Miracle-dz/UniFAR-FTUs huggingface dataset:
Differing effects of IFN beta vs IFN gamma in MS: gene expression in cultured astrocytes.

BACKGROUND Recent clinical trials indicate that interferon-beta (IFN beta) is effective in reducing exacerbations in relapsing-remitting MS, whereas IFN gamma provokes acute relapses. However, the molecular mechanisms underlying the beneficial effects of IFN beta and the detrimental effects of IFN gamma in MS remain to be characterized. Previously, the authors showed that IFN beta inhibited IFN gamma-induced major histocompatibility complex (MHC) class II expression on astrocytes. OBJECTIVE To clarify the gene expression profile in cultured fetal human astrocytes after exposure to IFN beta, IFN gamma, or IFN beta plus IFN gamma. METHODS Astrocytes were incubated for 24 hours in the culture medium with or without inclusion of 50 ng/mL recombinant human IFN beta, IFN gamma, or both. The gene expression profile was studied by analyzing a cDNA expression array containing clones of various functional classes. RESULTS Among 1,185 clones examined, the expression of six distinct genes was markedly induced after IFN treatment. Northern blot analysis verified a significant up-regulation of mRNA for interferon regulatory factor-7 (IRF-7) and pleiotrophin predominantly in astrocytes treated with IFN beta, both IRF-1 and intercellular adhesion molecule-1 mRNA mainly in astrocytes treated with IFN gamma, and signal transducer and activator of transcription-1 alpha and MHC class I HLA-C mRNA equally in astrocytes exposed to either type of IFN. In contrast, the treatment of astrocytes with either IFN beta or IFN gamma did not alter the levels of expression of mRNA for brain-derived neurotrophic factor, 27-kd heat shock protein, prion protein, or defender against apoptotic cell death-1. No antagonistic action was observed between IFN beta and IFN gamma in the pattern of gene induction in astrocytes. CONCLUSION A preferential induction of IRF-7 in IFN beta-treated astrocytes and a predominant expression of IRF-1 in IFN gamma-exposed astrocytes might contribute to one of the molecular mechanisms underlying the clinically opposite effects of IFN beta and IFN gamma in MS.
Optimized digital counting colonies of clonogenic assays using ImageJ software and customized macros: Comparison with manual counting

Abstract Purpose: To develop a digital method for counting colonies that highly replicates manual counting. Materials and methods: Breast cancer cells were treated with trastuzumab-conjugated gold nanoparticles in combination with X-ray irradiation, 111In labeled trastuzumab, or γ-radiation, followed by clonogenic assays. Colonies were counted manually or digitally using ImageJ software with customized macros. Key parameters, intensity threshold and minimum colony size, were optimized based on three preliminary manual counts or blindly chosen. The correlation of digital and manual counting and inter- and intra-experimenter variability were examined by linear regression. Survival curves derived from digital and manual counts were compared by F-test (P < 0.05). Results: Using optimized parameters, digital counts corresponded linearly to manual counts with slope (S) and R2 value close to 1 and a small y-intercept (y0): SK-BR-3 (S = 0.96 ± 0.02, R2 = 0.969, y0 = 5.9 ± 2.2), MCF-7/HER2-18 (S = 0.98 ± 0.03, R2 = 0.952, y0 = 0.74 ± 0.47), and MDA-MB-231 cells (S = 1.00 ± 0.02, R2 = 0.995, y0 = 3.3 ± 4.5). Both reproducibility and repeatability of digital counts were better than the manual method. Survival curves generated from digital and manual counts were not significantly different; P-values were 0.3646 for SK-BR-3 cells and 0.1818 for MCF-7/HER2-18 cells. Using blind parameters, survival curves generated by both methods showed some differences: P-values were 0.0897 for SK-BR-3 cells and 0.0024 for MCF-7/HER2-18 cells. Conclusions: The colony counting using ImageJ and customized macros with optimized parameters was a reliable method for quantifying the number of colonies.
Vascular rings: a rare cause of common respiratory symptoms

Upper airway symptoms or dysphagia may be caused by vascular anomalies, forming a ring around the trachea, oesophagus or both. To analyse the clinical presentation, use of various diagnostic techniques, treatment and follow‐up we carried out a retrospective study of 38 children who had been diagnosed with a vascular ring between 1981 and 1996. We found 74% of the vascular rings to be symptomatic, with inspiratory stridor and wheezing as the main complaints. The delay between the onset of symptoms and diagnosis of a vascular ring in patients without associated anomalies ranged from 1 to 84 mo. Associated anomalies were found in 53% of cases and 80% of these anomalies consisted of associated cardiovascular malformations. Oesophagography proved to be a valuable diagnostic technique when a vascular ring was suspected. Echocardiography appeared to be of little value for the diagnosis of a vascular ring, but was essential to exclude associated cardiovascular malformations. Although angiography has always been considered to be the gold standard in the determination of the exact anatomy of vascular rings, increasing evidence is available that CT scan or MRI may replace this role. Mortality was related to co‐existent tracheal deformities in 5/6 cases. Of the remaining, preoperatively symptomatic patients, relief of symptoms was achieved immediately after surgery in 43% and within 4 y after surgery in 57%. Prolonged and recurrent respiratory complaints or dysphagia in infancy or childhood should alert the paediatrician to the possibility of a vascular ring. □Associated cardiovascular malformations, childhood, clinical presentation, diagnostic techniques, follow‐up, surgical management, vascular ring
First Principles Simulations of Nanoscale Silicon Devices With Uniaxial Strain

We report parameter-free first principle atomistic simulations of quantum transport in Si nanochannels under uniaxial strain. Our model is based on the density functional theory (DFT) analysis within the Keldysh nonequilibrium Green's function (NEGF) formalism. By employing a recently proposed semi-local exchange along with the coherent potential approximation we investigate the transport properties of two-terminal Si nanodevices composed of large number of atoms and atomic dopants. Simulations of the two-terminal device based on the NEGF-DFT are compared quantitatively with the traditional continuum model to establish an important accuracy benchmark. For bulk Si crystals, we calculated the effects of uniaxial strain on band edges and effective masses. For two-terminal Si nanochannels with their channel length of ~ 10 nm, we study the effects of uniaxial strain on the electron transport. With 0.5% uniaxial tensile strain, the conductance along [110] direction is increased by ~ 8% and that along [001] is increased by ~ 2%, which are comparable with the other reported results. This paper qualitatively and quantitatively shows the current capability of first principle atomistic simulations of nanoscale semiconductor devices.
A novel ripple-based constant on-time control with virtual inductor current ripple for Buck converter with ceramic output capacitors

Ripple-based constant on-time (RBCOT) control has found applications because of its fast load transient response, small component count, and good light-load efficiency. However, this control scheme often encounters instability issue of subharmonic oscillation when ceramic capacitors are used for converter output filter capacitors. In the paper, a novel RBCOT control with virtual inductor current ripple was proposed to alleviate this problem. The novel control scheme improves system stability of RBCOT control without adding extra pins and converter components in IC implementation. Thus resulting in less component count and controller cost. Describing function method was used to derive the model and stability criterion of the proposed scheme, including the effect of delay-time. The scheme was implemented in an IC. Simulation and experimental results also confirm the proposed concept and the accuracy of the stability criterion developed.
Development and Evaluation of a Genus-Specific, Probe-Based, Internal-Process-Controlled Real-Time PCR Assay for Sensitive and Specific Detection of Blastocystis spp

ABSTRACT Blastocystis is a common intestinal parasite of unsettled clinical significance, which is not easily detected by standard parasitological methods. The genus comprises at least 13 subtypes (STs) (which likely represent separate species), 9 of which have been found in humans. Recent data indicate that at least one of the subtypes is associated with intestinal disease. A quantitative TaqMan 5′ nuclease real-time PCR (TaqMan PCR) including an internal process control (IPC) was developed for the detection of Blastocystis and shown to be applicable to genomic DNAs extracted directly from feces. The assay enabled successful amplification of DNAs from all relevant subtypes within the genus (ST1 to ST9). For assay evaluation, 153 samples previously tested by xenic in vitro culture (XIVC) were screened by the TaqMan assay. A total of 49/51 samples positive by XIVC and 13/102 samples negative by XIVC were positive by the TaqMan assay; samples positive by the TaqMan assay and negative by XIVC were subsequently tested by conventional PCR, and amplicons could be identified to the subtype level by sequencing in 69% of the cases. Compared to the TaqMan assay, XIVC had a sensitivity of 79%. This is the first time that a genus-specific, probe-based, internal-process-controlled real-time PCR assay for the detection Blastocystis has been introduced.
Effects of spinal cord lesion level upon thermoregulation during exercise in the heat.

PURPOSE This study examined the effects of the level of spinal cord injury upon the thermoregulatory responses of wheelchair athletes during prolonged wheelchair exercise in warm conditions. METHODS Eight tetraplegic (TP), 10 high-level paraplegic (HP), and 10 low-level paraplegic (LP) athletes exercised for 60 min at 60% [OV0312]O(2peak) in a warm environment (31.5 +/- 1.7 degrees C, 42.9 +/- 8.0% relative humidity). Skin temperature and aural temperature were monitored. RESULTS Aural temperature increased gradually during the exercise period by 1.1 +/- 0.3 and 1.4 +/- 0.5 degrees C for the HP and LP groups, with a more marked increase observed for the TP group (2.1 +/- 0.5 degrees C; P < 0.05). Upper-arm skin temperature was higher for the TP when compared with the HP and LP between 30 and 60 min (P < 0.05). Back skin temperature was higher for the TP when compared with the HP and LP between 45 and 60 min (P < 0.05). No differences were noted between groups for the thigh or calf skin temperatures. During recovery, skin temperature remained elevated for the TP group when compared with the HP and LP groups (P < 0.05). Heat storage was greatest for the TP athletes at the end of exercise and remained elevated throughout recovery (P < 0.05). CONCLUSIONS All athletes completed the exercise task even though the gradual increase in aural temperature observed for the HP and LP groups suggests a degree of thermal imbalance. However, this was much less than observed for TP athletes, who demonstrated a much greater imbalance in temperature regulation. Increasing the exercise or environmental strain may result in the thermoregulatory responses of athletes with a spinal cord injury being compromised.
Age‐related influences on the clinical characteristics of new‐onset hallucinations in Parkinson's disease patients

The objective of this study was to determine the demographic influences on the sensory characteristics (pure visual vs. nonvisual or mixed visual/nonvisual) of new‐onset hallucinations in Parkinson's disease (PD). We utilized 6‐year longitudinal interview data from 60 PD patients who had never hallucinated at baseline and reinterviewed them at 6, 18, 48, and 72 months to assess the presence and type of hallucination that developed as the first form of hallucination. We analyzed data by Generalized Estimating Equations methods and by nonparametric tests. Over 6 years, 37 of 60 patients developed hallucinations, and the first hallucinations were pure visual in 18, pure nonvisual in 9, and mixed visual/nonvisual in 10. At the time of first onset of hallucinations, patients whose hallucinations were nonvisual or mixed were significantly older than those with purely visual hallucinations (mean age, 69.8 ± 8.3 vs. 61.9 ± 10.6; P = 0.031). PD duration in the two groups, however, was statistically comparable (9.6 ± 4.4 vs. 12.9 ± 8.6 years). Though classically described as visual, hallucinations in PD frequently involve other sensory modalities. Age‐related disinhibition may facilitate wider cortical activation in PD and potentiate aberrant signaling that invokes other types of hallucinations besides the classic visual forms. © 2005 Movement Disorder Society
Reproducibility of coronary arteriographic reading in the coronary artery surgery study (CASS).

Eight hundred seventy arteriograms from the Coronary Artery Surgery Study (CASS) were independently read by readers at two different clinics to evaluate the reproducibility of the interpretation of coronary arteriograms. Among proximal segments, the interpretation of lesions of the left main coronary artery were the least reproducible, P less than . 02. When one angiographer reads a stenosis of 50% or more in the left main coronary artery, it is estimated that a second reader will report no lesion 18.6% of the time. In 94.7% of the films, the number of significantly (greater than or equal to 70% stenosis) diseased vessels was the same for both readers (72.1%) or differed by one vessel (22.6%). The reproducibility of interpretation of films of good or acceptable quality or completeness was better than the reproducibility of readings of arteriograms judged to be of poor quality or incomplete studies. The mean absolute difference between readings of the percent stenosis decreased over the time of the patient enrollment, 1975 to 1978. This may have resulted from major collaborative efforts made during the course of the study to improve the quality of angiography and to standardize the reading of the cine films.
Pretreatment clinical and psychosocial predictors of remission from depression after short-term psychodynamic psychotherapy and solution-focused therapy: a 1-year follow-up study

Abstract The mutual importance of different predictors of remission was studied in 163 outpatients with depression receiving either short-term psychodynamic psychotherapy or solution-focused therapy. After a 1-year follow-up, the percentage of remission significantly varied between sociodemographic subgroups and was dependent on severity of symptoms, personality disorder, and psychosocial factors but not on psychiatric history, previous psychiatric treatment, or type of therapy received. Simultaneous study showed that the most significant predictors were sense of coherence (based on Sense of Coherence Scale [SOCS]), symptom severity (based on Symptom Checklist-90 [SCL-90] Global Severity Index [GSI]), and education. The relative risks of remission between the lowest and highest quartiles of SOCS and SCL-90 GSI were 0.06 and 0.22 (95% confidence intervals = 0.01–0.35 and 0.05–0.97), respectively. In conclusion, several background factors, especially sense of coherence, predict remission.
The Oxidative Processes Induced in Cell Suspensions of Solanum Species by Culture Filtrate of Phytophthora infestans

Abstract Solanum genotypes that differ in the level of polygenic resistance to the oomycete plant pathogen Phytophthora infestans were studied for their oxidative response to culture filtrate (CF) of the pathogen. Reactive oxygen species (ROS) production, peroxidase activity and lipid peroxidation have been studied in the CF-treated cell suspensions derived from leaves of the resistant S. nigrum (nonhost) and 5. tuberosum cv. Bzura as well as from the susceptible S. tuberosum cv. Tarpan and clone H-8105. In both the resistant and susceptible cells the CF induced similar processes, but these varied with respect to the kinetics and intensity. In all cells probably the membrane-bound NADPH oxidase, was responsible for the ROS production. This process was more intensive and prolonged in the susceptible cells than in the resistant ones. The CF treatment slightly affected peroxidase activity in all cells studied. Lipid peroxidation that occurred as a consequence of the ROS accumulation was pronounced mainly in the susceptible cells. We suggest that lack of stringent control of the oxidative processes and sensitivity to the pathogen toxins may be decisive for limited polygenic resistance in potato.
PhoE signal peptide inserts into micelles as a dynamic helix-break-helix structure, which is modulated by the environment. A two-dimensional 1H NMR study.

Proteins that are destined for export out of the cytoplasm of Escherichia coli cells are synthesized as precursor proteins with N-terminal extensions or signal sequences, which are essential for translocation of the protein across the inner membrane. Signal sequences contain very little primary sequence homology, and therefore recognition of these sequences is thought to involve specific folding. To assess the conformational flexibility of signal sequences, we have studied the signal peptide of PhoE (MKKSTLALVVMGIVASASVQA) by two-dimensional nuclear magnetic resonance and circular dichroism in different membrane mimetic environments. The secondary structure of the PhoE signal peptide was analyzed via interresidue nuclear Overhauser enhancement measurements, chemical shifts of backbone protons, and by measuring amide proton exchange. The membrane mimetic environments studied were trifluoroethanol (TFE) and micelles of sodium dodecyl sulfate (SDS) or dodecylphosphocholine (DPC). In all systems alpha-helix formation was observed. In TFE, the alpha-helix stretches from the positively charged N-terminus to Ser18. In SDS and DPC micelles, the N- and C-terminal alpha-helical half are separated from each other by a kink at the Gly12 position, with the helical content being higher at the N-terminus and lower at the C-terminus. In zwitterionic DPC micelles, the C-terminal region has a less regular or more flexible structure compared to SDS. The insertion of the PhoE signal peptide into the hydrophobic environment of the micelles was demonstrated by the effect of spin-labeled 12-doxylstearate on the line widths of the peptide proton resonances. (ABSTRACT TRUNCATED AT 250 WORDS)
UPLC-MS/MS Profile of Alkaloids with Cytotoxic Properties of Selected Medicinal Plants of the Berberidaceae and Papaveraceae Families

Cancer is one of the most occurring diseases in developed and developing countries. Plant-based compounds are still researched for their anticancer activity and for their quantity in plants. Therefore, the modern chromatographic methods are applied to quantify them in plants, for example, UPLC-MS/MS (ultraperformance liquid chromatography tandem mass spectrometry). Therefore, the aim of the present study was to evaluate the content of sanguinarine, berberine, protopine, and chelidonine in Dicentra spectabilis (L.) Lem. , Fumaria officinalis L. , Glaucium flavum Crantz, Corydalis cava L. , Berberis thunbergii DC. , Meconopsis cambrica (L.) Vig. , Mahonia aquifolium (Pursh) Nutt. , Macleaya cordata Willd. , and Chelidonium majus L. For the first time, N,N-dimethyl-hernovine was identified in M. cambrica, B. thunbergii, M. aquifolium, C. cava, G. flavum, and C. majus; methyl-hernovine was identified in G. flavum; columbamine was identified in B. thunbergii; and methyl-corypalmine, chelidonine, and sanguinarine were identified in F. officinalis L. The richest source of protopine among all the examined species was M. cordata (5463.64 ± 26.3 μg/g). The highest amounts of chelidonine and sanguinarine were found in C. majus (51,040.0 ± 1.8 μg/g and 7925.8 ± 3.3 μg/g, resp.), while B. thunbergi contained the highest amount of berberine (6358.4 ± 4.2 μg/g).
Tinea faciei incognito due to Trichophyton rubrum as a result of autoinoculation from onychomycosis

The localisation of a dermatophytosis on the face is rare. Differential diagnoses include a broad range of dermatological disorders, e. g. contact dermatitis, psoriasis vulgaris, seborrhoeic dermatitis, demodicosis, and polymorphic photo eruptions. Two patients suffering from tinea faciei incognito caused by Trichophyton rubrum are presented. Diagnosis was based on mycological diagnostics of skin scrapings using Calcofluor preparation and cultivation of the causative dermatophyte. Both patients were suffering from tinea pedis and tinea unguium caused by the same dermatophyte species. An infection caused by Trichophyton rubrum of the face always occurs following autoinoculation from a pre‐existing tinea pedis and tinea unguium of feet and toenails, sometimes of the fingernails.
Bidirectional plasticity in the primate inferior olive induced by chronic ethanol intoxication and sustained abstinence

The brain adapts to chronic ethanol intoxication by altering synaptic and ion-channel function to increase excitability, a homeostatic counterbalance to inhibition by alcohol. Delirium tremens occurs when those adaptations are unmasked during withdrawal, but little is known about whether the primate brain returns to normal with repeated bouts of ethanol abuse and abstinence. Here, we show a form of bidirectional plasticity of pacemaking currents induced by chronic heavy drinking within the inferior olive of cynomolgus monkeys. Intracellular recordings of inferior olive neurons demonstrated that ethanol inhibited the tail current triggered by release from hyperpolarization (Itail). Both the slow deactivation of hyperpolarization-activated cyclic nucleotide-gated channels conducting the hyperpolarization-activated inward current and the activation of Cav3.1 channels conducting the T-type calcium current (IT) contributed to Itail, but ethanol inhibited only the IT component of Itail. Recordings of inferior olive neurons obtained from chronically intoxicated monkeys revealed a significant up-regulation in Itail that was induced by 1 y of daily ethanol self-administration. The up-regulation was caused by a specific increase in IT which (i) greatly increased neurons’ susceptibility for rebound excitation following hyperpolarization and (ii) may have accounted for intention tremors observed during ethanol withdrawal. In another set of monkeys, sustained abstinence produced the opposite effects: (i) a reduction in rebound excitability and (ii) a down-regulation of Itail caused by the down-regulation of both the hyperpolarization-activated inward current and IT. Bidirectional plasticity of two hyperpolarization-sensitive currents following chronic ethanol abuse and abstinence may underlie persistent brain dysfunction in primates and be a target for therapy.
Ureaplasma urealyticum in a neonatal intensive care population

The incidence of Ureaplasma colonization at birth and its effect on the development of chronic lung disease (CLD) and on mortality was studied in a neonatal intensive care population. Ureaplasma colonization was associated with a birthweight < 1000 g (odds ratio [OR] 3.45 confidence intervals [CI] 2.13‐5.60) and a gestational age < 30 weeks (OR 2.54 CI 1.71–3.79). In a case‐controlled study of 112 infants, significant associations with Ureaplasma colonization were maternal pyrexia in labour (n= 38 vs 21; P= 0.015), the requirement for antibiotics in labour (n= 39 vs 16; P= 0.0005) and vaginal delivery (n= 78 vs 58; P= 0.009). Risk factors associated with the development of CLD were birthweight < 1000 g (OR 3.77 CI 2.53–5.62) and delivery by Caesarean section (OR 1.65 CI 1.11–2.43). Within the group delivered by Caesarean section. Ureaplasma colonization was also associated with an increased risk of CLD (OR 1.97 CI 1.08–3.62). Ureaplasma colonization of infants at birth is associated with factors suggestive of maternal chorioamnionitis as well as preterm birth and low birthweight. In infants delivered by Caesarean section, Ureaplasma colonization is associated with an increased risk of chronic lung disease.