Miracle-dz/UniFAR-FTUs huggingface dataset:
Cre recombinase: The universal reagent for genome tailoring

In September 1998 the workshop for “Conditional Genome Alterations” in Cold Spring Harbor had a simple but important take-home message: “Cre works” (Rossant and McMahon, 1999). After several years of careful investigations, geneticists are now certain that the Cre recombinase of the P1 bacteriophage efficiently catalyzes recombination between two of its consensus 34 base pair DNA recognition sites (loxP sites) in any cellular environment and on any kind of DNA. Obviously mouse geneticists, including myself, are among those who are most excited about this finding. The reason is obvious: When we acquired the Cre/loxP recombinase system as a tool, we reached the level of sophistication of “no more practical limitation” in tailoring the mouse genome. The well-established practice of transgenesis allows the addition of functional DNA pieces into the mouse genome. Furthermore, with the advent of mouse embryonic stem (ES) cells and homologous recombinationbased gene targeting, we are capable of removing any existing gene from the genome. By adding the Cre recombinase system, we can excise or invert loxP-flanked DNA segments or create intermolecular recombination between different DNA molecules. By combining all of these tools, we are capable of creating any desired modification of the mouse genome, from introducing specific point mutations to large site-specific chromosomal aberrations. Furthermore, using the recombinase activity as a genetic activation or inactivation switch, conditional transgenesis or conditional knock-outs became available. The strategies are designed; the proof of principles are given. Many of these strategies utilize a common set of reagents, namely transgenic mouse lines that express the Cre recombinase in a tissue-specific manner and with high fidelity with respect to the recombinase activity. The bottleneck for taking full advantage of these powerful technologies seems to be the realization of this universal set of reagents, the Cre transgenic lines. The purpose of this introductory review in this special issue of Genesis is to summarize the recent status of mouse genetic strategies that apply the Cre recombinase system. BASIC PROPERTIES OF CRE RECOMBINASE
Volume Changes in the Mushroom Bodies of Adult Honey Bee Queens

The volume of the mushroom bodies of the brains of honey bee queens (Apis mellifera) was estimated using the method of Cavalieri. Tissue sampled was obtained from queens in five different behavioral and reproductive states: 1-day-old virgin queens, 14-day-old virgin queens, 14-day-old instrumentally inseminated queens, 9- to 13-day old naturally mated queens, and 5-month-old naturally mated queens. There were significant volume changes within the mushroom bodies during the first 2 weeks of adult life. The volume occupied by the somata of the intrinsic neuronal population (Kenyon cells) of the mushroom bodies decreased by approximately 30% and the volume of the neuropil of the mushroom bodies increased between 25 and 50%. These volume changes are strikingly similar to those previously reported to occur for worker honey bees switching from hive activities to foraging (Withers, Fahrbach, & Robinson, 1993). However, in this study they were found even in queens that had no flight experience. In addition, queens exhibiting these volume changes were found to have low blood levels of juvenile hormone, while previous studies have shown that foraging worker honey bees have high hormone levels. These results suggest that some aspect of behavioral development common to both the queen and the worker castes is fundamental to protocerebral volume changes early in adulthood in honey bees. If juvenile hormone regulates this process, results from queens suggest that it may play an organizational role.
Data Quality Through Business Rules

Good quality data is a valuable asset for any enterprise in this information age. Though volumes of data have grown, their utility for decision making has been meagre. This is a result of poor quality data that enterprises generally possess. Data generation process goes through a number of stages from capture through exchange, integration, migration to storage and data can get corrupted at any stage. Information systems/business applications built with business rules embedded in the code are inadequate to overcome data quality problems. This paper presents a framework that enables enterprise develop business applications that externalize centralized business logic through business rules. Decoupling business rules from the application provides a number of benefits to enterprises including enhanced data quality conforming to defined rules and agility in responding to the ever changing demands of the business environment.
Uveitis: A Potentially Blinding Disease

Uveitis (intraocular inflammation) is a potentially blinding group of, probably autoimmune, conditions predominantly occurring in the working age group. Although the aetiology is unknown in most cases, many patients have an associated underlying systemic disease. Central vision loss, in the form of cystoid macular oedema, is the commonest type of visual impairment. Although historical incidence and prevalence data exists, little is known about the degree of vision loss experienced, and the social and financial consequences of having temporary or permanent visual impairment in this age group. The literature is also full of uncontrolled studies and case reports of different modalities of drug therapy for uveitis. This article attempts to raise the awareness of uveitis as an important sight-threatening group of conditions by highlighting the paucity of evidence-based data on epidemiological, quality of life, socioeconomic, and therapeutic aspects.
A Software Architecture for Data Pre-Processing using Data Mining and Decision Support Models

A new software architecture is proposed that integrates several key data mining and decision support techniques used in the SolEuNet Project. The software is aimed at providing data-pre-processing services to Zeno-for-RAMSYS, a methodology and support system for use in rapid remote collaborative data mining projects. The architecture extends Sumatra, a scripting language for the speci cation of data transformation tasks, with the capability to use various data mining and decision support models, for data pre-processing for instance decision trees and hierarchical multi-attribute models. The integration of models takes place at the level of representation, which is common for all models and based on PMML, an emerging standard for sharing models.
Hibiscus Chlorotic Ringspot Virus Coat Protein Is Essential for Cell-to-Cell and Long-Distance Movement but Not for Viral RNA Replication

Hibiscus chlorotic ringspot virus (HCRSV) is a member of the genus Carmovirus in the family Tombusviridae. In order to study its coat protein (CP) functions on virus replication and movement in kenaf (Hibiscus cannabinus L.), two HCRSV mutants, designated as p2590 (A to G) in which the first start codon ATG was replaced with GTG and p2776 (C to G) in which proline 63 was replaced with alanine, were constructed. In vitro transcripts of p2590 (A to G) were able to replicate to a similar level as wild type without CP expression in kenaf protoplasts. However, its cell-to-cell movement was not detected in the inoculated kenaf cotyledons. Structurally the proline 63 in subunit C acts as a kink for β-annulus formation during virion assembly. Progeny of transcripts derived from p2776 (C to G) was able to move from cell-to-cell in inoculated cotyledons but its long-distance movement was not detected. Virions were not observed in partially purified mutant virus samples isolated from 2776 (C to G) inoculated cotyledons. Removal of the N-terminal 77 amino acids of HCRSV CP by trypsin digestion of purified wild type HCRSV virions resulted in only T = 1 empty virus-like particles. Taken together, HCRSV CP is dispensable for viral RNA replication but essential for cell-to-cell movement, and virion is required for the virus systemic movement. The proline 63 is crucial for HCRSV virion assembly in kenaf plants and the N-terminal 77 amino acids including the β-annulus domain is required in T = 3 assembly in vitro.
Multi-model, multi-objective tuning of fixed-structure controllers

We present a new technique for tuning arbitrary linear control structures against multiple plant models, multiple H2 and H∞ performance requirements, and additional constraints on open-loop stability and closed-loop pole locations. Our approach relies on non-smooth optimization and strikes a good balance between flexibility and effectiveness. Its capabilities are illustrated on two challenging applications.
A Comparison Study of Three Degree-of-Freedom Micro-motion Parallel Kinematic Machines with/without Actuation Redundancy

This paper presents a comparison study of two unique micro-motion parallel kinematic manipulators (PKM): a three degrees of freedom (DOF) micro-motion PKM and a 3-DOF micro-motion PKM with actuation redundancy. The 3-DOF micro-motion PKM has three linear-motion driving units, while the 3-DOF micro-motion PKM with actuator redundancy has four of these units. For both designs, the linear motion driving units are identical and both machines have the same passive link in the middle of the structure. The manipulator with actuator redundancy is designed to prevent singularity and to improve stiffness. The inverse kinematics and Jacobian of these two PKMs are analyzed, the stiffness properties are determined and global stiffness is optimized using genetic algorithm. A comparison of the global stiffness indicates that the 3-DOF micro motion PKM with actuator redundancy outperforms the one without actuator redundancy.
Segmentation of small structures in MR images: Semiautomated tissue hydration measurement

Segmentation of small anatomic structures In noisy magnetic resonance (MR) images is inherently challenging because the edge Information is contained in the same high‐frequency image component as the noise. The authors overcame this obstacle in the analysis of the sural nerve in the ankle by processing images to reduce noise and extracting edges with an edge detection algorithm less sensitive to noise. Anatomic accuracy of the segmentation was confirmed by a neuroradiologist. A nerve hydration coefficient was determined from the signal intensity of the nerve in these segmented images. These semiautomated measurements of hydration agreed closely with those obtained with a previously described manual method (n=44, P=.76). Each image in the study was analyzed identically, with no modification of the computer algorithm parameters. The data suggest that this robust method may be useful in a multicenter evaluation of diabetes treatment protocols.
Mixed cycle-E-super magic decomposition of complete bipartite graphs

An H-magic labeling in a H-decomposable graph G is a bijection f : V (G) ∪ E(G) → {1, 2, . , p + q} such that for every copy H in the decomposition, ∑νeV (H) f(v) + ∑νeE (H) f(e) is constant. f is said to be H-E-super magic if f(E(G)) = {1, 2, · · · , q}. A family of subgraphs H1,H2, · · · ,Hh of G is a mixed cycle-decomposition of G if every subgraph Hi is isomorphic to some cycle Ck, for k ≥ 3, E(Hi) ∩ E(Hj) = ∅ for i ≠ j and ∪hi=1E(Hi) = E(G). In this paper, we prove that K2m,2n is mixed cycle-E-super magic decomposable where m ≥ 2, n ≥ 3, with the help of the results found in [1].
Intestinal microbiota composition in fishes is influenced by host ecology and environment

The digestive tracts of vertebrates are colonized by complex assemblages of micro‐organisms, collectively called the gut microbiota. Recent studies have revealed important contributions of gut microbiota to vertebrate health and disease, stimulating intense interest in understanding how gut microbial communities are assembled and how they impact host fitness ( Sekirov et al. 2010 ). Although all vertebrates harbour a gut microbiota, current information on microbiota composition and function has been derived primarily from mammals. Comparisons of different mammalian species have revealed intriguing associations between gut microbiota composition and host diet, anatomy and phylogeny ( Ley et al. 2008b ). However, mammals constitute <10% of all vertebrate species, and it remains unclear whether similar associations exist in more diverse and ancient vertebrate lineages such as fish. In this issue, Sullam et al. (2012) make an important contribution toward identifying factors determining gut microbiota composition in fishes. The authors conducted a detailed meta‐analysis of 25 bacterial 16S rRNA gene sequence libraries derived from the intestines of different fish species. To provide a broader context for their analysis, they compared these data sets to a large collection of 16S rRNA gene sequence data sets from diverse free‐living and host‐associated bacterial communities. Their results suggest that variation in gut microbiota composition in fishes is strongly correlated with species habitat salinity, trophic level and possibly taxonomy. Comparison of data sets from fish intestines and other environments revealed that fish gut microbiota compositions are often similar to those of other animals and contain relatively few free‐living environmental bacteria. These results suggest that the gut microbiota composition of fishes is not a simple reflection of the micro‐organisms in their local habitat but may result from host‐specific selective pressures within the gut ( Bevins & Salzman 2011 ).
Enhanced gas sensing properties of flower-like ZnO nanostructure to acetylene

Abstract Well dispersed flower-like and rod-like zinc oxide (ZnO) microstructures were successfully synthesised by hydrothermal method with the assistance of hexadecyl trimethyl ammonium bromide. Microstructures and surface morphologies for both samples were characterised by X-ray diffraction, field emission scanning electron microscopy, transmission electron microscopy and high resolution transmission electron microscopy. Gas sensors were fabricated by screenprinting the as prepared ZnO nanostructures onto planar ceramic substrates. Then, their gas sensing properties were systematically investigated towards acetylene gas (C2H2). The products exhibit a high, reversible and fast response to C2H2 gas, and the flower-like ZnO architecture exhibits a better activity.
Systematic Review of the Literature and Evidence-Based Recommendations for Antibiotic Prophylaxis in Trauma: Results from an Italian Consensus of Experts

Background Antibiotic prophylaxis is frequently administered in severe trauma. However, the risk of selecting resistant bacteria, a major issue especially in critical care environments, has not been sufficiently investigated. The aim of the present study was to provide guidelines for antibiotic prophylaxis for four different trauma-related clinical conditions, taking into account the risks of antibiotic-resistant bacteria selection, thus innovating previous guidelines in the field. Methods The MEDLINE database was searched for studies comparing antibiotic prophylaxis to controls (placebo or no antibiotic administration) in four clinical traumatic conditions that were selected on the basis of the traumatic event frequency and/or infection severity. The selected studies focused on the prevention of early ventilator associated pneumonia (VAP) in comatose patients with traumatic brain injury, of meningitis in severe basilar skull fractures, of wound infections in long-bone open fractures. Since no placebo-controlled study was available for deep surgical site-infections prevention in abdominal trauma with enteric contamination, we compared 24-hour and 5-day antibiotic prophylaxis policies. A separate specific research focused on the question of antibiotic-resistant bacteria selection caused by antibiotic prophylaxis, an issue not adequately investigated by the selected studies. Randomised trials, reviews, meta-analyses, observational studies were included. Data extraction was carried out by one author according to a predefined protocol, using an electronic form. The strength of evidence was stratified and recommendations were given according to the Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria. Results Uncertain evidence deserving further studies was found for two-dose antibiotic prophylaxis for early VAP prevention in comatose patients. In the other cases the risk of resistant-bacteria selection caused by antibiotic administration for 48 hours or more, outweighed potential benefits. Conclusions When accounting for antibiotic-resistant bacteria selection we found no evidence in favour of antibiotic prophylaxis lasting two or more days in the studied clinical conditions.
BPS D-branes on Non-supersymmetric Cycles

In certain regions of the moduli space of K3 and Calabi-Yau manifolds, D-branes wrapped on non-supersymmetric cycles may give rise to stable configurations. We show that in the orbifold limit, some of these stable configurations can be described by solvable boundary conformal field theories. The world-volume theory of N coincident branes of this type is described by a non-supersymmetric U(N) gauge theory. At the boundary of the region of stability, there are marginal deformations connecting the non-supersymmetric brane to a pair of D-branes wrapped on supersymmetric cycles. We also discuss various relationships between BPS and non-BPS D-branes of type II string theories.
Finite element modelling (including material grain refinement prediction) when turning advanced aerospace alloys

The overall aim of the project/research was to develop finite element modelling/process simulation capability to predict workpiece surface integrity following machining of advanced aerospace alloys. The modelling work employed the general-purpose commercial finite element (FE) software ABAQUS, due to its robust solver for handling complex, dynamic non-linear problems as well as the facility to define custom algorithms/subroutines. Both 2D and 3D fully coupled thermo-mechanical FE models were formulated to simulate the orthogonal turning of Ti-6Al-4V titanium alloy and Inconel 718 nickel based superalloy. The performance of various material models and associated damage criteria were assessed, with high strain rate (up to ~ 6000 s\(^-\)\(^1\)) / temperature (up to ~ 850°C) flow stress data for Inconel 718 obtained from compression tests using SHPB and Gleeble systems. In addition to evaluating the influence of operating conditions on response measures such as cutting forces, temperatures and chip morphology, the FE models were extended to enable prediction of grain size distribution due to dynamic recrystallisation (DRX) of workpiece microstructure following machining. This was accomplished by developing a VUMAT user customised subroutine that included material constitutive modelling, damage initiation/propagation as well as a novel material model to predict workpiece grain refinement due to DRX.
Measuring epileptogenicity in kainic acid injected rats

The present work aims at improving the validation of therapeutic approaches to treat temporal lobe epilepsy. Today's antiepileptic drugs perform only poorly for this form of epilepsy, and electrical stimulation might be an alternative for these patients. Finding the optimal stimulation parameters, however, is difficult as the underlying mechanisms, both of the disease and the stimulation procedure, and even the evaluation of the therapeutic effect are still poorly understood. Here we used a method to obtain a quantitative measure - the relative phase clustering index (rPCI) - of the epileptogenicity of a brain region in a simple and straightforward way.
Optimal sequential waveform design for cognitive radar

This paper addresses the problem of adaptive sequential waveform design for system parameter estimation. This problem arises in several applications such as radar, sonar, or tomography. In the proposed technique, the transmit/input signal waveform is optimally determined at each step, based on the measurements in the previous steps. The waveform is determined to minimize the Bayesian Cramér-Rao bound (BCRB) for estimation of the unknown system parameter at each step. The algorithm is tested for spatial transmit waveform design in multiple-input multiple-output radar target angle estimation at very low signal-to-noise ratio. The simulations show that the proposed adaptive waveform design achieves significantly higher rate of performance improvement as a function of the pulse index, compared to identical signal transmission.
CGS 35601 and its Orally Active Prodrug CGS 37808 as Triple Inhibitors of Endothelin-converting Enzyme-1, Neutral Endopeptidase 24.11, and Angiotensin-converting Enzyme

CGS 35601 is a potent triple inhibitor of endothelinconverting enzyme-1, neutral endopeptidase 24.11, and angiotensinconverting enzyme. It inhibited the activities of these three enzymes with IC50 values of 55, 2 and 22 nM, respectively. In conscious rats, CGS 35601 suppressed the big endothelin-1-induced pressor response by 82% and 72% at 30 and 120 minutes, respectively, following injection at a dose of 10 mg/kg, intravenously. At the same dose, CGS 35601 increased plasma atrial natriuretic peptide (ANP) immunoreactivity by 170% for up to 4 hours in conscious rats infused with ANP, and it inhibited the angiotensin I-induced pressor response by 74-94% within the first 2 hours after dosing. Similar in vivo activities were also observed with its orally active prodrug, CGS 37808. This compound blocked the big endothelin-1- induced pressor response by 71% and 67% at 30 and 120 minutes, respectively, after an oral dose of 10 mgEq/kg in conscious rats. It also increased plasma ANP immunoreactivity by 103% for up to 4 hours and inhibited the angiotensin I-induced pressor response by an average of 49% within the first 4 hours after the same dosing regimen. By suppressing the biosyntheses of endothelin-1 and angiotensin II, two potent vasoconstrictors, while simultaneously potentiating the circulating levels of ANP, a vasorelaxant and diuretic, CGS 35601 and CGS 37808 may represent novel agents for the treatment of cardiovascular and renal diseases.