Miracle-dz/UniFAR-FTUs huggingface dataset:
Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII

To elucidate the mechanism of action of restriction endonucleases MvaI and EcoRII a study was made of their interaction with a set of synthetic substrates in which the heterocyclic bases or the sugar–phosphate backbone had been modified; individual nucleotide residues had been removed or replaced with hydrocarbon bridges, and mismatched base pairs had been introduced. The groups of atoms in the heterocyclic bases and the phosphates in the recognition site that produce the most significant influence on the functioning of endonucleases MvaI and EcoRII were discerned. Profound differences were found in the functioning of the MvaI and EcoRII neo‐schizomers. The catalytic activity of EcoRII is significantly affected by any alteration in the recognition site structure and conformation, with a modification in one strand of the substrate causing the same decrease in the hydrolysis rate of both strands. Endonuclease MvaI is tolerant to a number of structural abnormalities; the latter sometimes affect only hydrolysis of one strand of the recognition site. The enzyme can preferentially cleave one of the substrate strands. Mismatched base pairs retard and sometimes block the hydrolysis. The effect depends on the particular enzyme, mismatch and its location.
Robot-assisted therapy for autism spectrum disorders with (partially) autonomous control: Challenges and outlook

Robot-assisted therapy (RAT) is an emerging field that has already seen some success and is likely to develop in the future. One particular application area is within therapies for autism spectrum disorders, in which the viability of the approach has been demonstrated.The present paper is a vision paper with the aim of identifying research directions in the near future of RAT. Specifically, we argue that the next step in such therapeutic scenarios is the development of more substantial levels of autonomy which would allow the robot to adapt to the individual needs of children over longer periods of time (while remaining under the ultimate supervision of a therapist). We argue that this requires new advances on the level of robot controllers as well as the ability to infer and classify intentions, goals and emotional states of the robot’s interactants. We show that the state of the art in a number of relevant disciplines is now at the point at which such an endeavour can be approached in earnest.
Observations on a liver mitotic stimulant present in tumor tissue.

1. An increase in the liver mitotic index and a relationship between tumor size and the liver mitotic index was observed in strains C3H/He and C3Hf/He mice bearing transplanted mammary carcinoma C3HBA. 2. A significant increase in the host liver mitotic index was also observed 48 hours after the injection of 0.4 ml. of C3HBA mammary tumor brei. The number of mitotic figures in the host liver increased as the concentration of tumor brei injected was increased. 3. A saline extract of C3HBA mammary tumor brei also resulted in a significant increase in the host liver mitotic index at 48 hours. No increase in the host liver mitotic index was observed following the injection of the nuclear, nucleoprotein, mitochondria, and microsome cell fractions obtained from C3HBA mammary tumor tissue. 4. The subcutaneous injection of 0.4 ml. normal C3H/He and C3Hf/He tissue brei (liver, kidney, embryo) into normal strain C3H/He and C3Hf/He mice did not result in an increase in the host liver mitotic index 1 through 3 days after injection.
Relationship of Glycosyltransferases and mRNA Levels to Ganglioside Expression in Neuroblastoma and Melanoma Cells

Abstract : Most human neuroblastoma tumors are characterized by the high expression of GD2 (or GD2 and/or GM2) gangliosides, whereas melanomas characteristically express GD3 ganglioside. The molecular basis for these patterns was investigated by examining the relationship between ganglioside levels, glycosyltransferase (GM2/GD2 synthase and GD3 synthase) activity, and corresponding mRNA levels in a panel of human neuroblastoma and melanoma cell lines. In general, the ganglioside patterns could be explained by the levels of the transferases and their mRNA, indicating control at the level of transcription. A key role was noted for GD3 synthase. Notably, it was found that neuroblastoma cell lines with high GD2 ganglioside levels had low levels of GD3, its synthase, and mRNA for the enzyme even though this step provides the substrate for GD2 synthesis. The key role for GD3 synthase was also examined by stably transfecting GD3 synthase cDNA into a neuroblastoma cell line (SH‐SY5Y) not expressing GD3 and GD2. The resulting cell line had high levels of GD2 ganglioside and altered morphology and growth characteristics.
Modeling software maintenance requests: a case study

Software maintenance costs often total twice the original development cost in the lifetime of application software. Modeling the changes of software maintenance activities might improve software maintenance planning. Current studies model software activities only covering a portion of software lifetimes. This study investigates the changes of maintenance requests during the lifetime of large application software. It discusses the modeling of different software maintenance requests such as: user support, repair and enhancement. We found four distinct stages. User support reaches its peak in the first stage, repair inundates in the second stage. In the third stage, enhancement is the dominant factor. The frequencies of all three different maintenance requests are small in the last stage, when the IS department is looking for new software to replace the existing one
In vivo 1H MRS of brain injury and repair during acute SIV infection in the macaque model of neuroAIDS

The metabolic response of the rhesus macaque brain during acute simian immunodeficiency virus (SIV) infection was investigated with in vivo 1H MR spectroscopy. Fifteen rhesus macaques were studied before inoculation, and once or twice after infection. In all, 13/15 macaques had elevations of Cho/NAA at 11–13 days postinoculation (dpi); all 10 macaques measured after 13 dpi had subsequent reduction of this ratio (ANOVA, P < 10‐6). There were significant increases in Cho/Cr (20%, P = 0.04) and MI/Cr (14%, P = 0.003) at 11 dpi. At 13 dpi a 7.7% decrease (P = 0.02) in NAA/Cr was observed, while Cho/Cr was no longer significantly different from baseline. At 27 dpi Cho/Cr was decreased to 18% (P = 0.004) below preinoculation values, while NAA/Cr and MI/Cr were at baseline values. Absolute concentrations of Cho, MI, and NAA showed a similar time course, with no observed changes in Cr. There was a strong correlation between Cho/Cr change and plasma viral load (rs = 0.79, P < 0.01). Acute SIV produces extensive metabolic abnormalities in the brain, which may reflect inflammation and neuronal injury, which are reversed with immunological control of the virus. Similar events are likely to occur in acutely HIV‐infected people, and may explain the neurobehavioral symptoms associated with acute HIV infection. Magn Reson Med 51:1108–1114, 2004. © 2004 Wiley‐Liss, Inc.
Antibody-mediated rejection in kidney transplantation: an update

Introduction: Acute antibody-mediated rejection (AMR) in renal-transplant recipients is generally less responsive to conventional antirejection therapy and has a worse prognosis than acute cellular rejection. Areas covered: This review provides a broad understanding of the pathogenesis of AMR, recent advances in its therapy, and future directions. Conventional therapeutic approaches to AMR have minimal impact on mature plasma cells, the major source of antibody production. Emerging therapies include bortezomib, a proteasome inhibitor, and eculizumab, an anti-C5 antibody. In several reports, bortezomib therapy resulted in prompt reversal of rejection, decreased titers of donor-specific antibodies (DSA), and improved renal allograft function. Eculizumab also reversed AMR and prevented its development in patients with high post-transplantation DSA levels. Expert opinion: Despite the small sample size and lack of controls, these studies are encouraging, and although larger studies and long-term follow-up are needed, bortezomib and eculizumab may play a major future role in AMR therapy.
Novel Spectinomycin/Streptomycin Resistance Gene, aadA14, from Pasteurella multocida

ABSTRACT A novel spectinomycin/streptomycin resistance gene, designated aadA14, was detected on the mobilizable 5,198-bp plasmid pCCK647 from Pasteurella multocida. The aadA14 gene encodes an aminoglycoside adenylyltransferase of 261 amino acids. Sequence comparisons revealed that the AadA14 protein showed less than 60% identity to the AadA proteins known so far.
Pilus-Mediated Adherence of Haemophilus influenzae to Human Respiratory Mucins

ABSTRACT Haemophilus influenzae, especially the nontypeable strains, are among the most common pathogens encountered in patients with chronic lung disease and otitis media. We and others have demonstrated that respiratory isolates of nontypeable H. influenzae bind to human mucins, but the mechanism of binding is not entirely clear. We have therefore examined the role of pili in the adherence of both type b and nontypeable H. influenzae to human respiratory mucins. We used isogenic H. influenzaestrains with a mutation in the structural gene for pilin (hifA), a laboratory H. influenzae strain transformed with a type b pilus gene cluster (from strain C54), antibodies raised against H. influenzae HifA, andEscherichia coli strains carrying a cloned type b pilus gene cluster (from strain AM30) in these studies. All bacteria lacking HifA or the pilus gene cluster had decreased adherence of piliatedH. influenzae to mucins, and Fab fragments of anti-HifA antibodies inhibited the adherence. E. coli strains carrying the cloned type b pilus gene cluster were six to seven times more adhesive than strains carrying the vector. The role of other putative adhesins was not examined and thus cannot be excluded, but these studies support a role for pili in the binding of H. influenzae to human respiratory mucins.
Risk Factors for Early Epithelial to Mesenchymal Transition in Renal Grafts

Epithelial‐to‐mesenchymal transition (EMT) of tubular epithelial cells (TECs) may participate in the pathogenesis of renal fibrosis. We performed a prospective study of EMT markers in protocol biopsies obtained 3 months after engraftment from 56 patients who received deceased donor kidneys and who had stable renal function. The presence of EMT was examined, and quantified by immunohistochemical staining for vimentin and translocation of β‐catenin to the cytoplasm. EMT status was defined as the presence of EMT markers in ≥10% of TECs. EMT features were virtually absent in implantation biopsies, whereas 41% of the grafts were EMT‐positive in the absence of advanced chronic allograft nephropathy. Thirteen patients (23%) had borderline changes or acute rejection. EMT features were more frequent in these patients than in those with normal kidney grafts (vimentin expression, p = 0.003; β‐catenin translocation, p = 0.002). EMT in grafts corresponded with elevated serum creatinine of the donor before the recovery of kidney (p = 0.02) and longer cold ischemia time (p = 0.02). In contrast, the donor age had no influence on the expression of EMT markers. These results suggest that EMT is an early and frequent phenomenon in kidney transplants that could be triggered by immunological and/or ischemic tubular injury.
Brief Report: Respondent-driven Sampling Estimators Under Real and Theoretical Recruitment Conditions of Female Sex Workers in China

We compare the performance of multiple respondent-driven sampling estimators under different sample recruitment conditions in hidden populations of female sex workers in the midst of China’s ongoing epidemic of sexually transmitted infections. We first examine empirically calibrated simulations grounded in survey data to evaluate the relative performance of each estimator under ideal sampling conditions consistent with respondent-driven sampling assumptions and under conditions that mimic observed respondent-driven sampling recruitment processes. One estimator, which incorporates respondents’ reports on their network of contacts, substantially out-performs the others under all conditions. We then apply the estimators to empirical samples of female sex workers collected in two Chinese cities that include unique data on respondents’ networks. These empirical results are consistent with the simulation results, suggesting that traditional respondent-driven sampling estimators overestimate the proportion of female sex workers working in low tiers of sex work and are likely to overstate the sexually transmitted infection risk profiles of these populations.
Focal Nodular Hyperplasia and Hepatocellular Adenoma: Current views

Abstract Focal Nodular Hyperplasia (FNH) is a rare benign hepatic lesion believed to generate upon a hyperplastic response of the hepatocyte. Hepatocellular Adenoma (HA) occurs predominantly in young women receiving oral contraceptive medication. These two lesions have drawn significant attention throughout the recent years due to their specific clinical and pathological features as well as their challenging management. Although Focal Nodular Hyperplasia is managed conservatively in the majority of cases, it can albeit pose a difficult diagnostic dilemma. On the other hand, Hepatocellular Adenoma can be complicated with catastrophic hemorrhage or malignant transformation and therefore mandates surgical excision in many cases. The aim of this work is to review the current literature pertaining to these two clinical entities regarding their pathogenesis, diagnostic approach and genetics, as well as to shed light on specific differential diagnostic issues arising in many cases these lesions are encountered.
Prognostic significance of Philadelphia chromosome-positive cells detected by the polymerase chain reaction after allogeneic bone marrow transplant for chronic myelogenous leukemia.

Although rare cells expressing the bcr/abl fusion transcript can be detected by the polymerase chain reaction (PCR) in patient blood or marrow after allogeneic bone marrow transplant (BMT) for Philadelphia chromosome (Ph+)-positive chronic myelogenous leukemia (CML), the prognostic significance of this finding is unknown. This paper reports clinical, cytogenetic, and molecular data derived from 64 CML patients following allogeneic BMT. Nested primer PCR was performed on patient blood and bone marrow samples to detect the presence of residual bcr/abl (+) cells in CML patients considered to be in clinical remission at the time of study. Bcr/abl transcripts were detected in 37 of 64 patients for at least one timepoint post-BMT. Thirteen of these 37 bcr/abl (+) patients have subsequently relapsed, as defined by clinical and/or persistent cytogenetic findings, in contrast to 0 relapses among the 27 bcr/abl (-) patients (P = .0025). The median time from first (+) bcr/abl PCR signal to relapse was 150 days (range 90 to 832). Fifty-four patients were studied at two or more timepoints post-BMT: five of eight patients persistently bcr/abl (+) have relapsed; 5 of 23 patients with both bcr/abl (+) and (-) assays during follow-up have relapsed; and none of 23 patients persistently (-) have relapsed (cumulative actuarial relapse rates 77%, 20%, and 0%, respectively, P = .0017). These data indicate that among CML patients in apparent clinical remission after BMT, nested primer bcr/abl PCR can define subgroups with low, intermediate, and high risk of relapse. The pattern of bcr/abl PCR detection after transplant may aid in the development of trials designed to reduce the risk of relapse, or allow for early intervention in patients who fail to clear the malignant clone.
Facial-Attractiveness Choices Are Predicted by Divisive Normalization

Do people appear more attractive or less attractive depending on the company they keep? A divisive-normalization account—in which representation of stimulus intensity is normalized (divided) by concurrent stimulus intensities—predicts that choice preferences among options increase with the range of option values. In the first experiment reported here, I manipulated the range of attractiveness of the faces presented on each trial by varying the attractiveness of an undesirable distractor face that was presented simultaneously with two attractive targets, and participants were asked to choose the most attractive face. I used normalization models to predict the context dependence of preferences regarding facial attractiveness. The more unattractive the distractor, the more one of the targets was preferred over the other target, which suggests that divisive normalization (a potential canonical computation in the brain) influences social evaluations. I obtained the same result when I manipulated faces’ averageness and participants chose the most average face. This finding suggests that divisive normalization is not restricted to value-based decisions (e.g., attractiveness). This new application to social evaluation of normalization, a classic theory, opens possibilities for predicting social decisions in naturalistic contexts such as advertising or dating.
Light‐dependent regulation of the transcriptional activity of the mammalian gene for arrestin

The purpose of this investigation was to determine if the cyclic variations in the amount of arrestin mRNA that occur in the mouse retina during the light/dark cycle are controlled by light, a circadian clock, or both. In this study, an experimental paradigm was designed and used to distinguish among these molecular mechanisms. The data show that the initiation and the maintenance of an increased rate of syntheses of arrestin mRNA requires light and is not dependent on the time of day. Therefore the changes in transcriptional activity of the mouse arrestin gene are controlled by light, independent of circadian clock. The mechanism for this light‐dependent regulation of gene transcription in the retina is distinct from the light‐dependent increases in mRNA concentrations of early response genes which occur in the suprachiasmatic nucleus and a comparative analysis of such changes in these different regions of the CNS may lead to the identification of the molecular relationship between light‐ and circadian‐dependent gene regulation. © 1994 Wiley‐Liss, Inc.
Temperature Gradient Gel Electrophoresis of Fecal 16S rRNA Reveals Active Escherichia coli in the Microbiota of Patients with Ulcerative Colitis

ABSTRACT Previous studies of the endogenous microbiota in patients with ulcerative colitis (UC) have not taken bacterial activity into account, yet bacteria with high transcriptional activity might have a more important pathophysiological role than inactive bacteria. We therefore analyzed the biodiversity of active bacteria in the fecal microbiota of UC patients, in comparison with that of healthy subjects. Feces were collected from nine patients with active UC and from nine healthy controls. Total DNA and RNA were extracted, and 16S ribosomal DNA and RNA were amplified by PCR and reverse transcription-PCR, respectively. Amplification products were compared by means of temporal temperature gradient gel electrophoresis (TTGE). Bands of interest were excised, sequenced, and identified by comparison with the GenBank database (NCBI). The dominant-species diversity based on RNA-derived TTGE profiles was significantly lower for UC patients than for healthy controls (P = 0.01). The mean similarity index between the “present” and “active” microbiota was 74% ± 18% for UC patients. Comparison of the individual “active” microbiota identified a band that was present for eight UC patients and only two controls (89% versus 22%; P = 0.008). The band was sequenced for 6 patients and always corresponded to Escherichia coli. The biodiversity of active bacteria in the dominant fecal microbiota of patients with UC is lower than that of healthy subjects. E. coli is more represented in the active microbiota of UC patients. The possible pathophysiological role of this difference remains to be determined.
Transovarial Transmission of Babesia ovis by Rhipicephalus sanguineus and Hyalomma marginatum

Background Rhipicephalus sanguineus and Hyalomma marginatum are the most common species in sheep herds in Northeast of Iran. There is preliminary evidence that these species may be the vectors of Babesia ovis in Iran. We carried out two experiments in Mashhad area, Khorasan Razavi Province to determine whether B. ovis could be transovarially transmitted by R. sanguineus and H. marginatum. Methods In experiment 1, adults of laboratory reared H. marginatum and R.sanguineus were infected with B. ovis isolated from naturally infected sheep in Mashhad area by feeding the ticks on the sheep inoculated intravenously by infected blood samples. The inoculated sheep showed clinical signs with parasitaemia while the adult ticks were engorging on them. The engorged females were collected and kept at 28°C and 85% relative humidity in incubator. Then, larval, nymphal and adult stages derived from engorged females were used to infest the clean sheep. In experiment 2, two splenectomized sheep were infested only with the same adult ticks of two species. Results Examination of smears and PCR of blood samples to detect of B. ovis in infested sheep in two experiments were negative. Conclusion It seems that R. sanguineus and H. marginatum can not transovarially transmit B. ovis in sheep.
Transient Transcriptional Regulation of the CYS-C1 Gene and Cyanide Accumulation upon Pathogen Infection in the Plant Immune Response1[C][W]

The analysis of a mutant in the main enzyme responsible for cyanide detoxification, the mitochondrial β-cyanoalanine synthase, uncovers a new signaling role for cyanide in the plant response to pathogens. Cyanide is produced concomitantly with ethylene biosynthesis. Arabidopsis (Arabidopsis thaliana) detoxifies cyanide primarily through the enzyme β-cyanoalanine synthase, mainly by the mitochondrial CYS-C1. CYS-C1 loss of function is not toxic for the plant and leads to an increased level of cyanide in cys-c1 mutants as well as a root hairless phenotype. The classification of genes differentially expressed in cys-c1 and wild-type plants reveals that the high endogenous cyanide content of the cys-c1 mutant is correlated with the biotic stress response. Cyanide accumulation and CYS-C1 gene expression are negatively correlated during compatible and incompatible plant-bacteria interactions. In addition, cys-c1 plants present an increased susceptibility to the necrotrophic fungus Botrytis cinerea and an increased tolerance to the biotrophic Pseudomonas syringae pv tomato DC3000 bacterium and Beet curly top virus. The cys-c1 mutation produces a reduction in respiration rate in leaves, an accumulation of reactive oxygen species, and an induction of the alternative oxidase AOX1a and pathogenesis-related PR1 expression. We hypothesize that cyanide, which is transiently accumulated during avirulent bacterial infection and constitutively accumulated in the cys-c1 mutant, uncouples the respiratory electron chain dependent on the cytochrome c oxidase, and this uncoupling induces the alternative oxidase activity and the accumulation of reactive oxygen species, which act by stimulating the salicylic acid-dependent signaling pathway of the plant immune system.