Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence and Organization of pXO1, the Large Bacillus anthracis Plasmid Harboring the Anthrax Toxin Genes

ABSTRACT The Bacillus anthracis Sterne plasmid pXO1 was sequenced by random, “shotgun” cloning. A circular sequence of 181,654 bp was generated. One hundred forty-three open reading frames (ORFs) were predicted using GeneMark and GeneMark.hmm, comprising only 61% (110,817 bp) of the pXO1 DNA sequence. The overall guanine-plus-cytosine content of the plasmid is 32.5%. The most recognizable feature of the plasmid is a “pathogenicity island,” defined by a 44.8-kb region that is bordered by inverted IS1627 elements at each end. This region contains the three toxin genes (cya, lef, and pagA), regulatory elements controlling the toxin genes, three germination response genes, and 19 additional ORFs. Nearly 70% of the ORFs on pXO1 do not have significant similarity to sequences available in open databases. Absent from the pXO1 sequence are homologs to genes that are typically required to drive theta replication and to maintain stability of large plasmids in Bacillus spp. Among the ORFs with a high degree of similarity to known sequences are a collection of putative transposases, resolvases, and integrases, suggesting an evolution involving lateral movement of DNA among species. Among the remaining ORFs, there are three sequences that may encode enzymes responsible for the synthesis of a polysaccharide capsule usually associated with serotype-specific virulent streptococci.
Presynaptic Calcium Current Modulation by a Metabotropic Glutamate Receptor

Metabotropic glutamate receptors (mGluRs) regulate transmitter release at mammalian central synapses. However, because of the difficulty of recording from mammalian presynaptic terminals, the mechanism underlying mGluR-mediated presynaptic inhibition is not known. Here, simultaneous recordings from a giant presynaptic terminal, the calyx of Held, and its postsynaptic target in the medial nucleus of the trapezoid body were obtained in rat brainstem slices. Agonists of mGluRs suppressed a high voltage-activated P/Q-type calcium conductance in the presynaptic terminal, thereby inhibiting transmitter release at this glutamatergic synapse. Because several forms of presynaptic modulation and plasticity are mediated by mGluRs, this identification of a target ion channel is a first step toward elucidation of their molecular mechanism.
A phenylalanine ammonia‐lyase gene from parsley: structure, regulation and identification of elicitor and light responsive cis‐acting elements.

We demonstrate that phenylalanine ammonia‐lyase (PAL) in parsley (Petroselinum crispum) is encoded by a small family of at least four genes. The levels of mRNA from three identified PAL genes increase considerably upon treatment of cultured parsley cells with UV light or fungal elicitor and upon wounding of parsley leaves or roots. In cultured cells these changes were shown to involve transcriptional activation. We present the first primary structure of a plant PAL gene (parsley PAL‐1) and the deduced amino acid sequence of the enzyme. Inducible in vivo footprints in the PAL‐1 promoter define two nucleotide sequences, within the motifs CTCCAACAAACCCCTTC and ATTCTCACCTACCA, involved in the responses to both UV irradiation and elicitor application. These motifs are conserved at similar positions in several elicitor or light‐responsive genes from different species. In two cases they are found within short regions known to confer elicitor or UV‐light inducibility. The conserved motifs in the parsley 4‐coumarate:CoA ligase gene, which is coordinately regulated with PAL, also display UV‐light inducible in vivo footprints. Taken together, our findings suggest a general role of these putative cis‐acting elements in the responses of plants to such stresses.
Cervical artificial disc extrusion after a paragliding accident

Background: Cervical total disc replacement (TDR) is an established alternative to anterior cervical discectomy and fusion (ACDF) with excellent long-term outcomes and low failure rates. Cases of implant failure and migration are scarce and primarily limited to several years postoperatively. The authors report a case of anterior extrusion of a C4-C5 ProDisc-C (DePuy Synthes, West Chester, PA, USA) cervical artificial disc (CAD) 14 months after placement due to minor trauma. Case Description: A 33-year-old female who had undergone C4-C5 CAD implantation presented with neck pain and spasm after experiencing a paragliding accident. A 4 mm anterior protrusion of the CAD was seen on x-ray. She underwent removal of the CAD followed by anterior fusion. Other cases of CAD extrusion in the literature are discussed and the device's durability and testing are considered. Conclusion: Overall, CAD extrusion is a rare event. This case is likely the result of insufficient osseous integration. Patients undergoing cervical TDR should avoid high-risk activities to prevent trauma that could compromise the disc's placement, and future design/research should focus on how to enhance osseous integration at the interface while minimizing excessive heterotopic ossification.
Hirschsprung's disease with infantile nephropathic cystinosis

The case of a 3-year-old boy diagnosed to have Hirschsprung′s disease with infantile nephropathic cystinosis is being reported. Both these conditions are etiologically and genetically different as per current understanding and available information. The association is incidental and has not reported before in the English literature.
Eye-Tracking Technology for Construction Safety: A Feasibility Study

A construction site is a harsh environment demanding entire human senses and attention, even for regular scheduled tasks. Many accidents occur on construction sites because of inability of workers to identify hazards and make timely decisions. To understand why some hazards go unseen, it is crucial to study how workers perceive the site. The objective of this research is to leverage eye-tracking technology to study workers’ gazing pattern in a construction environment. A real picture from an active construction site is modified to introduce hazards and a desktop experiment is conducted, in which, subjects are asked to identify the hazards. A different group of subjects are made to make similar observations on a 2D sketch-representation of the same construction scenario. Eye-tracking data gathered from their observations is analyzed to understand when, how, and which hazards do they recognize and the pattern of recognition is studied. The results of this study will enhance our understanding on the visual factors that govern attention and help workers recognize potential hazards in a construction site. The comparison between the observation pattern in real and sketch-representation is done to assess how subjects respond to artificial images compared to real images. This comparison will test the feasibility of using virtual reality for safety training and simulations.
OMIP‐016: Characterization of antigen‐responsive macaque and human T‐cells

PURPOSE AND APPROPRIATE SAMPLE TYPES The present panel was optimized to assess the quality and phenotype of antigenspecific CD4 and CD8 T cells in both cynomolgus macaques and humans. The use of an identical protocol for specimens collected in the two species allows for an immediate translation of research from the macaque model to humans. Our protocol works well with cryopreserved and freshly collected PBMC. Following the fixing and permeabilization procedure, we introduced a freezing step that breaks the experimental procedure and allows the shipment of freshly stimulated and permeabilized samples to facilities equipped with instruments able to measure ten distinct fluorescences. Our procedure is thus adapted to multicenter studies where stimulation is performed on fresh PBMC and flow cytometry acquisition is done in a centralized facility.
Transmission and scanning electron microscopy of the male reproductive system of Schistosoma margrebowiei Le Roux, 1933

ABSTRACT The structure of the male reproductive system of Schistosoma margrebowiei as viewed by light, scanning and transmission electron microscopy is described. The cirrus tube opens at the genital pore without the presence of a cirrus and is spongy and leaf-like. The structure of the germinal and non-germinal cells of the testes are described. The spermatozoon consists of a head, without an acrosome, and a flagellum with a 9+0 arrangement of microtubles in the axial filament. A large mass of mitochondria is situated in the anterior end of the head and cortically arranged longitudinally running microtubles are present. The apical region of the epithelial cells of the vas deferens extends into the lumen of the duct forming convoluted lamellae. This arrangement, together with the presence of dense bodies within the cells, suggests that these cells have a secretory function.
Direct manipulation vs. interface agents

B en Shneiderman is a long-time proponent of direct manipulation for user interfaces. Direct manipulation affords the user control and predictability in their interfaces. Pattie Maes believes direct manipulation will have to give way to some form of delegation— namely software agents. Should users give up complete control of their interaction with interfaces? Will users want to risk depending on " agents " that learn their likes and dislikes and act on a user's behalf? Ben and Pattie debated these issues and more at both IUI 97 yourself where the future of interfaces should be headed—and why.
Ectopic Ossification in the Scar Tissue of Rats with Myocardial Infarction

We describe the occurrence of bone-like formations in the left ventricular wall of infarcted rats treated or not with bone marrow cells injected systemically or locally into the myocardium. The incidence of ectopic calcification in hearts has been reported in rare cases in children with infarcts without previous coronary artery disease. Recently, ventricular calcification has been correlated with unselected bone marrow cell transplantation into infarcted rat hearts. Echocardiographic analysis of large infarction in rats frequently reveals the presence of echogenic structures in the left ventricular wall, sometimes projecting to the lumen of the chamber. The histological examination of these echogenic structures exhibited bone, cartilage, and marrowlike formations extending from the collagen-rich matrix of the ventricle wall. Microanalytical techniques verified the presence of hydroxyapatite in the mineral phase. Ossification was found in 25 out of 30 hearts evaluated 90 days postinfarct, being observed in 14 out of 17 animals submitted to cell therapy and in 11 out of 13 infarcted rats not submitted to cell therapy. Our study indicates that chondro-osteogenic differentiation can take place in the pathological rat heart independent of animal treatment with marrow cells.
N-gram-based machine translation enhanced with neural networks

Neural Network Language Models (NNLMs) have been applied to Statistical Machine Translation (SMT) outperforming the translation quality. N -best list rescoring is the most popular approach to deal with the computational problems that appear when using huge NNLMs. But the question of “how much improvement could be achieved in a coupled system” remains unanswered. This open question motivated some previous work of us in order to speed the evaluation of NNLMs. Now, this work integrates the NNLM evaluation in the core of the SMT decoder. NNLMs are used in combination with statistical standard N -gram language models under the maximum entropy framework in an N -gram-based SMT system. A reordering decoder builds a reordering graph coupled during a Viterbi decoding. ThisN -gram-based SMT system enhanced with NNLMs for the French-English BTEC task of the IWSLT’10 evaluation campaign is described in detail. An improvement between1.8 and2.4 BLEU points was obtained from the baseline system to the official primary system. This system has been positioned as second in the automatic evaluation of the IWSLT’10 official results.
The developmental anatomy of the human superior hypogastric plexus: A morphometrical investigation with clinical and surgical correlations

The superior hypogastric plexus (SHP) is the part of the autonomic nervous system, which is responsible for the sympathetic innervation of pelvic organs and extrapelvic genitals in humans of both sexes. The SHP also functions as the anatomic pathway for the major part of visceral sensitive fibers originating from pelvic viscera. In this study, the morphology of the SHP was analyzed through anatomical dissections performed both in human adult and fetal cadavers. A computerized morphometrical investigation of the SHP was also performed and the resulting quantitative data statistically assessed. The comparison between fetal and adult SHP revealed that in the male group there was a developmental increase of six times (in height) and of about five times (in width); while in the female group, there was a developmental increase of 3.5 times both in height and width values. In addition, the distance from the superior border of the SHP to the bifurcation of the common iliac arteries presented a developmental increase of about six times in the male group, and about four times in the female group. We propose an original morphological classification with six types, based upon the anatomical arrangement of the nervous fibers in this autonomic plexus. Clin. Anat. 23:962–970, 2010. © 2010 Wiley‐Liss, Inc.
Direct current electrical characteristics of nano-CB/LDPE composite

Electric field distortion caused by the space charge accumulation in the insulation is considered to be one of the obstacles for the operation of high voltage DC cables. In this paper, nano-CB/LDPE composites were fabricated by using the melt blending method. Space charge characteristics and field distortions of nanocomposite films were measured under direct current (DC) field by pulsed electro-acoustic (PEA) method. Dielectric properties and DC breakdown strength were also investigated. Experimental results indicate that, by adding appropriate doping content of CB nanoparticles, the space charge injection threshold of the films was increased, which suppressed homo-polarity space charge injection and ameliorated the field distribution. Breakdown strength of nanocomposite decreased whereas the dielectric permittivity and dielectric loss tangent increased slightly. However, too much CB nanoparticles mixed in LDPE could weaken the suppression effect on charge injection and field distortion, and the LDPE with 0.03wt% of CB nano-particle showed a relative better ability of inhibiting field distortion.
Security framework for mobile banking

The banking sector is always looking for new services delivery platforms to improve customer confidence and satisfaction. To achieve this, the banking service delivery platform must provide end-to-end security to safeguard the information exchange between the bank and the customer. With the increased penetration of mobile phones in the market place the banks are looking for mobile phones as the major revenue generating platform for the delivery of banking and financial services. Today a number of banks offer mobile banking service to their customers. However, still banks have been adopting the generic user authentication systems that was developed for the desktop environment or other complex authentication systems with a number of user intrusive activities. Therefore, the usability and adoption of the mobile banking technology has been extremely slow. This paper presents a novel authentication and authorization framework for secure mobile banking applications. The proposed protocol enables users to authenticate with the banking services with minimum user interactions but with novel advance security features.
Surviving the passage

In plants, mitogen-activated protein kinases (MAPK) have been implicated in signalling associated with many processes, including cellular differentiation, organ development, cell death and stress/hormone signalling. While MAPK cascades are known to act in the cytosol and the nucleus, sequence analysis of the Arabidopsis MAPK cascade proteins predicts the presence of import signals that would target some of them to other organelles. In vitro uptake experiments confirm the predicted import of an oxidant-responsive MAPKK, AtMKK4, into the chloroplast. Unexpectedly, the imported MKK4 protein was not processed through stromal peptidase-dependent cleavage of the N-terminal signal peptide, thus leaving the pre-protein intact. Nevertheless, the N-terminal region was shown to be essential both for the import process and for the ability of MKK4 to activate its cognate MAPK targets in vivo. MKK4 import also occurred irrespective of the activation status of the kinase. The import of this primarily cytosolic oxidant-stimulated AtMKK4 into the chloroplasts, organelles with high redox fluxes, suggests that one of the functions of MKK4 might be to help coordinate intercompartment responses to cellular redox imbalances.
A Survey of Packet Collision Minimization Algorithms in Wireless Mesh Networks

— This article analyzes the existing algorithms used to minimize packet collision in Wireless Mesh Networks (WMNs). We illustrate a clear sympathetic of this vigorous research area, by identifying clear guidelines used when packet collision minimization algorithms are designed. We compare strength and weakness of existing solutions and highlight the key research areas for further development. Finally, the paper presents some future perspectives on how the identified shortcomings on exiting solutions can be solved. This paper serves as a guide and a starting point for anyone willing to delve into research on packet collision minimization algorithms in WMNs.
What happens when one picks up the Greek text

A few issues of hermeneutic nature related to Bible translation are considered. It is argued that the chosen philosophical framework (for instance, a modernist or postmodern approach) determines the way in which any process of translation is approached. Attention then shifts to some of the presuppositions and assumptions of literal translations. These presuppositions are discussed critically. Another factor determining the nature of a translation is the intended function of that particular translation. If, for instance, the intended function is to be understandable for ordinary, present-day readers, a meaning-orientated translation would be preferable. Lastly, the role of interpretation in the translation process is considered. The assumption that no interpretation takes place in the case of word-for word translations is critiqued.
Langmuir probe-based observables for plasma-turbulence code validation and application to the TORPEX basic plasma physics experiment

The methodology for plasma-turbulence code validation is discussed, with focus on the quantities to use for the simulation-experiment comparison, i.e., the validation observables, and application to the TORPEX basic plasma physics experiment [A. Fasoli , Phys. Plasmas 13, 055902 (2006)]. The considered validation observables are deduced from Langmuir probe measurements and are ordered into a primacy hierarchy, according to the number of model assumptions and to the combinations of measurements needed to form each of them. The lowest levels of the primacy hierarchy correspond to observables that require the lowest number of model assumptions and measurement combinations, such as the statistical and spectral properties of the ion saturation current time trace, while at the highest levels, quantities such as particle transport are considered. The comparison of the observables at the lowest levels in the hierarchy is more stringent than at the highest levels. Examples of the use of the proposed observables are applied to a specific TORPEX plasma configuration characterized by interchange-driven turbulence.
Stress Responses in Mycobacteria

Mycobacterium tuberculosis is a successful pathogen that overcomes numerous challenges presented by the immune system of the host. This bacterium usually establishes a chronic infection in the host where it may silently persist inside a granuloma until, a failure in host defenses, leads to manifestation of the disease. None of the conventional anti‐tuberculosis drugs are able to target these persisting bacilli. Development of drugs against such persisting bacilli is a constant challenge since the physiology of these dormant bacteria is still not understood at the molecular level. Some evidence suggests that the in vivo environment encountered by the persisting bacteria is anoxic and nutritionally starved. Based on these assumptions, anaerobic and starved cultures are used as models to study the molecular basis of dormancy. This review outlines the problem of persistence of M. tuberculosis and the various in vitro models used to study mycobacterial latency. The basis of selecting the nutritional starvation model has been outlined here. Also, the choice of M. smegmatis as a model suitable for studying mycobacterial latency is discussed. Lastly, general issues related to oxidative stress and bacterial responses to it have been elaborated. We have also discussed general control of OxyR‐mediated regulation and emphasized the processes which manifest in the absence of functional OxyR in the bacteria. Lastly, a new class of protein called Dps has been reviewed for its important role in protecting DNA under stress.IUBMB Life, 57: 149‐159, 2005
Strategies to Reduce Glucose Exposure in Peritoneal Dialysis Patients

Glucose has been used successfully for more than two decades in peritoneal dialysis, and in this regard, must be considered a safe and effective osmotic agent. Recently, however, insight has been growing about the potential for metabolic and peritoneal effects arising from long-term exposure to high glucose concentrations—for example, hyperlipidemia and loss of peritoneal ultrafiltration. Clinical concerns over exposure to excessive glucose and glucose degradation products (GDPs) during peritoneal dialysis can be significantly ameliorated by the use of non-glucose-based peritoneal dialysis (PD) solutions, in combination with more biocompatible glucose-based formulations. Peritoneal exposure to GDPs can be reduced by using low-GDP-containing glucose formulations and non glucose solutions such as amino acids and icodextrin. Peritoneal glucose exposure, hyperosmolar stress, and carbohydrate absorption can be reduced by using a combination of icodextrin and amino acids.