Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and Biochemical Characterization of the Chromosomal Class A β-Lactamases of Raoultella (formerly Klebsiella) planticola and Raoultella ornithinolytica

ABSTRACT Enterobacterial strains of Raoultella spp. display a penicillinase-related β-lactam resistance pattern suggesting the presence of a chromosomal bla gene. From whole-cell DNA of Raoultella planticola strain ATCC 33531T and Raoultella ornithinolytica strain ATCC 31898T, bla genes were cloned and expressed into Escherichia coli. Each gene encoded an Ambler class A β-lactamase, named PLA-1 and ORN-1 for R. planticola and R. ornithinolytica, respectively. These β-lactamases (291 amino acids), with the same pI value of 7.8, had a shared amino acid identity of 94%, 37 to 47% identity with the majority of the chromosome-encoded class A β-lactamases previously described for Enterobacteriaceae, and 66 to 69% identity with the two β-lactamases LEN-1 and SHV-1 from Klebsiella pneumoniae. However, the highest identity percentage (69 to 71%) was found with the plasmid-mediated β-lactamase TEM-1. PLA-1, which displayed very strong hydrolytic activity against penicillins, also displayed significant hydrolytic activity against cefepime and, to a lesser extent, against cefotaxime and aztreonam, but there was no hydrolytic activity against ceftazidime. Such a substrate profile suggests that the Raoultella β-lactamases PLA-1 and ORN-1 should be classified into the group 2be of the β-lactamase classification of K. Bush, G. A. Jacoby, and A. A. Medeiros (Antimicrob. Agents Chemother. 39:1211-1233, 1995). The highly homologous regions upstream of the blaPLA-1A and blaORN-1A genes comprised a nucleotide sequence identical to the −35 region and another one very close to the −10 region of the blaLEN-1 gene. From now on, as the bla gene sequences of the most frequent Raoultella and Klebsiella species are available, the bla gene amplification method can be used to differentiate these species from each other, which the biochemical tests currently carried out in the clinical laboratory are unable to do.
Preclinical Evaluation of MEDI0641, a Pyrrolobenzodiazepine-Conjugated Antibody–Drug Conjugate Targeting 5T4

Antibody–drug conjugates (ADC) are used to selectively deliver cytotoxic agents to tumors and have the potential for increased clinical benefit to cancer patients. 5T4 is an oncofetal antigen overexpressed on the cell surface in many carcinomas on both bulk tumor cells as well as cancer stem cells (CSC), has very limited normal tissue expression, and can internalize when bound by an antibody. An anti-5T4 antibody was identified and optimized for efficient binding and internalization in a target-specific manner, and engineered cysteines were incorporated into the molecule for site-specific conjugation. ADCs targeting 5T4 were constructed by site-specifically conjugating the antibody with payloads that possess different mechanisms of action, either a DNA cross-linking pyrrolobenzodiazepine (PBD) dimer or a microtubule-destabilizing tubulysin, so that each ADC had a drug:antibody ratio of 2. The resulting ADCs demonstrated significant target-dependent activity in vitro and in vivo; however, the ADC conjugated with a PBD payload (5T4-PBD) elicited more durable antitumor responses in vivo than the tubulysin conjugate in xenograft models. Likewise, the 5T4-PBD more potently inhibited the growth of 5T4-positive CSCs in vivo, which likely contributed to its superior antitumor activity. Given that the 5T4-PBD possessed both potent antitumor activity as well as anti-CSC activity, and thus could potentially target bulk tumor cells and CSCs in target-positive indications, it was further evaluated in non-GLP rat toxicology studies that demonstrated excellent in vivo stability with an acceptable safety profile. Taken together, these preclinical data support further development of 5T4-PBD, also known as MEDI0641, against 5T4+ cancer indications. Mol Cancer Ther; 16(8); 1576–87. ©2017 AACR.
Clinically significant differences in acute pain measured on self-report pain scales in children.

OBJECTIVES The objective was to determine the minimum and ideal clinically significant differences (MCSD, ICSD) in pain intensity in children for the Faces Pain Scale-Revised (FPS-R) and the Color Analog Scale (CAS) and to identify any differences in these estimates based on patient characteristics. METHODS This was a prospective study of children aged 4 to 17 years with acute pain presenting to two urban pediatric emergency departments. Participants self-reported their pain intensity using the FPS-R and CAS and qualitatively described their changes in pain. Changes in pain score reported using the FPS-R and CAS that were associated with "a little less" and "much less" pain (MCSD and ICSD, respectively) were identified using a receiver operating characteristic-based method and expressed as raw change score and percent reductions. Estimates of MCSD and ICSD were determined for each category of initial pain intensity (mild, moderate, and severe) and patient characteristics (age, sex, and ethnicity). Post hoc exploratory analyses evaluated categories of race, primary language, and etiology of pain. RESULTS A total of 314 children with acute pain were enrolled; mean (±SD) age was 9.8 (±3.8) years. The FPS-R raw change score and percent reduction MCSD estimates were 2/10 and 25%, with ICSD estimates of 3/10 and 60%. For the CAS, raw change score and percent reduction MCSD estimates were 1/10 and 15%, with ICSD estimates of 2.75/10 and 52%. For both scales, raw change score and percent reduction estimates of the MCSD remained unchanged in children with either moderate or severe pain. For both scales, estimates of ICSD were not stable across categories of initial pain intensity. There was no difference in MCSD or ICSD based on age, sex, ethnicity, race, primary language, or etiology of pain. CONCLUSIONS The MCSD estimates can be expressed as raw change score and percent reductions for the FPS-R and CAS. These estimates appear stable for children with moderate to severe pain, irrespective of age, sex, and ethnicity. Estimates of ICSD were not stable across different categories of initial pain intensity, therefore limiting their potential generalizability.
Comorbidity of borderline personality disorder with other personality disorders in hospitalized adolescents and adults.

OBJECTIVE The authors examined the comorbidity of borderline personality disorder with other personality disorders in a series of consecutively admitted adolescents. For comparison, the comorbidity of borderline personality disorder with other personality disorders was also examined in a series of adults consecutively admitted to the same hospital during the same period. METHOD A total of 138 adolescents and 117 adults were reliably assessed with the Personality Disorder Examination, a semistructured diagnostic interview for DSM-III-R personality disorders. Sixty-eight adolescents and 50 adults met the diagnostic criteria for borderline personality disorder. The co-occurrence of other personality disorders in the group of subjects with borderline personality disorder was statistically compared to that in the group without borderline personality disorder, for adolescents and adults separately. RESULTS For the adults, Bonferroni-corrected chi-square analysis revealed significant diagnostic co-occurrence with borderline personality disorder for antisocial personality disorder only. For the adolescents, borderline personality disorder showed significant co-occurrence with schizotypal and passive-aggressive personality disorders. CONCLUSIONS In the adults, borderline personality disorder was significantly comorbid only with another cluster B disorder. The adolescents, by comparison, displayed a broader pattern of comorbidity of borderline personality disorder, encompassing aspects of clusters A and C. These results suggest that the borderline personality disorder diagnosis may represent a more diffuse range of psychopathology in adolescents than in adults.
Mutual Authentication in IoT Systems Using Physical Unclonable Functions

The Internet of Things (IoT) represents a great opportunity to connect people, information, and things, which will in turn cause a paradigm shift in the way we work, interact, and think. IoT devices are usually small, low cost, and have limited resources, which makes them vulnerable to physical, side-channel, and cloning attacks. Therefore, any protocol designed for IoT systems should not only be secure but also efficient in terms of usage of chip area, energy, storage, and processing. To address this issue, we present light-weight mutual authentication protocols for IoT systems based on physical unclonable functions. Protocols for two scenarios are presented, one when an IoT device and server wish to communicate and the other when two IoT devices want to establish a session. A security and performance analysis of the protocols shows that they are not only robust against different types of attacks, but are also very efficient in terms of computation, memory, energy, and communication overhead. The proposed protocols are suitable for real time applications and are an attractive choice for implementing mutual authentication in IoT systems.
A novel enzymatic pathway leading to 1-methylinosine modification in Haloferax volcanii tRNA.

Transfer RNAs of the extreme halophile Haloferax volcanii contain several modified nucleosides, among them 1-methylpseudouridine (m1 psi), pseudouridine (psi), 2'-0-methylcytosine (Cm) and 1-methylinosine (m1l), present in positions 54, 55, 56 and 57 of the psi-loop, respectively. At the same positions in tRNAs from eubacteria and eukaryotes, ribothymidine (T-54), pseudouridine (psi-55), non-modified cytosine (C-56) and non-modified adenosine or guanosine (A-57 or G-57) are found in the so-called T psi-loop. Using as substrate a T7 transcript of Haloferax volcanii tRNA(Ile) devoid of modified nucleosides, the enzymatic activities of several tRNA modification enzymes, including those for m1 psi-54, psi-55, Cm-56 and m1l-57, were detected in cell extracts of H.volcanii. Here, we demonstrate that modification of A-57 into m1l-57 in H.volcanii tRNA(Ile) occurs via a two-step enzymatic process. The first step corresponds to the formation of m1A-57 catalyzed by a S-adenosylmethionine-dependent tRNA methyltransferase, followed by the deamination of the 6-amino group of the adenine moiety by a 1-methyladenosine-57 deaminase. This enzymatic pathway differs from that leading to the formation of m1l-37 in the anticodon loop of eukaryotic tRNA(Ala). In the latter case, inosine-37 formation preceeds the S-adenosylmethionine-dependent methylation of l-37 into m1l-37. Thus, enzymatic strategies for catalyzing the formation of 1-methylinosine in tRNAs differ in organisms from distinct evolutionary kingdoms.
The influence of surface nanoroughness, texture and chemistry of TiZr implant abutment on oral biofilm accumulation.

OBJECTIVES The aim of the study was to examine surface nanoroughness, texture and chemistry of dental implant abutment and to investigate how these parameters influence oral biofilm formation in healthy subjects. MATERIALS AND METHODS Eight different nanorough TiZr surfaces were produced by polishing, machining, cathodic polarization and acid etching. Surface topography was examined using field emission scanning electron microscope and a blue light laser profilometer. Surface chemistry was analyzed by secondary ion mass spectrometry and X-ray photoelectron spectroscopy. Surface hydrophilicity was tested by measuring contact angle on the surfaces. A human in vivo study using a splint model was employed to evaluate oral biofilm accumulation on these surfaces. RESULTS Different surface textures (flat, grooved and irregular) were created with nanoroughness from 29 to 214 nm. Some test surfaces were incorporated with hydrogen by cathodic polarization and/or acid etching with HCl/H(2)SO(4). Nanoroughness (S(a)) positively correlated with microbial adhesion. Biofilm accumulation was less pronounced on flat and grooved than on irregular surfaces. No significant association between hydrogen content or hydrophilicity of the surface and biofilm accumulation was observed. CONCLUSIONS Nanoroughness (< 214 nm) and surface texture influence oral biofilm accumulation independent of surface chemistry and hydrophilicity. Surface hydrogen, which has previously been shown to promote fibroblast growth, does not affect biofilm formation.
Germinal centers.

Germinal centers develop in the B cell follicles of secondary lymphoid tissues during T cell-dependent (TD) antibody responses. The B cells that give rise to germinal centers initially have to be activated outside follicles, in the T cell-rich zones in association with interdigitating cells and T cell help. After immunization with a single dose of protein-based antigen, the germinal centers formed are oligoclonal; on average three B blasts colonize each follicle. These blasts undergo massive clonal expansion and activate a site-directed hypermutation mechanism that acts on their immunoglobulin-variable (Ig-v)-region genes. Mature germinal centers are divided into dark and light zones. The proliferating blasts, centroblasts, occupy the dark zone and give rise to centrocytes that are not in cell cycle and fill the light zone. The light zone contains a rich network of follicular dendritic cells (FDC) that have the capacity to take up antigen and hold this on their surface for periods of more than a year. The antigen is held as an immune complex in a native unprocessed form; but the antigen may be taken up from FDC by B cells, which can process this and present it to T cells. Centrocytes appear to be selected by their ability to interact with antigen held on FDC. There is a high death rate among centrocytes in vivo, and when these cells are isolated in vitro, they undergo apoptosis within hours on culture. The onset of apoptosis can be delayed by cross-linking centrocytes' surface Ig, and long-term survival is achieved by signalling through their surface CD40. After activation through CD40 the centrocytes increase their surface Ig and acquire characteristics of memory and processing of antigen held on FDC and its presentation to T cells that can be induced to express CD40 ligand at the point of cognate interaction. Other signals that induce a proportion of germinal center cells to become plasma cells have also been described. Germinal centers persist for about 3 weeks following immunization, but after this, memory B blasts continue to proliferate in follicles throughout the months of T cell-dependent antibody responses. These cells are probably the source of plasma cells and memory cells required to maintain long-term antibody production and memory after the first 3 weeks of T cell-dependent antibody responses.
Vascular endothelial growth factor‐D is a survival factor for human breast carcinoma cells

Vascular endothelial growth factor‐D (VEGF‐D) stimulates growth of vascular and lymphatic endothelial cells by signaling through the tyrosine kinase receptors KDR (VEGFR‐2) and Flt‐4 (VEGFR‐3). In the present study, we examined the effects of VEGF‐D on apoptosis in human MCF‐7 and MDA‐MB‐231 breast carcinoma cells. Because VEGF‐D was not expressed constitutively in vitro, stable VEGF‐D transfectants were produced. The VEGF‐D‐expressing MCF‐7 and MDA‐MB‐231 lines displayed resistance to apoptosis induced by hypoxia, staurosporin and cycloheximide. Increased Bcl‐2 expression, decreased homogenous caspase activities and inhibition of poly(ADP‐ribose) polymerase cleavage were associated with inhibition of apoptosis in VEGF‐D‐expressing clones. Also, caspase‐3 activation was suppressed in the VEGF‐D expressing MDA‐MB‐231 clone. The antiapoptotic effect of VEGF‐D in vitro was recapitulated in vivo using VEGF‐D‐expressing MDA‐MB‐231 xenografts. The lack of VEGFR‐2 protein expression by Western blot and ineffectiveness of a neutralizing VEGFR‐2 antibody in eliminating the antiapoptotic effects of VEGF‐D suggest a different and yet unknown signaling mechanism. Our findings indicate that VEGF‐D has a novel function as a survival factor of breast carcinoma cells in addition to its established functions as an angiogenic and lymphangiogenic factor. © 2005 Wiley‐Liss, Inc.
Controlling Aggregation in Distributed Object Systems: A Graph-Based Approach

The Distributed Object Kernel is a federated database system providing a set of services which allow cooperative processing across different databases. The focus of this paper is the design of a DOK security service that provides for enforcing both local security policies, related to the security of local autonomous databases, and federated security policies, governing access to data aggregates composed of data from multiple distributed databases. We propose Global Access Control, an extended access control mechanism enabling a uniform expression of heterogeneous security information. Mappings from existing Mandatory and Discretionary Access Controls are described. To permit the control of data aggregation, the derivation of unauthorized information from authorized data, our security framework provides a logic-based language, the Federated Logic Language (FELL), which can describe constraints on both single and multiple states of the federation. To enforce constraints, FELL statements are mapped to state transition graphs which model the different subcomputations required to check the aggregation constraints. Graph aggregation operations are proposed for building compound state transition graphs for complex constraints. To monitor aggregation constraints, two marking techniques, called Linear Marking Technique and Zigzag Marking Technique, are proposed. Finally, we describe a three-layer DOK logical secure architecture enabling the implementation of the different security agents. This includes a Coordination layer, a Task layer, and a Database layer. Each contains specialized agents that enforce a different part of the federated security policy. Coordination is performed by the DOK Manager, enforcing security is performed by a specialized Constraint Manager agent, and the database functions are implemented by user and data agents.
Connective Tissue Growth Factor Is Responsible for Transforming Growth Factor-Beta-Induced Peritoneal Mesothelial Cell Apoptosis

Background: Previous studies found that transforming growth factor-β (TGF-β) induces mesothelial production of connective tissue growth factor (CTGF), which may be downstream mediators of TGF-β. Since high dose TGF-β induces apoptosis of peritoneal mesothelial cells (PMC), we study the effect of CTGF blockade in the system of TGF-β-induced PMC apoptosis. Method: We examined the effect of TGF-W in primary culture of rat peritoneal mesothelial cells (PMC). PMC apoptosis was studied by flow cytometry. The effect of CTGF was blocked by antibody and short-interfering RNA (siRNA). Expression of apoptotic gene was studied by real-time polymerase chain reaction. Result: In cultured unstimulated rat PMC, there is a low but definite incidence of spontaneous apoptosis. Stimulation with TGF-β 50 pg/ml induces an upregulation of apoptotic gene BAX expression and a downregulation of anti-apoptotic gene BCL-2L expression, and a 4-fold increase in PMC apoptosis. The effect of TGF-β-induced PMC apoptosis was partly prevented by antibody against CTGF, and completely abolished by CTGF-specific siRNA, while CTGF-blockade by siRNA had no effect on PMC necrosis. CTGF silencing by siRNA prevented the down-regulation of BCL-2L expression induced by TGF-β, had no effect on the BAX expression. Conclusion: Our results indicate that CTGF is an important downstream mediator of TGF-β-induced PMC apoptosis.
Current Status and Future Perspectives in Articles about Coding and Programming Learning at Early Ages Published from 2009 to 2017: A Content Anaysis Study

In recent years, remarkable attention has been paid to coding and computer programming learning and teaching at pre-university level. Many countries are taking important steps in this field every passing year. Examining the studies on coding learning enriched by use of different tools based on specific periods may be guiding for researchers in this field, in which there is an ever-growing interest. In this regard, the purpose of this study is to make a thorough examination of the articles on coding learning and teaching at pre-university level published in international journals from 2009 to 2017 and to show the general trend. The study examined 34 articles published in this field from 2009 to 2017 through content analysis. The data collected by use of Article Classification Form were descriptively analyzed. The research findings show that most articles published in this field covered robotic tools at elementary education level. They also indicate that quantitative – quasi-experimental method was the most preferred method, and various data collection tools, achievements tests being in the first place, were employed. The majority of studies reached positive results from different perspectives while few studies reported neutral results. The results of the present study are considered to be revealing the current situation in this field and lighting the way for other studies to be carried out in the future.
Xenobiotic Nuclear Receptors Pregnane X Receptor and Constitutive Androstane Receptor Regulate Antiretroviral Drug Efflux Transporters at the Blood-Testis Barrier

Poor antiretroviral drug (ARV) penetration in the testes could be due, in part, to the presence of ATP-binding cassette (ABC) membrane–associated drug efflux transporters such as P-glycoprotein (P-gp), breast cancer resistance protein (BCRP), and multidrug resistance–associated proteins (MRPs) expressed at the blood-testis barrier (BTB). The functional expression of these transporters is known to be regulated by ligand-activated nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) in various tissues. This study aimed to investigate in vitro and ex vivo the role of PXR and CAR in the regulation of ABC transporters at the BTB. Both PXR and CAR proteins were expressed in human testicular tissue and in mouse TM4 Sertoli cells (an in vitro cell line model of the BTB). In addition, we demonstrated an upregulation of P-gp, Bcrp, and Mrp4 mRNA and protein expression, after exposure to PXR or CAR ligands in TM4 cells. Small interfering RNA downregulation of PXR or CAR attenuated the expression of these transporters, suggesting the direct involvement of these nuclear receptors in regulating P-gp, Bcrp, and Mrp4 in this system. In an ex vivo study using freshly isolated mouse seminiferous tubules, we found that exposure to PXR or CAR ligands, including ARVs, significantly increased P-gp expression and function. Together, our data suggest that ABC transporters could be regulated at the BTB during chronic treatment with ARVs that can serve as ligands for PXR and CAR, which could in turn further limit testicular ARV concentrations.