Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characteristics of KPC-Producing Enterobacteriaceae at the Early Stage of Their Dissemination in Poland, 2008–2009

ABSTRACT After the first report in May 2008, the National Reference Center for Susceptibility Testing confirmed 113 cases of infection or colonization by KPC-producing members of the family Enterobacteriaceae in Poland by the end of 2009. The vast majority of patients were found in 18 hospitals; three patients were diagnosed at outpatient clinics. Most of the institutions were in the Warsaw area, including three hospitals with the highest numbers of cases. When available, the data on previous hospitalizations often indicated that these hospitals were the probable acquisition sites; one patient arrived from New York. The group of 119 unique isolates consisted of Klebsiella pneumoniae (n = 114), followed by Klebsiella oxytoca (n = 3), and Escherichia coli (n = 2). The K. pneumoniae isolates were dominated by the clone sequence type 258 (ST258) (n = 111); others were ST11 and ST23. The ST258 group was heterogeneous, with 28 pulsed-field gel electrophoresis (PFGE) subtypes, ∼25 plasmid profiles, and nine β-lactamase patterns differing by KPC variants (KPC-2 mainly), and SHV-12, CTX-M-3, and TEM-1-like enzymes. Plasmids carrying blaKPC genes varied in size (∼48 to 250 kb), structure, and conjugation potential. Transferable IncFIIK plasmids of ∼110 to 160 kb, probably pKpQIL or its derivatives, were observed in all K. pneumoniae clones and in K. oxytoca. Also prevalent were nontypeable pETKp50-like plasmids of ∼50 kb, found in K. pneumoniae ST258 and E. coli isolates (ST93 and ST224). Two K. pneumoniae-E. coli pairs from single patients might represent the in vivo transfer of such plasmids. The striking diversity of KPC producers at the early stage of dissemination could result from several introductions of these bacteria into the country, their multidirectional evolution during clonal spread, and transfer of the plasmids.
Establishment and characterization of a pair of non-malignant and malignant tumor derived cell lines from an African American prostate cancer patient.

Research into molecular and genetic mechanisms underlying prostate carcinogenesis in high-risk African American men would be greatly advanced by in vitro models of African American prostate tumors representing primary tumors. However, the generation of immortalized primary African American prostate cancer cells that will accurately reflect the in situ characteristics of malignant epithelium is currently limited but is greatly needed. We have successfully established immortalized cell lines of a pair of non-malignant and malignant tumors derived from an African American prostate cancer patient with HPV-16E6E7 (RC-77N/E and RC-77T/E). RC-77N/E and RC-77T/E cells are currently growing well at passage 40. Both cells exhibit epithelial morphology and are androgen sensitive. The RC-77T/E cells produced tumors in SCID mice whereas the RC-77N/E cells produced no tumor in SCID mice. These cells expressed androgen-regulated prostate-specific homobox gene, NKX 3.1, epithelial cell specific cytokeratn 8, androgen receptor (AR), prostate specific antigen (PSA), and p16. Chromosome analysis showed that both cell lines are similar; near diploid human male (XY) with most chromosome counts in the 45-48 range. However, RC-77T/E cell line has new marker chromosomes: M1B=del/t(4;? )(q28;? ), M5=16q+ in addition to those observed in the RC-77N/E cell line (M1=del(4)(q28q34)+hsr in some, M1A=t(4q;? ),M2=der(9? ),M2A=del(M2p-),M3=iso(? ), M4=der(22? )). This is the first documented case of the establishment of pair of non-malignant and malignant tumors derived from an African American prostate cancer patient. These models will provide novel tools to study the molecular and genetic mechanisms of prostate carcinogenesis, especially for high-risk African American men.
Circular Patch Sensor Based on Distributed Fiber Optic Technology for Tensile and Bending Loads Identification

The design, manufacturing, and preliminary testing of a smart patch sensor named MonitoRing are herein presented. The sensor is conceived to identify amplitude and direction of structural loads by distributed strain profile detection along its circular geometry. The sensor is manufactured by using flexible glass/epoxy laminates hosting a single standard telecom fiber optic. The fiber optic is embedded according to three loops, different by radius and quote. The sensor is then externally bonded on a structural element and able to follow the deformations under tensile and bending loading condition. The optical Rayleigh backscattering technology provides an interrogation of strain with high spatial resolution all along the fiber path. The load and direction identification is hence, provided by comparing amplitude, phase and sign of deformation spectrum of each loop. Preliminary numerical and experimental result, are reported and analyzed for simple test cases.
Identifying free text plagiarism based on semantic similarity

It is common knowledge that plagiarism in academia goes as back in time as research itself. However, in the last two decades this phenomenon of academic deception has turned into an academic plague. Undoubtedly, the rapid expansion of the Web and the vast amount of publicly available information and documents facilitate the unethical malpractice of computer-aided plagiarism, which in turn has inflated the problem. Anti-plagiarism techniques build upon technological solutions and especially the development of task-specific software. The role of anti-plagiarism software for text is to process a document and identify the pieces of text that have been reproduced from another source. This work presents a semantic-based approach to text-plagiarism detection which improves the efficiency of traditional keyword matching techniques. Our semantic matching technique is able to detect a larger variety of paraphrases, including the use of synonym terms, the repositioning of words in the sentences etc. We evaluate our methodology in a dataset comprising positive and negative plagiarism samples and present comparative results of both supervised and unsupervised methods.
Telomerase Immortalization of Human Corneal Endothelial Cells Yields Functional Hexagonal Monolayers

Human corneal endothelial cells (HCEnCs) form a monolayer of hexagonal cells whose main function is to maintain corneal clarity by regulating corneal hydration. HCEnCs are derived from neural crest and are arrested in the post-mitotic state. Thus cell loss due to aging or corneal endothelial disorders leads to corneal edema and blindness–the leading indication for corneal transplantation. Here we show the existence of morphologically distinct subpopulations of HCEnCs that are interspersed among primary cells and exhibit enhanced self-renewal competence and lack of phenotypic signs of cellular senescence. Colonies of these uniform and hexagonal HCEnCs (HCEnC-21) were selectively isolated and demonstrated high proliferative potential that was dependent on endogenous upregulation of telomerase and cyclin D/CDK4. Further transduction of HCEnC-21 with telomerase yielded a highly proliferative corneal endothelial cell line (HCEnT-21T) that was devoid of oncogenic transformation and retained critical corneal endothelial cell characteristics and functionality. This study will significantly impact the fields of corneal cell biology and regenerative medicine.
Three dimensional digital reconstruction of the jaw adductor musculature of the extinct marsupial giant Diprotodon optatum

The morphology and arrangement of the jaw adductor muscles in vertebrates reflects masticatory style and feeding processes, diet and ecology. However, gross muscle anatomy is rarely preserved in fossils and is, therefore, heavily dependent on reconstructions. An undeformed skull of the extinct marsupial, Diprotodon optatum, recovered from Pleistocene sediments at Bacchus Marsh in Victoria, represents the most complete and best preserved specimen of the species offering a unique opportunity to investigate functional anatomy. Computed tomography (CT) scans and digital reconstructions make it possible to visualise internal cranial anatomy and predict location and morphology of soft tissues, including muscles. This study resulted in a 3D digital reconstruction of the jaw adductor musculature of Diprotodon, revealing that the arrangement of muscles is similar to that of kangaroos and that the muscle actions were predominantly vertical. 3D digital muscle reconstructions provide considerable advantages over 2D reconstructions for the visualisation of the spatial arrangement of the individual muscles and the measurement of muscle properties (length, force vectors and volume). Such digital models can further be used to estimate muscle loads and attachment sites for biomechanical analyses.
Bounds on the distribution of a sum of independent lognormal random variables

The distribution function of a sum of lognormal random variables (RVs) appears in several communication problems. Approximations are usually used for such distribution as no closed form nor bounds exist. Bounds can be very useful in assessing the performance of any given system. In this letter, we derive upper and lower bounds on the distribution function of a sum of independent lognormal RVs. These bounds are given in a closed form and can be used in studying the performance of cellular radio and broadcasting systems.
Paradigms for Statistical Inference Murray Aitkin

This paper expresses the different theories of statistical inference in terms of the competition between scientific paradigms as described in Kuhn (1996). The conflict among the major schools is examined in Kuhn’s terms, with extensive quotes, which helps to illuminate the discussion. Critical issues among the schools are evaluated with canonical examples. The scientific and social implications of conflicting conclusions from the same data by different schools are considered, and proposals are made for extending the current Bayesian paradigm, through both reformulating model comparisons, and incorporating sample survey analysis.
Heat-inactivated proteins are rescued by the DnaK.J-GrpE set and ClpB chaperones.

Functional chaperone cooperation between Hsp70 (DnaK) and Hsp104 (ClpB) was demonstrated in vitro. In a eubacterium Thermus thermophilus, DnaK and DnaJ exist as a stable trigonal ring complex (TDnaK.J complex) and the dnaK gene cluster contains a clpB gene. When substrate proteins were heated at high temperature, none of the chaperones protected them from heat inactivation, but the TDnaK.J complex could suppress the aggregation of proteins in an ATP- and TGrpE-dependent manner. Subsequent incubation of these heated preparations at moderate temperature after addition of TClpB resulted in the efficient reactivation of the proteins. Reactivation was also observed, even though the yield was low, if the substrate protein alone was heated and incubated at moderate temperature with the TDnaK.J complex, TGrpE, TClpB, and ATP. Thus, all these components were necessary for the reactivation. Further, we found that TGroEL/ES could not substitute TClpB.
Eyeless Mexican Cavefish Save Energy by Eliminating the Circadian Rhythm in Metabolism

The eyed surface form and eyeless cave form of the Mexican tetra Astyanax mexicanus experience stark differences in the daily periodicities of light, food and predation, factors which are likely to have a profound influence on metabolism. We measured the metabolic rate of Pachón cave and surface fish at a fixed swimming speed under light/dark and constant dark photoperiods. In constant darkness surface forms exhibited a circadian rhythm in metabolism with an increase in oxygen demand during the subjective daytime, whereas cave forms did not. The lack of circadian rhythm in metabolism leads to a 27% energy savings for Pachón cave fish compared to surface fish when comparing both forms in their natural photoperiods. When surface forms were tested under constant dark conditions they expended 38% more energy than cave forms under equivalent conditions. Elimination of the circadian rhythm in metabolism may be a general feature of animals that live in perpetually dark food-limited environments such as caves or the deep sea.
Did the One-Child Policy Generate Child Overweight in China in the 1990 s ? A Cross-Sectional and Longitudinal Analysis

The prevalence of overweight among children in China has increased, and the one-child policy has been suggested as a cause. Drawing on longitudinal data from the 1993, 1997 and 2000 waves of the China Health and Nutrition Survey, this analysis investigates the relationship between the one-child policy and overweight among young children. The policy is measured directly as policy strength and indirectly as sibship composition. Cross-sectional and longitudinal findings from multilevel models suggest that, first, overweight among preschoolers and primary school children increased in the 1990s at a slower pace than that documented in previous studies in China. Second, single children and those in strong policy communities do not differ from children with sibling(s) and those in weak policy communities, after adjusting for household and community characteristics. Thus, the policy does not seem to bear a relationship to child overweight risk directly or indirectly, and little evidence has emerged from this analysis to support the public perception that the one-child policy is associated with the rising epidemic of child overweight in transitional China. Paper prepared for the 2005 Annual Meeting of the Population Association of America at Philadelphia. The author thanks Susan Short, David Linstrom, Berna Torr, Zhanlian Feng, Frank Hu, Holly Reed and Michael White for helpful inputs on an earlier draft of this paper.
Structure Preserving Semantic Matching

A rotary potentiometer is provided with a switch, preferably as a final control element for the control of electrical machinery. An enclosed, prefabricated rotary potentiometer component with its own casing is inserted in a cup-shaped upper casing that is open on one side. Switching contact supports are housed in the upper casing by means of peripheral wall sections. These contact supports are actuated by a cam actuating member that is mounted on a fulcrum pin so as to permit play and simultaneously also effect rotation and retention of the potentiometer component in the upper casing.
Atlas registration for edema-corrected MRI lesion volume in mouse stroke models

Lesion volume measurements with magnetic resonance imaging are widely used to assess outcome in rodent models of stroke. In this study, we improved a mathematical framework to correct lesion size for edema which is based on manual delineation of the lesion and hemispheres. Furthermore, a novel MATLAB toolbox to register mouse brain MR images to the Allen brain atlas is presented. Its capability to calculate edema-corrected lesion size was compared to the manual approach. Automated image registration performed equally well in in a mouse middle cerebral artery occlusion model (Pearson r = 0.976, p = 2.265e-11). Information encapsulated in the registration was used to generate maps of edema induced tissue volume changes. These showed discrepancies to simplified tissue models underlying the manual approach. The presented techniques provide biologically more meaningful, voxel-wise biomarkers of vasogenic edema after stroke.
Creating portable, repeatable, realistic benchmarks for embedded systems and the challenges thereof

To appreciate the challenges of analysing embedded processor behaviour, step back in time to understand the evolution of embedded processors. Only a few decades ago, embedded processors were relatively simple devices (compared to today), represented by a host of 8- and 16-bit microcontrollers, and 32-bit microprocessors, with minimal integration. Today, these processors (even the so-called, low-end microcontrollers), have evolved into highly-integrated SoCs with a wide variety of architectures capable of tackling both specific and general-purpose tasks. Associated with these transformations, the benchmarks used to quantify the capabilities have also grown in complexity and range. At the simplest level, benchmarks such as CoreMark analyse the fundamental processor cores. At the other end of the spectrum, system benchmarks, such BrowsingBench, analyse the entire SoC as well as the system software stack and even the physical interfaces. This paper examines some of the challenges of applying such benchmarks, and explains the methodologies used at EEMBC to manage portability, repeatability, and realism.
Polinsar at Low Frequency and Ionospheric Effects

Global warming is now known to be the major environmental issue mankind will have to face in the next decade. Monitoring of vegetation and biomass is clearly an essential piece of information required at all levels ranging from the scientific studies to understand and forecast, to the political actors and government leaders responsible for drafting remediation policies and evaluating their impact. Microwave remote sensing with the low-frequency SAR technique can provide a useful characterization of forest (spatial coverage, species, density, height.) at a global scale, relying on the all-weather imaging capabilities of SAR linked with the significant penetration of the low-frequency EM wave in the canopy. The published techniques for forest characterization from low frequency SAR data include radiometry inversion, polarimetric inversion based on the anisotropy parameters and PolInSAR Random Volume Over Ground inversion. In this paper, we will more specifically concentrate on the PolInSAR technique and the impact of ionospheric effect on this inversion. PolInSAR at low frequency can be envisioned with two radar platforms flying in formation or as a repeat pass mission. The second alternative is more plausible given the cost and the size of a low frequency SAR instrument. However the two cases will be discussed in the paper.
Rectangular Microstrip Patch Antenna with U-Shaped DGS Structure for Wireless Applications

A compact micro strip patch antenna with wide operational bandwidth is presented. The proposed design consists of rectangular patch antenna in ring shaped with U-slots cut in ground. Antenna is fed by micro strip line. The performance of rectangular patch antenna has been discussed and analyzed by modification of the patch dimensions. The proposed antenna is having bandwidth of 1300 MHz, gain 2.65 dBi and return loss -28.82 dB. The proposed antenna has been analyzed using IE3D and simulated results are presented in terms of bandwidth, gain and return loss.
Design, optimization and control in systems and synthetic biology

How good is our understanding of the way cells treat information and make decisions? To what extend our current understanding enables us to reprogram and control the way cells behave? In this manuscript I describe several approaches developed for the computational analysis of the dynamics of biological networks. In particular I present work done on (i) the analysis of large gene networks with partial information on parameter values, (ii) the use of specification languages to express observations or desired properties in an abstract manner and efficiently search for parameters satisfying these properties, and (iii) recent efforts to use models to drive gene expression in real-time at the cellular level.
Gut endoderm is involved in the transfer of left-right asymmetry from the node to the lateral plate mesoderm in the mouse embryo

In the mouse, the initial signals that establish left-right (LR) asymmetry are determined in the node by nodal flow. These signals are then transferred to the lateral plate mesoderm (LPM) through cellular and molecular mechanisms that are not well characterized. We hypothesized that endoderm might play a role in this process because it is tightly apposed to the node and covers the outer surface of the embryo, and, just after nodal flow is established, higher Ca2+ flux has been reported on the left side near the node, most likely in the endoderm cells. Here we studied the role of endoderm cells in the transfer of the LR asymmetry signal by analyzing mouse Sox17 null mutant embryos, which possess endoderm-specific defects. Sox17–/– embryos showed no expression or significantly reduced expression of LR asymmetric genes in the left LPM. In Sox17 mutant endoderm, the localization of connexin proteins on the cell membrane was greatly reduced, resulting in defective gap junction formation, which appeared to be caused by incomplete development of organized epithelial structures. Our findings suggest an essential role of endoderm cells in the signal transfer step from the node to the LPM, possibly using gap junction communication to establish the LR axis of the mouse.
A Comparison of EFGM and FEM for Nonlinear Solid Mechanics Problems

In this paper, element free Galerkin method (EFGM) has been applied to solve nonlinear solid mechanics problems using updated Lagrangian approach. The nonlinear equations have been solved using Newton Raphson method. An associative J2 flow rule and isotropic hardening has been used for the modelling of elasto-plastic material behaviour. Elastic predictor and plastic corrector algorithm has been used for the integration of incremental stress-strain relation. Few test problems involving large deformations have been simulated and the results obtained by EFGM have been compared with those obtained by FEM.
Direct effect of a dynamic wrist and hand orthosis on reach and grasp kinematics in chronic stroke

Many stroke patients have impaired arm and hand function. Distal arm and hand devices may support functional use of the upper extremity in activities in daily life. The present study assessed the direct effects of a passive dynamic wrist and hand orthosis on hand and arm movements during the performance of a reach and grasp task in ten mildly to moderately impaired chronic stroke patients. The use of the orthosis resulted in an increase in hand opening, increase in trunk displacement and decrease in elbow ROM during the performance of the reach and grasp task. Therefore, the use of an additional device supporting the arm against gravity should be considered when using such an orthosis in future research, to counteract potential compensatory trunk movements. The findings obtained in this study are being taken into consideration for a longitudinal feasibility study using this orthosis in combination with a computerized gaming environment in chronic stroke at home.
Manipulative zero-stealthy attacks in cyber-physical systems: Existence space of feasible attack objectives

In this paper, we analyze the vulnerabilities due to novel integrity cyber attacks in CPS, which are modeled as a stochastic Linear Time-Invariant (LTI) system equipped with a Kalman filter, an LQG controller, and a χ2 failure detector from an attacker's standpoint. The attacks are designed by a sophisticated attacker so that the measurement residual of the compromised system coincides with the healthy one. Additionally, the attacked system state is manipulated to an objective which is designed by the adversary. We first show an existence condition and a design procedure of the stealthy attacks using invariant subspace property. Then, we formulate the stealthy attacks with a malicious objective, and the condition of the feasible objectives is derived. Finally, the dangerousness of the attacks is verified through a numerical simulation.