Miracle-dz/UniFAR-FTUs huggingface dataset:
Tracking sub-clonal TP53 mutated tumor cells in human metastatic renal cell carcinoma

Renal Cell Carcinomas (RCCs) are heterogeneous tumors with late acquisition of TP53 abnormalities during their evolution. They harbor TP53 abnormalities in their metastases. We aimed to study TP53 gene alterations in tissue samples from primary and metastatic RCCs in 36 patients followed up over a median of 4.2 years, and in xenografted issued from primary RCCs. In 36 primary RCCs systematically xenografted in mice, and in biopsies of metastases performed whenever possible during patient follow-up, we studied p53-expressing tumor cells and TP53 gene abnormalities. We identified TP53 gene alterations in primary tumors, metastases and xenografts. Quantification of tumors cells with TP53 gene alterations showed a significant increase in the metastases compared to the primary RCCs, and, strikingly, the xenografts were similar to the metastases and not to the primary RCCs from which they were derived. Using laser-microdissection of p53-expressing tumor cells, we identified TP53-mutated tumor cells in the xenografts derived from the primary RCC, and in a lung metastasis later developed in one patient. The mutation enabled us to track back their origin to a minority sub-clone in the primary heterogeneous RCC. Combining in situ and molecular analyses, we demonstrated a clonal expansion in a living patient with metastatic RCC.
Distance Protection of Lines Emanating From Full-Scale Converter-Interfaced Renewable Energy Power Plants—Part I: Problem Statement

The fault ride-through (FRT) requirement of modern grid codes results in interactions between full-scale converter-interfaced renewable energy power plants (CIREPPs) and the protection systems of high-voltage transmission grids, which normally involve distance elements either as the primary or the backup relay. Such interactions are influenced by the CIREPPs' exclusive fault behavior, and have been left largely unnoticed in relaying literature. Part I of this paper develops a CIREPP model suitable for relaying studies, and highlights the CIREPP properties by which the protection system is endangered the most. Then, the operating scenarios leading to the malfunction of a distance relay that is located at a CIREPP substation and protects the adjacent line are unveiled. These scenarios include in-zone short circuits missed by the relay and incorrect tripping for out-of-zone faults, which would, in turn, neutralize FRT schemes implemented inside CIREPPs. The findings of this study also hold true for the ac lines emanating from voltage-sourced converter-based HVDC connections.
Effect of Complement on HIV-2 Plasma Antiviral Activity Is Intratype Specific and Potent

ABSTRACT Human immunodeficiency virus type 2 (HIV-2)-infected individuals develop immunodeficiency with a considerable delay and transmit the virus at rates lower than HIV-1-infected persons. Conceivably, comparative studies on the immune responsiveness of HIV-1- and HIV-2-infected hosts may help to explain the differences in pathogenesis and transmission between the two types of infection. Previous studies have shown that the neutralizing antibody response is more potent and broader in HIV-2 than in HIV-1 infection. In the present study, we have examined further the function of the humoral immune response and studied the effect of complement on the antiviral activity of plasma from singly HIV-1- or HIV-2-infected individuals, as well as HIV-1/HIV-2 dually infected individuals. The neutralization and antibody-dependent complement-mediated inactivation of HIV-1 and HIV-2 isolates were tested in a plaque reduction assay using U87.CD4. CCR5 cells. The results showed that the addition of complement increased intratype antiviral activities of both HIV-1 and HIV-2 plasma samples, although the complement effect was more pronounced with HIV-2 than HIV-1 plasma. Using an area-under-the-curve (AUC)-based readout, multivariate statistical analysis confirmed that the type of HIV infection was independently associated with the magnitude of the complement effect. The analyses carried out with purified IgG indicated that the complement effect was largely exerted through the classical complement pathway involving IgG in both HIV-1 and HIV-2 infections. In summary, these findings suggest that antibody binding to HIV-2 structures facilitates the efficient use of complement and thereby may be one factor contributing to a strong antiviral activity present in HIV-2 infection.
Pro-Coagulant Endothelial Dysfunction Results from EHEC Shiga Toxins and Host Damage-Associated Molecular Patterns

Hemolytic uremic syndrome (HUS) from enterohemorrhagic Escherichia coli infection is a leading cause of kidney failure in otherwise healthy U.S. children. The bacterial Shiga toxins (Stx) induce the characteristic coagulopathy of HUS, but the damage to toxin-receptor expressing cells and organ injury due to ischemia likely also releases inflammatory damage-associated molecular patterns (DAMPs), which may exacerbate injury along with the toxins. To examine this, human aortic and renal glomerular cell anti-coagulant and barrier functions were studied after in vitro challenge with Stx1, Stx2, and DAMPs. There was significant loss of surface anti-coagulant protein C pathway molecules, increased expression of pro-thrombotic PAR1 and reduced protein C activation capability by 15–27%. Histones nearly completely prevented the activated protein C protection of endothelial cells from thrombin-induced permeability. In mice, lethal Stx2 challenge elevated plasma HMGB1 (day 2, 321 ± 118%; p < 0.01) and extracellular histones (day 3, 158 ± 62%; p < 0.01). Mice colonized with Stx2-expressing Citrobacter rodentium developed increased HMGB1 (day 5, 155 ± 55%; p < 0.01) and histones (day 3, 378 ± 188%; p < 0.01). Anti-histone antibody reduced both DAMPs to baseline, but was not sufficient to improve survival outcome or kidney function. Together, these data suggest a potential role Stx to produce DAMPs, and DAMPs to produce endothelial injury and a pro-thrombotic environment.
The Utility of Health States After Stroke: A Systematic Review of the Literature

Background— To perform decision analyses that include stroke as one of the possible health states, the utilities of stroke states must be determined. We reviewed the literature to obtain estimates of the utility of stroke and explored the impact of the study population and the elicitation method. Summary of Review— We searched various databases for articles reporting empirical assessment of utilities. Mean utilities of major stroke (Rankin Scale 4 to 5) and minor stroke (Rankin Scale 2 to 3) were calculated, stratified by study population and elicitation method. Additionally, the modified Rankin Scale was mapped onto the EuroQol classification system. Utilities were obtained from 23 articles. Patients at risk for stroke assigned utilities of 0.26 and 0.55 to major and minor stroke, respectively. Stroke survivors assigned higher utilities to both major (0.41) and minor stroke (0.72). The EuroQol completed by stroke survivors revealed a utility of 0.32 and 0.71 for major and minor stroke, respectively. Utilities elicited by the Standard Gamble were generally higher, while those obtained by the Visual Analogue Scale were lower than the Time Trade Off values. Remaining variation between utilities may be caused by differences in definitions of the health states. The mapped EuroQol indicated a utility of 0.64 for minor stroke and a value just below zero for major stroke. Conclusions— For minor stroke, a utility between 0.50 and 0.70 seems to be reasonable for both decision analyses and cost-effectiveness studies. The utility of major stroke may range between 0 and 0.30 and may possibly be negative.
Preparation and Viscoelastic Properties of Waterborne Polyurethane/Cellulose Nanocrystals Composites

The objective of this work is to study the viscoelastic properties by which nanofillers produce mechanical reinforcement in polymers using dynamic mechanical analysis (DMA). To this purpose, waterborne polyurethane (WBPU) and cellulose nanocrystals (CNCs) composites films with various filler contents were prepared by ultrasonic dispersion followed by emulsion casting process. In frequency sweep tests, the storage modulus and loss modulus were recorded and modeled by the Power Law equation. CNCs precipitation significantly increased the steady state viscous properties of cellulose nanocoposite films but decreased the dynamic viscoelastic properties and frequency sensitivity of nanocomposite films.
Multiple Imputation for Missing Data in Repeated Measurements Using MCMC and Copulas

This paper presents two imputation methods: Markov Chain Monte Carlo (MCMC) and Copulas to handle missing data in repeated measurements. Simulation studies were performed using the Monte Carlo technique to generate datasets in different situations. Each subject unit in each dataset was measured on three occasions under the following conditions: 1. data had a multivariate normal distribution under two types of correlation structures: Compound Symmetry (CS) and Autoregressive (AR (1)), 2. the correlation among repeated observations under each subject was determined at low level (ρ =0.3), middle level (ρ =0.5), and high level (ρ=0.7), 3. sample sizes consisted of 30, 70, and 100 subject units, and 4. data were assigned missing at random (MAR) at the last occasion of measurement with missing rate of 5%, 10%, 20% and 30%, respectively. All possible combinations of these conditions gave rise a total of 72 different situations. Each defined situation was repeated 1,000 times by SAS programming and each missing value was replaced with a set of five plausible values that represent the uncertainty about the right value to impute under the MCMC method. The performance of each imputation method was evaluated using mean square error (MSE). The lower MSE would indicate the more effective method. The results from the simulation studies showed that the Copulas method was superior effective than other methods in all situations. The MCMC method was more effective than the simple mean imputation method when the correlation structure was AR1. For application, both imputation methods were applied with two datasets in practices: 1) waist circumference data on healthy project and 2) monthly rainfall data. The results also confirmed that the Copulas was the most effective method which was consistent with the simulation studies.
Teenagers, sex and contraception.

Since 1967 Planned Parenthood in San Francisco and Oakland has operated Teen Clinics which provide sex education, contraception, pregnancy and VD testing on a drop-in basis for girls under the age of 18.1 These centers have been enthusiastically received by the teenagers; they are attended by 2,400 new young people each year, mainly nulliparae, three out of four of whom come in for contraceptive care, the rest for pregnancy testing. If the pregnancy tests are positive, the young women are referred for abortion or prenatal care, whichever they decide is appropriate; if negative, they are offered contraceptive services. Such a group of sexually active young girls has rarely been isolated either for service or for study. They represent three quite distinct groups: contraceptors acting openly and realistically to prevent unwanted births; those seeking abortion referral; and those continuing their out-ofwedlock pregnancies to term. A study was undertaken to explore the sexual knowledge, attitudes and contraceptive practices of girls in each group and to elucidate the possible differences among them. Girls in the first two groups were attending Planned Parenthood's San Francisco or Oakland Teen Centers while girls in the third group were residents of two Bay Area maternity homes, the Florence Crittenton Home in San Francisco and the Booth Memorial Home of the Salvation Army in Oakland. * The study was conducted between November 1969 and July 1970, by means of an anonymous, self-administered questionnaire. All girls in the study were 17 years of age or younger and unwed. * The contraception group consisted of 210 consecutive never-pregnant new patients. * The abortion group consisted of 100 consecutive new patients seeking abortion counseling for a problem pregnancy.f * The maternity group consisted of 67 girls living at the two maternity homes. The questionnaire was given at six-week intervals over a five-month period to all new residents younger than 18 at these homes. The questionnaire asked 60 questions, to be answered with a check or short phrase, eliciting information on the girls' background characteristics, sexual knowledge and attitudes, and contraceptive use. It was usually completed in 20-35 minutes. The purposes of the questionnaire were explained to each respondent, individually or in a group. All new teenage patients arriving at Planned Parenthood during the study period were given the questionnaire, and only five percent failed to complete the form. It was given to each girl before she attended a discussion group, counseling session or medical examination. Girls at the two maternity homes were sampled each six weeks during the study period and, therefore, some girls had already had a substantial time in residence before answering. Background and Characteristics
The Effect of Tuberculosis Treatment at Combination Antiretroviral Therapy Initiation on Subsequent Mortality: A Systematic Review and Meta-Analysis

Objective We aimed to perform a systematic review and meta-analysis examining the impact of TB treatment at the time of combination antiretroviral therapy (cART) initiation on subsequent mortality. Methods We searched PubMed, EMBASE, and selected conference proceedings for studies that report adult mortality on cART, stratified by TB treatment status at cART initiation. Stratified random-effects and meta-regression analyses were used to examine the influence of study and population characteristics. Results 22 eligible cohort studies reported data on 98,350 (range 74-15,225) adults, of whom 14,779 (15%) were receiving TB treatment at cART initiation. Studies of those receiving vs. not receiving TB treatment had an average mortality relative risk of 1.10 (95% confidence interval 0.87-1.40) at 1-3 months (based upon 8 estimates), 1.15 (0.94-1.41) at 6-12 months (11 estimates), and 1.33 (1.02-1.75) at 18-98 months (10 estimates) following cART initiation. However, there was a wide range of estimates and those at later time points were markedly heterogeneous. Meta-regression identified factors associated with elevated average risk estimates: lower median baseline CD4 counts and adjustment for baseline hemoglobin at 1-3 months; longer length of follow-up and women-only studies at 6-12 months; and not adjusting for BMI/weight at 18-98 months. Conclusions Patients receiving TB treatment at cART initiation did not have a statistically significant estimated increase in short-term risk of all-cause mortality as compared to those not receiving TB treatment. TB treatment was significantly associated with increased mortality after about a year of cART, suggesting that patients with concurrent TB treatment at cART initiation may benefit from continued support after TB treatment completion.
ACE inhibition prevents Na and water retention and MABP increase during reduction of renal perfusion pressure.

Two groups of six dogs were studied during 4 control days and 4 days of reduced renal perfusion pressure (rRPP) servo controlled at 20% below the individual dog's 24-h mean arterial blood pressure (MABP) during control days, i.e., below the threshold for renin release. On rRPP days, endogenous activation of plasma aldosterone and angiotensin II was inhibited by the angiotensin-converting enzyme inhibitor captopril. The dogs were kept on a high-Na and high-water intake. Unlike studies during rRPP alone, there was no Na and water retention during rRPP+captopril. Glomerular filtration rate dropped by approximately 9%, and MABP remained in the range of control days. Plasma renin activity rose to values 14 times greater than control, whereas plasma aldosterone decreased by approximately 60%. Atrial natriuretic peptide remained in the range of controls. In conclusion, angiotensin-converting enzyme inhibition can prevent the otherwise obligatory Na and water retention and systemic MABP increase during a 20% reduction in renal perfusion pressure. This is achieved most likely via the captopril-induced fall in angiotensin II and plasma aldosterone levels.
Virtual Reality in Stroke Rehabilitation: A Meta-Analysis and Implications for Clinicians

Background and Purpose— Approximately two thirds of stroke survivors continue to experience motor deficits of the arm resulting in diminished quality of life. Conventional rehabilitation provides modest and sometimes delayed effects. Virtual reality (VR) technology is a novel adjunctive therapy that could be applied in neurorehabilitation. We performed a meta-analysis to determine the added benefit of VR technology on arm motor recovery after stroke. Methods— We searched Medline, EMBASE, and Cochrane literature from 1966 to July 2010 with the terms “stroke,” “virtual reality,” and “upper arm/extremity. ” We evaluated the effect of VR on motor function improvement after stroke. Results— From the 35 studies identified, 12 met the inclusion/exclusion criteria totaling 195 participants. Among them, there were 5 randomized clinical trials and 7 observational studies with a pre-/postintervention design. Interventions were delivered within 4 to 6 weeks in 9 of the studies and within 2 to 3 weeks in the remaining 3. Eleven of 12 studies showed a significant benefit toward VR for the selected outcomes. In the pooled analysis of all 5 randomized controlled trials, the effect of VR on motor impairment (Fugl-Meyer) was OR=4.89 (95% CI, 1.31 to 18.3). No significant difference was observed for Box and Block Test or motor function. Among observational studies, there was a 14.7% (95% CI, 8.7%–23.6%) improvement in motor impairment and a 20.1% (95% CI, 11.0%–33.8%) improvement in motor function after VR. Conclusions— VR and video game applications are novel and potentially useful technologies that can be combined with conventional rehabilitation for upper arm improvement after stroke.
Handbook of Magnetic Measurements

Introduction to Magnetic Measurements Fundamentals of Magnetic Measurements Historical Background Main Terms The Magnetization Process of Ferromagnetic Materials Anisotropy and Texture Electromagnetic Loss Influence of the Magnetic Field on Physical Properties of a Material Magnetic Resonance Superconductivity Used in Magnetic Measurements Main Rules of Magnetics The Physical Principles of Magnetism The Magnetic Hysteresis Sources of a Magnetic Field The Samples and Circuits of the Material under Test Magnetic Shielding Magnetic Materials Soft Magnetic Materials: General Information Silicon Iron Electrical Steel Nickel- and Cobalt-Based Alloys Amorphous and Nanocrystalline Alloys Soft Ferrites Hard Magnetic Materials Special Magnetic Materials Magnetic Sensors General Remarks Induction Sensors Fluxgate Sensors Magnetoresistive and Magnetoimpedance Sensors Hall-Effect Sensors Resonance Sensors SQUID Sensors Resonance Sensors and Magnetometers Other Magnetic Sensors Testing of Magnetic Materials AC Testing of Soft Magnetic Materials DC Testing of Soft Magnetic Materials Testing of Hard Magnetic Materials Special Methods of Testing of Magnetic Materials Magnetic Field Measurements and Their Applications Environment Magnetic Fields Applications of Magnetic Field Measurements Magnetic Diagnostics Index References appear at the end of each chapter.
Resisting the Urge to Smoke and Craving during a Smoking Quit Attempt on Varenicline: Results from a Pilot FMRI Study

Background: Varenicline has been shown to reduce cigarette craving during a quit attempt. Objectives: Use BOLD fMRI to explore differences in smoking cue reactivity at baseline and after five weeks of varenicline smoking cessation treatment. Methods: Treatment-seeking nicotine-dependent adult smokers underwent BOLD fMRI scans with block presentation of visual smoking, neutral, and rest cues under two conditions: craving or resisting the urge to smoke at baseline and following 5 weeks of standard varenicline therapy. Data were analyzed using FMRI Expert Analysis Tool, version 5.98 of Functional Magnetic Imaging of the Brain Software Library focused on the smoking vs. neutral cue contrast at the individual and group level, Z>2.3 with cluster threshold p=0.05. Results: Twenty-one participants were scanned at baseline and 16 completed the study; 10 were abstinent at the 2nd session, confirmed with urinary cotinine. In the Crave Condition no significant differences were found between the abstinent and non-abstinent groups at either time point. During the baseline Resist Condition, the abstinent group compared to the non-abstinent group demonstrated activation in a distributed network involved in alertness, learning and memory. Additionally, within the abstinent group, increased activation of the superior frontal gyrus was found at baseline compared to week 5. Conclusion: Successful smoking cessation with varenicline is associated with increased activation, prior to a quit attempt, in brain areas related to attentiveness and memory while resisting the urge to smoke Scientific Significance: Varenicline may exert effects by both reducing craving and enhancing resistance to smoking urges during cue-elicited craving.
FEBRILE NEUTROPENIA AS THE PRESENTING SIGN OF APPENDICITIS IN AN ADOLESCENT WITH ACUTE MYELOGENOUS LEUKEMIA

The diagnosis and management of a surgical abdomen in patients with acute leukemia is quite difficult because of the complications and treatment of disease itself. A 13-year-old boy with acute myelogenous leukemia developed 2 episodes of febrile neutropenia during induction therapy. The second one was treated with a 5-day course of parenteral antimicrobial therapy, but the patient then presented with right lower quadrant abdominal tenderness, guarding, and rebound tenderness. Abdominal ultrasonography and computed tomography revealed appendicitis. Conservative medical management was unsuccessful, and appendectomy was performed 5 days after appendicitis was diagnosed. The patient's clinical manifestations resolved 5 days later. The case illustrates that fever may be the first manifestation of appendicitis in a child with acute myelogenous leukaemia who is neutropenic. Surgery is acceptable as first-line treatment in such cases.
Nitrate reductases in Hydrogenobacter thermophilus with evolutionarily ancient features: distinctive localization and electron transfer

Dissimilatory nitrate reductase (NAR) and assimilatory nitrate reductase (NAS) serve as key enzymes for nitrogen catabolism and anabolism in many organisms. We purified NAR and NAS from H. thermophilus, a hydrogen‐oxidizing chemolithoautotroph belonging to the phylogenetically deepest branch in the Bacteria domain. Physiological contribution of these enzymes to nitrate respiration and assimilation was clarified by transcriptomic analysis and gene disruption experiments. These enzymes showed several features unreported in bacteria, such as the periplasmic orientation of NAR anchored with a putative transmembrane subunit and the specific electron transfer from a [4Fe‐4S]‐type ferredoxin to NAS. While some of their enzymatic properties are shared with NARs from archaea and with NASs from phototrophs, phylogenetic analysis indicated that H. thermophilus NAR and NAS have deep evolutionary origins that cannot be explained by a recent horizontal gene transfer event from archaea and phototrophs. These findings revealed the diversity of NAR and NAS in nonphotosynthetic bacteria, and they also implied that the outward orientation of NAR and the ferredoxin‐dependent electron transfer of NAS are evolutionarily ancient features preserved in H. thermophilus.