Miracle-dz/UniFAR-FTUs huggingface dataset:
Rickettsial ompB Promoter Regulated Expression of GFPuv in Transformed Rickettsia montanensis

Background Rickettsia spp. (Rickettsiales: Rickettsiaceae) are Gram-negative, obligate intracellular, α-proteobacteria that have historically been associated with blood-feeding arthropods. Certain species cause typhus and spotted fevers in humans, but others are of uncertain pathogenicity or may be strict arthropod endosymbionts. Genetic manipulation of rickettsiae should facilitate a better understanding of their interactions with hosts. Methodology/Principal Findings We transformed a species never associated with human disease, Rickettsia montanensis, by electroporation with a TN5 transposon (pMOD700) containing green fluorescent protein (GFPuv) and chloramphenicol acetyltransferase (CAT) genes under regulation of promoters cloned from the Rickettsia rickettsii ompB gene, and isolated a Chloramphenicol-resistant GFP-fluorescent rickettsiae population (Rmontanensis700). The Rmontanensis700 rickettsiae contained a single transposon integrated near an acetyl-CoA acetyltransferase gene in the rickettsial chromosome. Northern blots showed that GFPuv and CAT mRNAs were both expressed as two transcripts of larger and smaller than predicted length. Western immunoblots showed that Rmontanensis700 and E. coli transformed with a plasmid containing the pMOD700 transposon both expressed GFPuv proteins of the predicted molecular weight. Conclusions/Significance Long-standing barriers to transformation of rickettsiae have been overcome by development of transposon-based rickettsial transformation vectors. The ompB promoter may be the most problematic of the four promoters so far employed in those vectors.
Allelic Variation of MHC Structure Alters Peptide Ligands to Induce Atypical Partial Agonistic CD8+ T Cell Function

T cell receptors recognize small changes in peptide ligands leading to different T cell responses. Here, we analyzed a panel of HLA-A2–Tax11-19 reactive T cell clones to examine how small allelic variations of MHC molecules could alter the functional outcome of antigen recognition. Similar to the effects induced by antigenic altered peptide ligands, weak or partial agonistic T cell functions were identified in individual T cell clones with the recognition of MHC-altered peptide ligands (MAPLs). Interestingly, one subtype of HLA-A2 molecules induced an unusual type of partial agonistic function; proliferation without cytotoxicity. Modeling of crystallographic data indicated that polymorphic amino acids in the HLA-A2 peptide binding groove, especially the D-pocket, were responsible for this partial agonism. Reciprocal mutations of the Tax peptide side chain engaging the D-pocket indeed restored the agonist functions of the MHC–peptide complex. Whereas early intracellular signaling events were not efficiently induced by these MAPLs, phosphorylated c-Jun slowly accumulated with sustained long-term expression. These data indicate that MAPLs can induce atypical partial agonistic T cell function through structural and biochemical mechanisms similar to altered peptide ligands.
A high-troughput radix-4 log-MAP decoder with low complexity LLR architecture

The throughput of turbo decoder is limited by the recursion architecture. In this paper, an improved radix-4 recursion architecture is presented. In order to decrease the critical path delay, a hybrid 4-inputs addition/subtraction structure is employed. Moreover, we present a modified trace-back architecture to decrease the hardware complexity of the log-likelihood ratios (LLR) architecture. The area of the proposed MAP decoder is 0.58 mm2 on UMC 0. 13µm standard cell technology and under the worst case a maximum throughput of 600 Mbps can be achieved.
GnRH antagonist multiple dose protocol with oral contraceptive pill pretreatment in poor responders undergoing IVF/ICSI

Objective To investigate the effectiveness of GnRH antagonist multiple-dose protocol (MDP) with oral contraceptive pill (OCP) pretreatment in poor responders undergoing IVF/ICSI, compared with GnRH antagonist MDP without OCP pretreatment and GnRH agonist low-dose long protocol (LP). Methods A total of 120 poor responders were randomized into three groups according to controlled ovarian stimulation (COS) options; GnRH antagonist MDP after OCP pretreatment (group 1), GnRH antagonist MDP without OCP pretreatment (group 2) or GnRH agonist luteal low-dose LP without OCP pretreatment (group 3). Patients allocated in group 1 were pretreated with OCP for 21days in the cycle preceding COS, and ovarian stimulation using recombinant human FSH (rhFSH) was started 5 days after discontinuation of OCP. Results There were no differences in patients' characteristics among three groups. Total dose and days of rhFSH used for COS were significantly higher in group 3 than in group 1 or 2. The numbers of mature oocytes, fertilized oocytes and grade I, II embryos were significantly lower in group 2 than in group 1 or 3. There were no significant differences in the clinical pregnancy rate and implantation rate among three groups. Conclusion GnRH antagonist MDP with OCP pretreatment is at least as effective as GnRH agonist low-dose LP in poor responders and can benefit the poor responders by reducing the amount and duration of FSH required for follicular maturation.
A marine oligobacterium harboring genes known to be part of aromatic hydrocarbon degradation pathways of soil pseudomonads

The far-ranging distribution of genes for aromatic hydrocarbon catabolism, predominantly studied in soil pseudomonads, is extended to a marine oligobacterium by finding five homologous sequences in a 5.7-kb chromosomal DNA from a new isolate, Cycloclasticus oligotrophus RB1. RB1 is capable of growth in unamended seawater or mineral salts media supplemented with a variety of aromatic compounds, including toluene, o-, m-, or p-xylenes, as sole carbon sources. The five open reading frames, designated xylM, K, G, C1, and C2, are 57% A+T-rich. XylM is predicted to be an integral membrane protein; XylK and XylG possess glutathione S-transferase (GST) and 2-hydroxy-5methyl-6-oxohexa2,4-dienoate dehydrogenase activities, respectively; XylC1C2 are homologs of the large and small subunits of the iron sulfur protein component of the biphenyl dioxygenase (e.g., BphA1A2).
The significance and workings of social movements as a part of the civil society: an approach from a learning angle

Abstract This article is intended to trace the meaning and workings of social movements during the 1990s from a learning angle. In the first section, the author outlines the theoretical background to the concept of ‘social movement’ and then develops a model within which to locate the internal and external workings of social movements. In the second part, the author considers our changing society and the consequences of this on social movements. From a theoretical point of view, social movements - and considering the recent White Movement as one - have three possible social functions in their external workings: animation and the formation of a network, education and training, and social as well as cultural activation and the promotion of interests. In the third part, the author points to three distinct types of social movement which can be traced: old and new social movements, and present-day action groups. Finally, the article looks into a number of challenges and necessary changes regarding the struggle.
Outcome of IUI Based on Sperm Morphology in Cases of Unex-plained and Male Factor Infertility.

Background: Objective: To evaluate the effects of sperm morphology on the success rate of IUI. Methods: This was a prospective study of 200 couples who underwent IUI in order to improve the likelihood of conception. The patients were divided into 2 groups, one consisting of 100 patients with a normal sperm morphology of ≤20%, and the other consisting of 100 patients with a normal semen morphology of >20%, and an otherwise normal semen analysis. Results: A total of 59 clinical pregnancies were obtained for a pregnancy rate / cycle of 10.5%. No significant differences were found between the two groups examined. Conclusion: There are no substantial differences in the success of intrauterine insemination when normal sperm morphology in semen analysis is more than 20% compared to when it is less than 20%.
Preferential Reduction of Fe(III) over Fumarate by Geobacter sulfurreducens

ABSTRACT The presence of Fe(III), but not that of Fe(II), resulted in ca. 20-fold-lower levels of mRNA for fumarate reductase, inhibiting fumarate reduction and favoring utilization of fumarate as an electron donor in chemostat cultures of Geobacter sulfurreducens, despite the fact that growth yield with fumarate was 3-fold higher than with Fe(III).
Speech , Hearing and Language : work in progress

It has been claimed that speech recognition with a cochlear implant is dependent on the correct frequency alignment of analysis bands in the speech processor with characteristic frequencies (CFs) at electrode locations. However the cochlear position of the most apical electrode often has a CF of 1 kHz or more, and the use of filters aligned in frequency to relatively basal electrode arrays leads to significant loss of lower frequency speech information. This study simulates a cochlear implant array with 8 electrodes spaced 2-mm apart, inserted to a relatively shallow depth within the typical range, such that the most apical element is at a CF of 1851 Hz. Two noiseexcited vocoder speech processors for this simulated electrode location have been compared, one with CF-matched filters, and one with filters matched to CFs at basilar membrane locations 6mm more basal than electrode locations. An extended crossover training design examined preand post-training performance in the identification of vowels and words in sentences for both processors. The shifted processor led to higher post-training scores than the frequency-aligned processor for a male talker with both vowels and sentences. For a female talker, post-training vowel scores did not differ significantly between processors, while sentence scores were higher with the frequency-aligned processor. Training effects were significant only for the shifted processor. The effects of upward spectral shifting were significantly reduced with a few hours of experience. In the case of a shallow electrode insertion, it seems likely that speech processors should cover the most informative frequency range irrespective of electrode position and frequency misalignment.
Constructing Microbial Consortia with Optimal Biomass Production Using a Genetic Algorithm

Typical natural microbial ecosystems contain many different member organisms that all interact with each other in a highly nonlinear way. Although historically most work in microbiology has focused on pure cultures of single organisms, the study of groups of organisms (consortia) still forms a major challenge. While genetic algorithms are capable of optimising nonlinear systems and they should therefore be very well suited for studying microbial ecology, they have only rarely been used in this field. In this work, a genetic algorithm was used to construct a microbial consortium with optimal biomass production from separate isolated strains.
An Energy Efficient Protocol for Target Localization in Wireless Sensor Networks

—Target tracking and localization are important applications in wireless sensor networks. In these applications, sensor nodes collectively monitor and track the movement of a target. They have limited energy supplied by batteries, so energy efﬁciency is essential for sensor networks. Most existing target tracking protocols need to wake up sensors periodically to perform tracking. Some unnecessary energy waste is thus introduced. In this paper, an energy efﬁcient protocol for target localization is proposed. In order to preserve energy, the protocol ﬁxes the number of sensors for target tracking, but it retains the quality of target localization in an acceptable level. By selecting a set of sensors for target localization, the other sensors can sleep rather than periodically wake up to track the target. Simulation results show that the proposed protocol saves a signiﬁcant amount of energy and also prolongs the network lifetime.
Vascular Remodeling Induced by Naturally Occurring Unsaturated Lysophosphatidic Acid In Vivo

Background—We previously identified unsaturated (16:1, 18:1, and 18:2) but not saturated (12:0, 14:0, 16:0, and 18:0) lysophosphatidic acids (LPAs) as potent factors for vascular smooth muscle cell (VSMC) dedifferentiation. Unsaturated LPAs strongly induce VSMC dedifferentiation via the coordinated activation of the extracellular signal–regulated kinase (ERK) and p38 mitogen–activated protein kinase (p38MAPK), resulting in the proliferation and migration of dedifferentiated VSMCs. Here, we investigated the effects of 18:1 and 18:0 LPAs (as representative unsaturated and saturated LPAs, respectively) on the vasculature in vivo. Methods and Results—Rat common carotid arteries (CCAs) were treated transiently with 18:1 or 18:0 LPA and then examined by histological and biochemical analyses. The 18:1 but not 18:0 LPA potently induced vascular remodeling that was composed primarily of neointima. The incorporation of [3H]18:1 LPA into the CCAs revealed that a sufficient amount of unmetabolized [3H]18:1 LPA to induce VSMC dedifferentiation was present in the vascular wall. The 18:1 LPA–induced neointimal formation in vivo was also dependent on the coordinated activation of ERK and p38MAPK. Unlike balloon-injured CCAs, the 18:1 LPA–treated CCAs showed a histological similarity to human atherosclerotic arteries. Conclusions—This is the first report demonstrating a role for a naturally occurring unsaturated LPA in inducing vascular remodeling in vivo and provides a novel animal model for neointimal formation.
Molecular Characterization of Rotavirus in Ireland: Detection of Novel Strains Circulating in the Population

ABSTRACT A collection of three hundred thirty rotavirus-positive stool samples from children with diarrhea in the southern and eastern regions of Ireland between 1997 and 1999 were submitted to the Molecular Diagnostics Unit of the Cork Institute of Technology, Cork, Ireland, for investigation. These strains were characterized by several methods, including polyacrylamide gel electropherotyping and G and P genotyping. A subset of the G types was confirmed by nucleic acid sequencing. The most prevalent types found in this collection included G1P[8] (n = 106; 32.1%), G2P[4] (n = 94; 28.5%), and G4P[8] (n = 37; 11.2%). Novel strains were also detected, including G1P[4] (n = 19; 5.8%), and G4P[4] (n = 2; 0.6%). Interestingly, mixed infections accounted for 18.8% (n = 62) of the total collection, with only 3% (n = 10) which were not G and/or P typeable. Significantly, six G8 and five G9 strains were identified as part of mixed infections. These strains have not previously been identified in Irish children, suggesting a greater diversity in rotavirus strains currently circulating in Ireland.
Projections for Future Research

This body of papers, selected from two related panels, brings into perspective a number of research problems concerning work in comparative administration within Latin America and the Caribbean-the diversity of bureaucratic experience to be considered, the variety of conceptual approaches available, the range of analytic units to be employed. Cross-national administrative studies within the region remain rare indeed. Efforts aimed at generating comparative data on bureaucratic performance and attitudes, beyond the unique, are few in number. Questions concerning the rationale behind continuing to press for the collection of new data on
AIDS‐related lymphomas: from pathogenesis to pathology

Human immunodeficiency virus (HIV)‐associated lymphomas include: (1) lymphomas also occurring, although sporadically, in the absence of HIV infection. The vast majority of these lymphomas are high‐grade B‐cell lymphomas: Burkitt lymphoma (BL), diffuse large B‐cell lymphoma (DLBCL) with centroblastic (CB) features and DLBCL with immunoblastic (IBL) features; (2) unusual lymphomas occurring more specifically in HIV‐positive patients and include two rare entities, namely ‘primary effusion lymphoma’ (PEL) and ‘plasmablastic lymphoma’ of the oral cavity. The pathological heterogeneity of acquired immunodeficiency syndrome‐associated non‐Hodgkin's lymphomas (AIDS‐NHL) reflects the heterogeneity of their associated molecular lesions. In AIDS‐BL, the molecular lesions involve activation of cMYC, inactivation of P53, and infection with Epstein–Barr virus (EBV). AIDS‐IBL infected with EBV are characterised by frequent expression of latent membrane protein 1 – an EBV oncoprotein. The biological heterogeneity of AIDS‐NHL is highlighted by their histogenetic differences. Kaposi's sarcoma‐associated herpesvirus/human herpesvirus 8 (KSHV/HHV8)‐associated lymphomas, which often develop in persons with advanced AIDS, present predominantly as PEL. KSHV/HHV8 has also been recently detected in solid extracavitary‐based lymphomas. The KSHV/HHV8‐associated solid lymphomas are (1) unusual lymphomas that occur more specifically in HIV‐positive patients; (2) extracavitary and arise in nodal and/or extranodal sites; and (3) histologically, they usually display a PEL‐like morphology and plasma cell‐related phenotype.
Surgical Treatment of Strabismus in Children

: Strabismus is a visual disorder in which the eyes are misaligned and point in different directions. This misalignment may be constant or intermittent. The aim of this study was to assess pediatric strabismus outcomes andcomplications in a tertiary hospital. The study was conducted at University Hospital Center “Mother Theresa” in Tirana, Albania over the period 2012 -2014.This study includes 82 cases, 49 (60%) males and 33(40%) females with mean age of 12.2 (±12.2) years. Exodeviation (51%) and esodeviation(39%) had more frequency than other deviation types. In all infantile types of strabismus, occurence age was less than 6 months.Male cases had more frequency of esotropia (55%) and DRS II (78%) than females while in other types females were more frequent (p<0.05). Twenty nine percent of cases had family history of strabismus. Congenital type of strabismus was the most common cause (68%) of pediatric strabismus.
Prevalence of sarcopenia in patients attending outpatient geriatric clinics: the ELLI study.

OBJECTIVES the aim of this study is to know the prevalence of sarcopenia in geriatric outpatient clinics using the EGWSOP (European Working Group on Sarcopenia in Older People) diagnostic criteria that include muscle mass, muscle strength and physical performance. METHODS subjects over 69 years old, able to walk without help and who attended five geriatric outpatient clinics were recruited. Body composition was assessed using bioimpedance analysis (BIA), grip strength using a JAMAR dynamometer and physical performance by the 4 m gait speed. Sarcopenia was diagnosed using the EGWSOP criteria (gait speed <0.8 m/s; grip strength <30 kg in men or <20 kg in women, and muscle mass index (MMI) <8.31 kg/m(2) in men or <6.68 kg/m(2) in women). RESULTS two hundred and ninety-eight subjects were included (median age 83.2 years, 63.1% women). 19.1% had sarcopenia (12.7% men, 22.9% women); 20.1% had low muscle mass; 68.8% had low gait speed and 81.2% low grip strength. Only 21.9% of the subjects with low grip strength and 19.5% of those with low gait speed had sarcopenia. No correlations between muscle mass and either muscle strength or gait speed were detected. CONCLUSIONS sarcopenia is present in one out of five subjects attending geriatric outpatient clinics.
Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters

Abstract Background. Characterization of textural features (spatial distributions of image intensity levels) has been considered as a tool for automatic tumor segmentation. The purpose of this work is to study the variability of the textural features in PET images due to different acquisition modes and reconstruction parameters. Material and methods. Twenty patients with solid tumors underwent PET/CT scans on a GE Discovery VCT scanner, 45–60 minutes post-injection of 10 mCi of [18F]FDG. Scans were acquired in both 2D and 3D modes. For each acquisition the raw PET data was reconstructed using five different reconstruction parameters. Lesions were segmented on a default image using the threshold of 40% of maximum SUV. Fifty different texture features were calculated inside the tumors. The range of variations of the features were calculated with respect to the average value. Results. Fifty textural features were classified based on the range of variation in three categories: small, intermediate and large variability. Features with small variability (range ≤ 5%) were entropy-first order, energy, maximal correlation coefficient (second order feature) and low-gray level run emphasis (high-order feature). The features with intermediate variability (10% ≤ range ≤ 25%) were entropy-GLCM, sum entropy, high gray level run emphsis, gray level non-uniformity, small number emphasis, and entropy-NGL. Forty remaining features presented large variations (range > 30%). Conclusion. Textural features such as entropy-first order, energy, maximal correlation coefficient, and low-gray level run emphasis exhibited small variations due to different acquisition modes and reconstruction parameters. Features with low level of variations are better candidates for reproducible tumor segmentation. Even though features such as contrast-NGTD, coarseness, homogeneity, and busyness have been previously used, our data indicated that these features presented large variations, therefore they could not be considered as a good candidates for tumor segmentation.
Phosphorylation of the 6-Phosphofructo-2-Kinase/Fructose 2,6-Bisphosphatase/PFKFB3 Family of Glycolytic Regulators in Human Cancer

Purpose: Fructose 2,6-bisphosphate (F2,6BP) is a potent activator of phosphofructokinase, which is a rate-limiting enzyme of glycolysis. The concentration of F2,6BP depends on the activity of the bifunctional enzyme, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK-2/FBPase). Four genes encoding PFK-2/FBPase have been identified and termed PFKFB1 to PFKFB4. PFKFB3 protein is expressed in high levels in human tumors in situ. The purpose of this study was to determine the role of functional interactions between the phosphorylation of PFKFB3 and activated glycolysis in human cancer cells. Experimental Design: cDNA from several human tumor cell lines and human colon carcinoma were analyzed by reverse transcription-PCR to identify different splicing variants of PFKFB3. The effect of phosphorylation of Ser461 was studied by recombinantly replacing this residue with glutamate (PFKFB3S461E). The phosphorylation of PFKFB3 protein in human cancer was determined by immunostaining using an anti-phospho-PFK-2(PFKFB3) antibody. Results: Two splicing variants of PFKFB3 are expressed in human cancer cell lines: PFKFB3-ACG and PFKFB3-AG. Quantitative, real-time PCR analysis confirmed the overexpression of PFKFB3 mRNA in colon carcinoma, with the dominant variant being the PFKFB3-ACG isoform that contains a phosphorylation site at Ser461. Forced expression of PFKFB3-ACG in COS-7 cells resulted in enhanced glycolysis. Introduction of PFKFB3-ACGS461E into COS-7 cells led to increased the lactate production and cell proliferation. Highly phosphorylated PFKFB3 protein was found in human tumor cells, vascular endothelial cells, and smooth muscle cells, as determined by immunostaining with an anti-phospho-PFK-2(PFKFB3) antibody. Conclusions: These findings support a potential role for the phosphorylation of PFKFB3 protein in the progression of cancer and angiogenesis.