Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer

ABSTRACT PCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus Methylocystis. A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.
Site-specific methylation of adenine in the nuclear genome of a eucaryote, Tetrahymena thermophila

DNA in the polyploid macronucleus of the ciliated protozoan Tetrahymena thermophila contains the modified base N6-methyladenine. We identified two GATC sites which are methylated in most or all of the 45 copies of the macronuclear genome. One site is 2 kilobases 5' to the histone H4-I gene, and the other is 5 kilobases 3' to the 73-kilodalton heat shock protein gene. These sites are de novo methylated between 10 and 16 h after initiation of conjugation, during macronuclear anlage development. The methylation states of these two GATC sites and four other unmethylated GATC sites do not change in the DNA of cells cultured under conditions which change the activity of the genes, including logarithmic growth, starvation, and heat shock.
Novel, Compound Heterozygous, Single‐Nucleotide Variants in MARS2 Associated with Developmental Delay, Poor Growth, and Sensorineural Hearing Loss

Novel, single‐nucleotide mutations were identified in the mitochondrial methionyl amino‐acyl tRNA synthetase gene (MARS2) via whole exome sequencing in two affected siblings with developmental delay, poor growth, and sensorineural hearing loss.We show that compound heterozygous mutations c.550C>T:p.Gln 184* and c.424C>T:p.Arg142Trp in MARS2 lead to decreased MARS2 protein levels in patient lymphoblasts. Analysis of respiratory complex enzyme activities in patient fibroblasts revealed decreased complex I and IV activities. Immunoblotting of patient fibroblast and lymphoblast samples revealed reduced protein levels of NDUFB8 and COXII, representing complex I and IV, respectively. Additionally, overexpression of wild‐type MARS2 in patient fibroblasts increased NDUFB8 and COXII protein levels. These findings suggest that recessive single‐nucleotide mutations in MARS2 are causative for a new mitochondrial translation deficiency disorder with a primary phenotype including developmental delay and hypotonia. Identification of additional patients with single‐nucleotide mutations in MARS2 is necessary to determine if pectus carinatum is also a consistent feature of this syndrome.
Language Use and Stereotyping: the Role of Approach and Avoidance Motivation Goals

The use of more abstract language to describe expected behaviors as opposed to unexpected behaviors has traditionally been considered a way of stereotype maintenance. This tendency is known as linguistic expectancy bias. Two experiments examined the influence of approach and avoidance motivational orientations on the production of this linguistic expectancy bias. It was predicted that approach strategic orientation is likely to describe expectancy consistent behaviors at a higher level of linguistic abstraction than expectancy inconsistent behaviors. In contrast, avoidance strategic orientation is likely to describe both expectancy consistent behaviors and expectancy inconsistent behaviors at a lower level of linguistic abstraction, thus facilitating the disappearance of linguistic expectancy bias. Two experiments confirmed these expectations, using strategic orientation manipulations based either on communication goals or on motor action, and measuring linguistic abstraction either on forced-choice answer format or on free descriptions. Implications for the generalisation of linguistic expectancy bias are discussed. El uso de un lenguaje más abstracto para describir los comportamientos congruentes con las expectativas que los comportamientos incongruentes con las expectativas es una forma de mantener los estereotipos. Esta tendencia se conoce como el sesgo lingüístico de expectativa. Dos experimentos analizan la influencia de las orientaciones motivacionales de aproximación y evitación en la producción del sesgo lingüístico de expectativa. Se predijo que la orientación estratégica de aproximación promovería que comportamientos consistentes con la expectativa se describiesen con un mayor nivel de abstracción lingüística que los comportamientos inconsistentes con la expectativa. En cambio, la orientación estratégica de evitación induciría a que tanto los comportamientos consistentes como los inconsistentes con las expectativas se describiesen a un menor nivel de abstracción, facilitando con ello la desaparición del sesgo lingüístico de expectativa. Los dos experimentos que se presentan confirmaron dichas predicciones utilizando manipulaciones de orientación estratégica de aproximación y evitación formuladas en forma de metas comunicativas y en forma de acción motora. Además, se midió la abstracción lingüística tanto en formato de respuesta de elección múltiple como en descripción libre. El artículo debate las implicaciones de los estudios para la generalización del sesgo lingüístico de expectativa.
Meta‐analysis of soy food and risk of prostate cancer in men

There has been considerable interest in recent years in the role of soy in cancer etiology. The purpose of this meta‐analysis was to evaluate epidemiologic studies available to date that related soy consumption to the risk of prostate cancer in men. We conducted a thorough Medline search for English‐language publications, supplemented with hand‐searching of articles' bibliographies and nonindexed medical and professional journals, on epidemiologic studies of soy and prostate cancer. We identified 2 cohort and 6 case‐control studies that met the following criteria for meta‐analysis: a study must have assessed soy as a food and provided a risk estimate (relative risk or odds ratio) and its 95% confidence interval. Data from the same study population appearing in different journals were only used once with the most recent publication chosen for the analysis. Studies on fermented soy food were not included. We conducted the meta‐analysis using a random‐effects model. An analysis of these studies yielded an overall risk estimate of 0.70 (95% CI = 0.59–0.83; p < 0.001). No publication bias was detected. In summary, results of the analysis showed that consumption of soy food was associated with a lower risk of prostate cancer in men. © 2005 Wiley‐Liss, Inc.
Is there anything distinctive about epileptic déjà vu?

Background Déjà vu can occur as an aura of temporal lobe epilepsy and in some psychiatric conditions but is also common in the general population. It is unclear whether any clinical features distinguish pathological and physiological forms of déjà vu. Methods 50 epileptic patients with ictal déjà vu, 50 non-epileptic patients attending general neurology clinics and 50 medical students at Edinburgh University were recruited. Data were collected on demographic factors, the experience of déjà vu using a questionnaire based on Sno's Inventory for Déjà Vu Experiences Assessment, symptoms of anxiety and depression using the Hospital Anxiety and Depression Scale as well as seizure characteristics, anti-epileptic medications, handedness, EEG and neuroimaging findings for epileptic patients. Results 73.5% of neurology patients, 88% of students and (by definition) all epilepsy patients had experienced déjà vu. The experience of déjà vu itself was similar in the three groups. Epileptic déjà vu occurred more frequently and lasted somewhat longer than physiological déjà vu. Epilepsy patients were more likely to report prior fatigue and concentrated activity, associated derealisation, olfactory and gustatory hallucinations, physical symptoms such as headaches, abdominal sensations and fear. After controlling for study group, anxiety and depression scores were not associated with déjà vu frequency. Conclusions Déjà vu is common and qualitatively similar whether it occurs as an epileptic aura or normal phenomenon. However ictal déjà vu occurs more frequently and is accompanied by several distinctive features. It is distinguished primarily by ‘the company it keeps’.
Growth and regression of thalamic efferents in the song‐control system of male zebra finches

A serial forebrain pathway in the songbird brain plays a critical role in vocal learning; Area X of the parolfactory lobe (X) projects to the medial portion of the dorsolateral nucleus of the anterior thalamus (DLM), which in turn projects to the lateral magnocellular nucleus of the anterior neostriatum (IMAN). Lesions of this pathway in juvenile birds disrupt vocal development, whereas identical lesions in adult birds do not influence the production of already learned song. During the course of vocal learning, IMAN undergoes a phase of massive neuronal loss, whereas the neuronal population of X more than doubles. In the present study, the development of neuron number in DLM was analyzed and found not to change during the course of vocal learning. Anterograde DiI labeling of DLM efferent fibers was then used to analyze the morphological development of this projection in relation to both the loss of neurons from IMAN and the loss of the ability of X‐DLM‐IMAN lesions to influence vocal production. We found that DLM axons arrive within IMAN by 15 days of age, prior to both the loss of neurons from IMAN and the onset of vocal production. The volume of anterograde DiI label over IMAN did not change between 15 and 20 days of age, but this volume more than doubled between 20 and 35 days of age. During this phase of exuberant growth, anterograde label matched the dorsal border of IMAN but extended beyond all other borders of IMAN into a surrounding “shell” of parvicellular neurons. By adulthood, the volume of both IMAN and anterograde DiI label declined substantially, but anterograde label continued to fill a parvicellular region of neostriatum surrounding all but the dorsal border of IMAN. Because DLM neuron number is stable during vocal development, these changes must reflect the growth and regression of some aspect(s) of DLM axonal morphology. Rearrangement of DLM axonal arborization may therefore be an important factor in the functional development of the X‐DLM‐IMAN pathway. © 1982 Wiley‐Liss, Inc. © 1992 Wiley‐Liss, Inc.
Studies on the infectivity of foot-and-mouth disease virus RNA using microinjection.

Foot-and-mouth disease virus (FMDV) RNA, isolated as virion RNA from purified virus particles or as total RNA from infected cells, has been microinjected into nuclei and cytoplasms of BHK cells. When injected directly into the nucleus FMDV RNA was not infectious, whereas cytoplasmic injection resulted in a high proportion of productive infections. Infectivity microinjection assays on dilution series of various FMDV RNAs showed that both single-stranded positive sense 35S RNA and double-stranded replicative form (Rf) RNA have an infectivity close to 1 p.f. u. per molecule, although only a minor fraction of BHK cells appeared able to support plaque formation following microinjection of Rf FMDV RNA. The infectivity of Rf FMDV RNA was not sensitive to inhibition by actinomycin D. The results are discussed in relation to the high virus particle to p.f. u. ratios observed for FMDV.
Tumor vessel biology in pediatric intracranial ependymoma.

OBJECT This study aimed to characterize the pediatric intracranial ependymoma vasculature in terms of angiogenic activity and maturation status so as to provide indications for the applicability of vessel-targeted therapy in cases of pediatric intracranial ependymoma. METHODS Tumor samples obtained in patients with ependymomas were immunohistochemically (double) stained for Ki 67/CD34, caspase 3a/CD34, vascular endothelial growth factor (VEGF)-A, -B, -C, -D, collagen Type IV, and smooth muscle actin to determine microvessel density, tumor and endothelial cell proliferation and apoptotic fraction, the relative expression of VEGF family members, and the coverage of the tumor endothelial cells by basal membrane and pericytes. Messenger RNA expression of angiopoietin-1 and -2 was analyzed by real-time reverse transcriptase polymerase chain reaction. These data were compared with those obtained in a glioblastoma series. RESULTS Despite a low endothelial cell turnover, the microvessel density of ependymomas was similar to that of glioblastomas. In ependymomas the expression of VEGF-A was within the range of the variable expression in glioblastomas. The staining intensities of VEGF-B, -C, and -D in ependymomas were significantly lower (p < 0.001). The expression of angiopoietin-1 was higher in ependymomas than in glioblastomas (p = 0.03), whereas angiopoietin-2 expression was similar. The coverage of tumor endothelial cells with basal membrane and pericytes was more complete in ependymomas (p = 0.009 and p = 0.022, respectively). CONCLUSIONS The ependymoma vasculature is relatively mature and has little angiogenic activity compared with malignant gliomas. Therefore, the window for vessel normalization as a therapeutic aim might be considered small. However, the status of the tumor vasculature may not be a reliable predictor of treatment effect. Therefore, possible benefits of antiangiogenic treatment cannot be excluded beforehand in patients with ependymomas.
Do ARTs affect the incidence of monozygotic twinning?

STUDY QUESTION Does the manipulation of gametes or embryos during ARTs increase the risk for monozygotic twinning (MZT)? SUMMARY ANSWER Frozen embryo transfer (ET) is associated with a lower MZT rate, while blastocyst culture is associated with an increased risk of monozygotic pregnancy. WHAT IS KNOWN ALREADY Monozygotic twins have a higher risk for perinatal complications. Although an increased incidence of monozygotic pregnancies after ART has been previously reported, data regarding the possible impact of different laboratory procedures are conflicting. STUDY DESIGN, SIZE, DURATION All clinical pregnancies after single ET carried out in our centre between 2004 and 2013 (n = 6096) were retrospectively analysed for the incidence of MZT. The effect of different laboratory procedures on the incidence of MZT was evaluated. PARTICIPANTS/MATERIALS, SETTING, METHODS The following ART risk factors were assessed: maternal age, type of ET (fresh versus frozen), zona pellucida (ZP) manipulation (specifically, ICSI, embryo biopsy and assisted hatching), use of donor oocytes, embryo stage at time of ET (cleavage, compaction, early or advanced blastocyst) and culture media. MAIN RESULTS AND THE ROLE OF CHANCE The overall MZT rate was 2.2% (136/6096). Frozen ET was associated with a significant reduction in MZT incidence (adjusted odds ratio (aOR) 0.48, 95% CI 0.29-0.80), while blastocyst transfer (early or advanced blastocyst) was associated with a significant increase in MZT risk (aOR 2.70, 95% CI 1.36-5.34; aOR 2.05, 95% CI 1.29-3.26, respectively). No significant differences were found between the MZT and singleton (non-MZT) groups regarding maternal age, the use of different ZP manipulation techniques, not type of culture media used. LIMITATION, REASONS FOR CAUTION This study is limited by its retrospective nature and the fact that monozygosity was not confirmed by genetic testing. Furthermore, since monozygotic pregnancy is a rare event, other ART parameters that may influence its incidence could not be assessed during our analysis. WIDER IMPLICATION OF THE FINDINGS Our findings warrant future studies designed to investigate the association between specific ART procedures and MZT, namely the potential risk of blastocyst transfer to increase MZT. STUDY FUNDING/COMPETING INTERESTS No external funding was used for this study. There are no conflicts of interest.
Value of a Single-Tube Widal Test in Diagnosis of Typhoid Fever in Vietnam

ABSTRACT The diagnostic value of an acute-phase single-tube Widal test for suspected typhoid fever was evaluated with 2,000 Vietnamese patients admitted to an infectious disease referral hospital between 1993 and 1998. Test patients had suspected typhoid fever and a blood culture positive for Salmonella typhi (n= 1,400) orSalmonella paratyphi A (n = 45). Control patients had a febrile illness for which another cause was confirmed (malaria [n = 103], dengue [n = 76], or bacteremia due to another microorganism [n = 156] or tetanus (n = 265). An O-agglutinin titer of ≥100 was found in 18% of the febrile controls and 7% of the tetanus patients. Corresponding values for H agglutinins were 8 and 1%, respectively. The O-agglutinin titer was ≥100 in 83% of the blood culture-positive typhoid fever cases, and the H-agglutinin titer was ≥100 in 67%. The disease prevalence in investigated patients in this hospital was 30.8% (95% confidence interval, 26.8 to 35.1%); at this prevalence, an elevated level of H agglutinins gave better positive predictive values for typhoid fever than did O agglutinins. With a cutoff titer of ≥200 for O agglutinin or ≥100 for H agglutinin, the Widal test would diagnose correctly 74% of the blood culture-positive cases of typhoid fever. However, 14% of the positive results would be false-positive, and 10% of the negative results would be false-negative. The Widal test can be helpful in the laboratory diagnosis of typhoid fever in Vietnam if interpreted with care.
Long‐term experience with burkitt's lymphoma in uganda

The cumulative results and long‐term follow‐up of all patients with Burkitt's lymphoma treated at the Uganda cancer Institute Kampala are reported. The annual admission rate is 29. The tumor patients commonly present with jaw swelling (72%), abdominal swelling (56%) and central nervous system involvement (30%). Complete response rate is achieved in a high proportion of patients (81 %). About 50% of these relapse, equal numbers relapsing before and after 3 months. The most important factor influencing remission duration and survival is disease stage. Other important factors are treatment protocols and, to a lesser extent, the type of relapse. Central nervous system relapse does not necessarily augur poor prognosis as second remissions and long‐term survival can be achieved with appropriate therapy. Presently 25% of all treated patients have survived free of disease well beyond 5 years.
Prevalence of self-medication practices and its associated factors in Urban Puducherry, India

Background and Objectives: Self medication is an important concern for health authorities at global level. This study was aimed to find the prevalence of self medication for allopathic drugs and associated factors among households of urban community. This study was also aimed at assessing the attitude of respondents who had experienced self-medication. Materials and Methods: This cross-sectional study was done in field practice area attached to a medical institution in urban Puducherry. A total of 352 subjects from 124 households were selected by random sampling. With pretested interview schedule, information regarding self-medication use in the past three months and associated sociodemographic factors, purpose, source of drug procurement, attitude toward self-medication use were collected. Results: Prevalence of self-medication was found to be 11.9%. Males, age >40 years and involving in moderate level activity of occupation, were found to be significantly associated with higher self-medication usage (P < 0.05). Fever (31%), headache (19%), and abdominal pain (16.7%) are most common illnesses where self-medication is being used. Telling the symptoms to pharmacist (38.1%) was the commonest method adopted to procure drugs by the users. Majority of the self-medication users expressed that self-medication is harmless (66.6%) and they are going to use (90%) and advice others also (73.8%) to use self-medication drugs. Conclusion: Self-medication is an important health issue in this area. Health education of the public and regulation of pharmacies may help in limiting the self-medication practices.
Pattern of cell death during optic cup formation in the tree shrew Tupaia belangeri

Developmental cell death during optic cup formation was investigated in the tree shrew Tupaia belangeri. Twenty‐six embryos from days 12 to 16 of prenatal ontogenesis were studied by light microscopy. Prior to the optic vesicle stage, a dorsal area of cell death surrounded the lumen of the V‐shaped optic evagination (phase 1). A ventral band of dead cells, found in the optic vesicle (phase 2), preceded a dorsal focus of cell death (phase 3) previously described as a characteristic avian feature. During further invagination (phase 4), a peak of cell death was represented by a ventrodorsal band extending from the diencephalon over the complete optic anlage. The main areas of cell death found in phases 2 to 4 were, topographically, segments of this band. Also, the distinct areas of cell death reported in the literature for the vertebrate species studied so far fit well into this ventrodorsal band found in Tupaia. Thus, most probably, a common spatio‐temporal sequence of cell death exists in all of them. In Tupaia, dead cells concentrated at the diencephalic insertion of the optic stalk, the suboptic necrotic center (SONC) reported by several authors, were part of the early ventral band of cell death originating from the median floor of the prosencephalon (phase 2). During optic cup formation, the SONC was part of the ventrodorsal band and, thus, was not secondarily formed by the subdivision of a pre‐existing distal ventral area of cell death as reported for several other vertebrates. J. Comp. Neurol. 401:352–366, 1998. © 1998 Wiley‐Liss, Inc.