Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancement and rescue of target capture in Tn10 transposition by site‐specific modifications in target DNA

The bacterial transposon Tn10 inserts preferentially into specific target sequences. This insertion specificity appears to be linked to the ability of target sites to adopt symmetrically positioned DNA bends after binding the transposition machinery. Target DNA bending is thought to permit the transposase protein to make additional contacts with the target DNA, thereby stabilizing the target complex so that the joining of transposon and target DNA sequences can occur efficiently. In the current work, we have asked whether the introduction of a discontinuity in a target DNA strand, a modification that is expected to make it easier for a DNA molecule to bend, can enhance or rescue target capture under otherwise suboptimal reaction conditions. We show that either a nick or a missing phosphate specifically at the site of reaction chemistry increases the ability of various target DNAs to form the target capture complex. The result suggests that the bends in the target DNA are highly localized and include the scissile phosphates. This raises the possibility that strand transfer is mechanistically linked to target capture. We have also identified specific residues in the target DNA and in transposase that appear to play an important role in target DNA bending.
Successful treatment of severe thrombotic thrombocytopenic purpura with the monoclonal antibody rituximab

The only established treatment for patients with thrombotic thrombocytopenic purpura (TTP) is plasma exchange against fresh frozen plasma. For cases refractory to plasma exchange, no generally treatment schedule exists. One option is immunosuppressive therapy with corticosteroids and vincristine. Rituximab is a chimeric monoclonal antibody directed against the CD20 antigen, and it has been successfully used in B‐cell malignancies and is being investigated in autoimmune diseases. Its efficacy in TTP has not yet been determined. We report two female patients with severe TTP refractory to multiple courses of plasmapheresis, high‐dose steroid treatment, and vincristine who responded after adding rituximab while continuing plasmapheresis. Am. J. Hematol. 71:105–108, 2002. © 2002 Wiley‐Liss, Inc.
Use of magnetic resonance imaging for in vivo measurements of water content in human brain: method and normal values.

OBJECT The authors present a quantitative in vivo magnetic resonance (MR) imaging method and propose its use for the accurate assessment of brain water in humans. METHODS With this technique, a pure T1-weighted image of a selected brain slice in a patient is generated, and the image is subsequently converted to a pure water image by means of an equation derived from a tissue relaxation model. The image intensity in the resulting water map directly yields absolute measures of water expressed in grams of water per gram of tissue at a given anatomical location. The method has been validated previously in a series of phantom experiments and in an infusion model of brain edema in cats. In this report, the authors evaluate the method by using samples of tissue harvested from patients who underwent surgery for brain tumor removal and apply the technique to a series of normal volunteers, providing average regional brain water content (f(w)) values for a range of tissues. Application of the method in pathological conditions such as head trauma, tumor, and hydrocephalus allows quantification of regional or global increases in f(w) that result from edema. CONCLUSIONS It is now possible to obtain accurate brain water measurements with the anatomical resolution of MR imaging. This permits monitoring of the development and resolution of edema in a variety of clinical circumstances, thus enhancing understanding of the underlying pathophysiological processes.
Arrhythmias and death after coronary artery occlusion in the rat. Continuous telemetric ECG monitoring in conscious, untethered rats.

BACKGROUND The onset of acute myocardial infarction (MI) is accompanied by a rapid increase in electrical instability and often fatal ventricular arrhythmias. The aim of this study was to assess the continuous arrhythmia profile during the initial 48 hours after coronary artery ligation in the rat in relation to time course, mortality, and infarct size. METHODS AND RESULTS Continuous ECG recording were obtained in 26 conscious, untethered rats for 24 hours before and 48 hours after coronary ligation by use of an implantable telemetry system. All episodes of ventricular tachycardia and fibrillation were counted and their durations summed. Infarct size was measured at 48 hours after MI or after spontaneous death. After ligation, two distinctly active arrhythmogenic periods developed (A1, 0 to 0.5 hours; A2, 1.5 to 9 hours), each followed by a quiescent phase of low ectopy (Q1, 0.5 to 1.5 hours; Q2, 10 to 48 hours). The total mortality rate of 65% was found within the two active periods, with 13 of 15 deaths occurring in A2. Rats with larger infarcts (> or = 50%) and nonsurvivors tended to have increased arrhythmia frequency and duration compared with both animals with smaller MIs (< 50%) and survivors. CONCLUSIONS Two distinct arrhythmogenic periods occur in rats with acute MI that may be caused by different mechanisms and correspond to the bimodal arrhythmia time course seen in dogs and humans after acute MI. Telemetric monitoring of the ECG in the conscious rat after infarction will be useful in assessment of the differential effects of therapeutic interventions on these two arrhythmogenic periods and in the study of potential mechanisms for the spontaneous resolution of ventricular ectopy and risk of sudden death.
Ideomotor apraxia test: a new test of imitation of gestures for elderly people

Ideomotor apraxia is one the earliest disturbances in Alzheimer's disease(AD); no test of this disturbance has yet been validated for elderly people. We propose a test of meaningless gesture imitation and its relevance;in elderly people is studied. The Ideomotor Aprazia Test (IAT) consists of showing 10 gestures. Each item is graded from 0 to 3. IAT was carried;out on 55 patients with AD (mean age:86.8 ± 6.8(71–100); mean MMS score: 14.6 ± 6.3) and 26 elderly patients without cognitive impairment (mean age:84.1 ± 7.5(70–100); mean MMS score:27.5 ± 1.9). The inter‐rater relilability, a threshold, the apparent sensitivity and specificity and the relationship bestween the MMS score and the ideomotor apraxia score were determined. The mean apraxia score was 14.9 ± 7.3 in the AD group and 28 ± 1.6 in the normal group (P < 0.0001). Inter‐rater agreement is excellent (P = 0.995). The threshold is 27. The apparent sensitivity and specificity are very good (95% and 98%, respectively). The correlataion between the MMS score and ideomotor apraxia score. IAT is the first test that evaluates meaningless gesture imitating capacity in an elderly population. It is easy and quick‐to‐perform test, useful routienly for diagnois of AD and is correlatead with the severity of cognitive impairment.
Nonamnestic mild cognitive impairment progresses to dementia with Lewy bodies

Objective: To determine the rate of progression of mild cognitive impairment (MCI) to dementia with Lewy bodies (DLB). Methods: We followed 337 patients with MCI in the Mayo Alzheimer's Disease Research Center (range 2–12 years). Competing risks survival models were used to examine the rates of progression to clinically probable DLB and Alzheimer disease (AD). A subset of patients underwent neuropathologic examination. Results: In this clinical cohort, 116 remained as MCI, while 49 progressed to probable DLB, 162 progressed to clinically probable AD, and 10 progressed to other dementias. Among nonamnestic MCI, progression rate to probable DLB was 20 events per 100 person-years and to probable AD was 1.6 per 100 person-years. Among amnestic MCI, progression rate to probable AD was 17 events per 100 person-years, and to DLB was 1.5 events per 100 person-years. In 88% of those who developed probable DLB, the baseline MCI diagnosis included attention and/or visuospatial deficits. Those who developed probable DLB were more likely to have baseline daytime sleepiness and subtle parkinsonism. In 99% of the clinically probable AD group, the baseline MCI diagnosis included memory impairment. Neuropathologic confirmation was obtained in 24 of 30 of those with clinically probable AD, and in 14 of 18 of those with clinically probable DLB. Conclusion: In a clinical sample, patients with nonamnestic MCI were more likely to develop DLB, and those with amnestic MCI were more likely to develop probable AD.
Quality of life is decreased after treatment for nonfunctioning pituitary macroadenoma.

OBJECTIVE Although a reduced quality of life (QoL) has been reported after long-term cure of functioning pituitary adenomas, the effect of successful treatment of nonfunctioning pituitary macroadenoma (NFMA) on QoL has not been fully addressed. Therefore, we evaluated a broad spectrum of QoL parameters in patients successfully treated for NFMA in our center. DESIGN We conducted a case-control study. PATIENTS AND METHODS We assessed QoL in 99 adult patients (mean age, 61.9 yr; range, 24-86 yr) in remission during long-term follow-up after surgical (n = 99) and additional radiotherapeutic (n = 37) treatment for NFMA by four validated health-related questionnaires (Hospital Anxiety and Depression Scale, Multidimensional Fatigue Index, Nottingham Health Profile, and Short Form-36). Patient outcomes were compared with 125 controls and with age-adjusted reference values derived from the literature. RESULTS NFMA patients reported significantly impaired QoL in all questionnaires compared with the 125 controls and the age-adjusted reference values. All subscales of fatigue, assessed using the Multidimensional Fatigue Index (general fatigue, physical fatigue, reduction in activity, reduction in motivation, and mental fatigue) were impaired. The scores in the Nottingham Health Profile pointed toward reduced energy and affected emotional reaction. In several subscales of the Short Form-36 (social functioning, role limitations due to physical problems, role limitations due to emotional problems, and general health perception), NFMA patients reported a reduced QoL. CONCLUSION QoL is considerably reduced in patients after successful treatment of NFMA.
Perforin is not co-expressed with granzyme A within cytotoxic granules in CD8 T lymphocytes present in lymphoid tissue during chronic HIV infection.

BACKGROUND Residual HIV-1-infected cells are poorly eliminated from lymphoid tissue (LT) reservoirs by effector cytotoxic T lymphocytes (eCTL) despite antiretroviral therapy. Perforin and granzyme A (grA) constitute major effector molecules within eCTL granules that induce apoptosis and lysis of virally infected cells. OBJECTIVE Expression of perforin and grA was studied at the single cell level in LT and blood from 16 patients infected with HIV-1 (stage A1-C) who were not taking antiretroviral therapy. METHOD Immunohistochemical analysis by in situ imaging of cells from blood and LT. RESULTS Quantitative in situ imaging showed that perforin-expressing CD8 T cells comprised 0.3-1.5% of total cells within the LT from recent HIV-1 seroconverters, while grA was found in 2.1-7.2% of total cells. However, despite high-level grA upregulation (1.5-4.5% of total cells) compared with that in non-infected individuals (0.4-0.9%), perforin expression remained low (< 0.1% of total cells) (P < 0.02) in LT from patients with chronic HIV-1 infection (stage A2-C). This contrasted with findings in peripheral blood mononuclear cells (PBMC) from the same HIV-1 infected cohort where perforin was detected in 13-31% of all PBMC, which was 10- to 100-fold higher than in lymphoid tissue (P < 0.001); grA was found in 14-32% of total PBMC. Two-colour staining showed that granular expression of perforin and grA was restricted to CD8 T cells in over 90% of total cells in both LT and blood. CONCLUSIONS These findings indicate that cytotoxic perforin expression is impaired at local sites of HIV replication within lymphoid tissue. Since perforin is required together with grA for granule-mediated cytolysis, the low perforin expression in the LT may limit the ability of eCTL to eliminate HIV-1 infected cells in lymphoid tissue.
Isolation of a Highly Clonogenic and Multipotential Subfraction of Adult Stem Cells from Bone Marrow Stroma

Attempts have been made to develop cell and gene therapies using the adult stem cells from bone marrow referred to as mesenchymal stem cells or marrow stromal cells (MSCs). However, the results have been variable in part because there are no standardized protocols for preparing and characterizing MSCs. In the experiments presented here, we developed a standardized assay by light scattering to measure the content of rapidly self‐renewing cells (RS cells) in preparations of MSCs. The assay quickly identifies preparations of MSCs that replicate rapidly in subsequent culture. In addition, the standardized assay enabled us to isolate RS cells that were up to 90% clonogenic and that generated single cell–derived colonies that differentiated into either mineralizing cells or adipocytes with appropriate additions to the medium.
The Negative Correlation Between Thyrotropin Receptor–Stimulating Antibodies and Bone Mineral Density in Postmenopausal Patients With Graves’ Disease

Graves’ disease is an autoimmune disorder with various clinical manifestations. Thyrotropin receptor antibodies (TRAbs), the circulating autoantibodies specific to Graves’ disease, are the cause for hyperthyroidism, the most prevalent abnormality. Hyperthyroidism leads to increased bone turnover and a negative bone balance. The aims of the present study were to determine the relationship between TRAbs and bone mineral density (BMD), to assess the extent of BMD change in patients with Graves’ disease, and to determine the impact of conservative and surgical therapy on BMD. Fifty female postmenopausal patients with Graves’ disease were chosen for this study. Twenty women had a recent diagnosis of Graves’ disease, 30 women presented with a compensated disease state after either conservative or surgical treatment, and 30 healthy postmenopausal women served as controls. Thyroid parameters were measured, and BMD values were obtained by dual energy x-ray absorptiometry scan. Femoral neck and lumbar spine BMD and T-scores were significantly lower in newly diagnosed patients compared with the control group, but a difference was not observed between the treated and control groups. Statistical analysis revealed a strong and significant negative correlation between femoral neck and lumbar spine BMD and TRAb values. Both surgical and conservative therapies are effective for restoring BMD in postmenopausal patients with Graves’ disease, and the increased level of TRAb can be a useful marker of bone density impairment.
Incorporating biological, chemical, and toxicological knowledge into predictive models of toxicity.

Complete List of Authors: Dix, David; US EPA, Nat'l Center for Computational Toxicology Houck, Keith; USEPA, NCCT Judson, Richard S. ; US EPA, National Center for Computational Toxicology Knudsen, Thomas; US EPA, NCCT Martin, Matthew; US EPA, Reif, David; US EPA, National Center for Computational Toxicology Richard, Ann; USEPA, MD B143-06 Shah, Imran; USEPA, NCCT Kleinstreuer, Nicole; U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology Sipes, Nisha; U.S. Environmental Protection Agency, Office of Research and Development/National Center for Computational Toxicology Kavlock, Robert; U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology; US EPA, NHEERL, MD-71
Central Nervous System Manifestations in Human Immunodeficiency Virus Infection Without AIDS

To characterize neurological and neuropsychological findings associated with human immunodeficiency virus type-I (HIV) infection, 77 seropositive homosexual or bisexual males with no or minor symptoms of HIV were compared prospectively to 44 HIV seronegative men by observers blinded to serological status of the subjects. Neurological symptoms and examination findings were not significantly different between seropositives and seronegatives except for cranial nerve findings, predominately mild hearing impairment. Mean performance scores for a 15-test neuropsychological battery were within an unimpaired range for both groups, although for five tests, mean scores were significantly poorer in seropositives. After adjustment for vocabulary score, and demographic and psychosocial variables, the mean score of seropositives was significantly worse only for the Benton Visual Retention Test. Magnetic resonance (MR) images of brain were abnormal in 14 (27%) of 52 seropositives and one of 10 seronegatives (value was not significant). HIV was isolated from cerebrospinal fluid (CSF) in 31 (61%) of 51 seropositives. The only clinical or laboratory difference between CSF culture positives and negatives was a higher CSF immunoglobulin synthesis rate in the former subjects (medians of 10.3 versus 0.1 mg/day; p = 0.03). An additional 13 seropositive subjects had immunologic evidence of central nervous system HIV infection, defined by a serum-to-CSF HIV antibody ratio of <5.5. Intracranial abnormalities on MR imaging were associated with CSF immunologic responses to HIV. Nervous system involvement occurred in the vast majority of men with early HIV infection, but clinically significant impairment was uncommon.
Psychological Factors Associated with Emotional Distress among Palestinian Arabs from East Jerusalem Accessing Psychiatric Care in Israel.

BACKGROUND The Palestinian population residing in East Jerusalem is characterized by high rates of poverty and unemployment and is subject to discrimination in various forms, including infrastructure of mental health services. Little is known about the help seeking needs and practices of East Jerusalem residents. METHOD We examined socio-demographic and clinical characteristics of a consecutive sample Palestinian residents from East Jerusalem (N=50) who accessed a specially assigned psychiatric clinic in Israel. In addition, we examined the psychological factors associated with emotional distress among these service-users upon entry to care. Participants completed a survey in Arabic that included a socio-demographic questionnaire and measures assessing emotional distress, perceived exposure to discrimination and social support, and mental health stigma. RESULTS Participants reported high levels of emotional distress. Female gender, low socioeconomic status, higher perceived exposure to discrimination and higher perceived social support were associated with increased emotional distress. CONCLUSIONS Findings add to the scarce body of knowledge on specific mental health characteristics of East Jerusalem Palestinian residents.
Clinical and Laboratory Evaluation of Upper Respiratory Symptoms in Elite Athletes

Objective:To characterize the etiology of upper respiratory symptoms in elite athletes presenting to a sports physician for treatment. Design:Prospective clinical and laboratory investigations. Setting:Sports medicine clinic. Participants:Seventy elite-level athletes. Main Outcome Measurements:Physician-recorded symptoms and diagnosis; health/training questionnaires; laboratory investigations of respiratory pathogens, white blood cell differential counts, and immune parameters. Results:Physicians characterized 89% of presentations as viral or bacterial upper respiratory tract infection. Only 57% of presentations were associated with an identified pathogen or other laboratory parameters indicative of infection. Demographic information, previous illness, and training history did not distinguish between presentations with or without objective measures of infection. Elevated white blood cell and neutrophil counts and lower vitamin D concentrations partially distinguished infectious episodes. The number of systemic symptoms/behaviors at presentation (cough, headache, earache, fatigue, fever/rigors, myalgia/arthralgia, or cessation of training before clinic attendance) had some predictive value for infection: odds ratio per symptom, 1.23 (90% confidence interval: 0.91 to 1.66); probability of infection, 48% with no symptoms to 77% with 6 symptoms. Laboratory investigation identified allergy in a considerable proportion of the cohort (39%). Conclusions:The discrepancy between physician and laboratory diagnosed infection in elite athletes highlights the need for consideration of alternate diagnostic options when evaluating upper respiratory symptoms in athletes. A considerable proportion of episodes of respiratory symptoms in athletes were not associated with identification of a respiratory pathogen; other potentially treatable causes of upper respiratory symptoms should be considered, particularly in athletes with recurrent symptoms.
In Vivo Overexpression of Tissue‐Nonspecific Alkaline Phosphatase Increases Skeletal Mineralization and Affects the Phosphorylation Status of Osteopontin

Functional ablation of tissue‐nonspecific alkaline phosphatase (TNAP) (Alpl−/− mice) leads to hypophosphatasia, characterized by rickets/osteomalacia attributable to elevated levels of extracellular inorganic pyrophosphate, a potent mineralization inhibitor. Osteopontin (OPN) is also elevated in the plasma and skeleton of Alpl−/− mice. Phosphorylated OPN is known to inhibit mineralization, however, the phosphorylation status of the increased OPN found in Alpl−/− mice is unknown. Here, we generated a transgenic mouse line expressing human TNAP under control of an osteoblast‐specific Col1a1 promoter (Col1a1‐Tnap). The transgene is expressed in osteoblasts, periosteum, and cortical bones, and plasma levels of TNAP in mice expressing Col1a1‐Tnap are 10 to 20 times higher than those of wild‐type mice. The Col1a1‐Tnap animals are healthy and exhibit increased bone mineralization by micro–computed tomography (µCT) analysis. Crossbreeding of Col1a1‐Tnap transgenic mice to Alpl−/− mice rescues the lethal hypophosphatasia phenotype characteristic of this disease model. Osteoblasts from [Col1a1‐Tnap] mice mineralize better than nontransgenic controls and osteoblasts from [Col1a1‐Tnap+/−; Alpl−/−] mice are able to mineralize to the level of Alpl+/− heterozygous osteoblasts, whereas Alpl−/− osteoblasts show no mineralization. We found that the increased levels of OPN in bone tissue of Alpl−/− mice are comprised of phosphorylated forms of OPN whereas wild‐type (WT) and [Col1a1‐Tnap+/−; Alpl−/−] mice had both phosphorylated and dephosphorylated forms of OPN. OPN from [Col1a1‐Tnap] osteoblasts were more dephosphorylated than nontransgenic control cells. Titanium dioxide‐liquid chromatography and tandem mass spectrometry analysis revealed that OPN peptides derived from Alpl−/− bone and osteoblasts yielded a higher proportion of phosphorylated peptides than samples from WT mice, and at least two phosphopeptides, p(S174FQVS178DEQY182PDAT186DEDLT191)SHMK and FRIp(S299HELES304S305S306S307)EVN, with one nonlocalized site each, appear to be preferred sites of TNAP action on OPN. Our data suggest that the promineralization role of TNAP may be related not only to its accepted pyrophosphatase activity but also to its ability to modify the phosphorylation status of OPN.