote KIR cross-reactive binding. Conclusions KIR2DL2/3 binding to C1 is more peptide selective than that of KIR2DL1 binding to C2, which provides an explanation for why KIR2DL3–C1 interactions appear weaker than KIR2DL1–C2. In addition, cross-reactive binding of KIR is characterized by even higher peptide selectivity. We demonstrate a hierarchy of functional peptide selectivity of KIR–HLA-C interactions with relevance to NK cell biology and human disease associations. This selective peptide sequence-driven binding of KIR provides a potential mechanism for pathogen as well as self-peptide to modulate NK cell activation through altering levels of inhibition.