Miracle-dz/UniFAR-FTUs huggingface dataset:
NMR structure and dynamics of human ephrin‐B2 ectodomain: The functionally critical C‐D and G‐H loops are highly dynamic in solution

Eph receptors and ephrins constitute the largest family of receptor tyrosine kinases with 15 individual receptors and nine ligands. Its ectodomains represent attractive targets not only for understanding fundamental mechanisms underlying axon guidance, cell migration, segmentation, tumorigenesis, and bone remodeling, but also for drug screening/design to treat cancers, bone diseases and viral infection. So far no NMR study on the ephrin ectodomains is available and as such their properties in solution still remain unknown. In this study, we presented the first NMR structure and dynamics of the human ephrin‐B2 ectodomain as well as its interaction with the receptor EphB2. Strikingly, the NMR study reveals a picture different from those previously obtained by X‐ray crystallography. Although in solution it still adopts the same Greek key fold, with the central β‐barrel (∼30% of the molecule) highly similar to that in crystal structures, the other regions are highly dynamic and accessible to the bulk solvent. In particular, the functionally critical C‐D and G‐H loops of the ephrin‐B2 ectodomain are highly flexible as reflected by several NMR probes including hydrogen exchange and 15N backbone relaxation data. Nevertheless, as revealed by ITC and NMR, the ephrin‐B2 ectodomain binds to EphB2 with a Kd of 22.3 nM to form a tight complex in which the tip of the C‐D loop and the C‐terminus still remain largely flexible. The present results may bear critical implications in understanding the molecular details as well as designing antagonists of therapeutic interest for Eph‐ephrin interactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Human umbilical cord mesenchymal stem cells promote peripheral nerve repair via paracrine mechanisms

Human umbilical cord-derived mesenchymal stem cells (hUCMSCs) represent a promising young-state stem cell source for cell-based therapy. hUCMSC transplantation into the transected sciatic nerve promotes axonal regeneration and functional recovery. To further clarify the paracrine effects of hUCMSCs on nerve regeneration, we performed human cytokine antibody array analysis, which revealed that hUCMSCs express 14 important neurotrophic factors. Enzyme-linked immunosorbent assay and immunohistochemistry showed that brain-derived neurotrophic factor, glial-derived neurotrophic factor, hepatocyte growth factor, neurotrophin-3, basic fibroblast growth factor, type I collagen, fibronectin and laminin were highly expressed. Treatment with hUCMSC-conditioned medium enhanced Schwann cell viability and proliferation, increased nerve growth factor and brain-derived neurotrophic factor expression in Schwann cells, and enhanced neurite growth from dorsal root ganglion explants. These findings suggest that paracrine action may be a key mechanism underlying the effects of hUCMSCs in peripheral nerve repair.
Antihypertensive treatment of acute cerebral hemorrhage*

Objective: To determine the feasibility and acute (i.e., within 72 hrs) safety of three levels of systolic blood pressure reduction in subjects with supratentorial intracerebral hemorrhage treated within 6 hrs after symptom onset. Design: A traditional phase I, dose-escalation, multicenter prospective study. Settings: Emergency departments and intensive care units. Patients: Patients with intracerebral hemorrhage with elevated systolic blood pressure ≥170 mm Hg who present to the emergency department within 6 hrs of symptom onset. Intervention: Intravenous nicardipine to reduce systolic blood pressure to a target of: (1) 170 to 200 mm Hg in the first cohort of patients; (2) 140 to 170 mm Hg in the second cohort; and (3) 110 to 140 mm Hg in the third cohort. Measurements and Main Results: Primary outcomes of interest were: (1) treatment feasibility (achieving and maintaining the systolic blood pressure goals for 18–24 hrs); (2) neurologic deterioration within 24 hrs; and (3) serious adverse events within 72 hrs. Safety stopping rules based on neurologic deterioration and serious adverse events were prespecified and approved by an NIH-appointed Data and Safety Monitoring Board, which provided oversight on subject safety. Each subject was followed-up for 3 months to preliminarily assess mortality and the clinical outcomes. A total of 18, 20, and 22 patients were enrolled in the respective three tiers of systolic blood pressure treatment goals. Overall, 9 of 60 patients had treatment failures (all in the last tier). A total of seven subjects with neurologic deterioration were observed: one (6%), two (10%), and four (18%) in tier one, two, and three, respectively. Serious adverse events were observed in one subject (5%) in tier two and in three subjects (14%) in tier three. However, the safety stopping rule was not activated in any of the tiers. Three (17%), two (10%), and five (23%) subjects in tiers one, two, and three, respectively, died within 3 months. Conclusions: The observed proportions of neurologic deterioration and serious adverse events were below the prespecified safety thresholds, and the 3-month mortality rate was lower than expected in all systolic blood pressure tiers. The results form the basis of a larger randomized trial addressing the efficacy of systolic blood pressure reduction in patients with intracerebral hemorrhage.
Scrapie PrP 27-30 is a sialoglycoprotein

The major scrapie prion protein, designated PrP 27-30, exhibited both charge and size heterogeneity after purification from infected hamster brains. Eight or more discrete charge isomers of PrP 27-30 with isoelectric points ranging from approximately pH 4.6 to 7.9 were found by using non-equilibrium pH gradient electrophoresis in the first dimension followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. The charge isomers were detected by silver staining as well as by radioiodination. The procedures used to disaggregate PrP 27-30 before electrophoresis in the first dimension do not appear to be responsible for the charge heterogeneity. However, heating PrP 27-30 to 100 degrees C for 15 min in 0.1 N NaOH or 0.1 N HCl resulted in modification of the protein and alteration of its electrophoretic pattern. A PrP 27-30 fragment (molecular weight, 17,100 to 21,900) obtained by cyanogen bromide cleavage also exhibited charge and size heterogeneity. Periodic acid-Schiff staining of PrP 27-30 electrophoresed into sodium dodecyl sulfate-polyacrylamide gels demonstrated that carbohydrate residues are attached to the protein. Digestion of PrP 27-30 with neuraminidase and endo-beta-N-acetylglucosaminidase H resulted in significant changes in the isoelectric pH of PrP 27-30 isomers, whereas digestion with alkaline phosphatase had no effect. Our results demonstrate that PrP 27-30 is a sialoglycoprotein; this is consistent with several properties of this protein and of the scrapie prion.
Urocortin 2 autocrine/paracrine and pharmacologic effects to activate AMP-activated protein kinase in the heart

Urocortin 2 (Ucn2), a peptide of the corticotropin-releasing factor (CRF) family, binds with high affinity to type 2 CRF receptors (CRFR2) on cardiomyocytes and confers protection against ischemia/reperfusion. The mechanisms by which the Ucn2-CRFR2 axis mitigates against ischemia/reperfusion injury remain incompletely delineated. Activation of AMP-activated protein kinase (AMPK) also limits cardiac damage during ischemia/reperfusion. AMPK is classically activated by alterations in cellular energetics; however, hormones, cytokines, and additional autocrine/paracrine factors also modulate its activity. We examined the effects of both the endogenous cardiac Ucn2 autocrine/paracrine pathway and Ucn2 treatment on AMPK regulation. Ucn2 treatment increased AMPK activation and downstream acetyl-CoA carboxylase phosphorylation and glucose uptake in isolated heart muscles. These actions were blocked by the CRFR2 antagonist anti–sauvagine-30 and by a PKCε translocation-inhibitor peptide (εV1-2). Hypoxia-induced AMPK activation was also blunted in heart muscles by preincubation with either anti–sauvagine-30, a neutralizing anti-Ucn2 antibody, or εV1-2. Treatment with Ucn2 in vivo augmented ischemic AMPK activation and reduced myocardial injury and cardiac contractile dysfunction after regional ischemia/reperfusion in mice. Ucn2 also directly activated AMPK in ex vivo-perfused mouse hearts and diminished injury and contractile dysfunction during ischemia/reperfusion. Thus, both Ucn2 treatment and the endogenous cardiac Ucn2 autocrine/paracrine pathway activate AMPK signaling pathway, via a PKCε-dependent mechanism, defining a Ucn2-CRFR2-PKCε-AMPK pathway that mitigates against ischemia/reperfusion injury.
The validity of the session-RPE method for quantifying training load in water polo.

CONTEXT The assessment of internal training load (ITL) using the session rating of perceived exertion (session RPE) has been demonstrated to provide valuable information, also in team sports. Nevertheless, no studies have investigated the use of this method during youth water polo training. PURPOSE To evaluate youth water polo training, showing the corresponding level of reliability of the session-RPE method. METHODS Thirteen male youth water polo players (age 15.6 ± 0.5 y, height 1.80 ± 0.06 m, body mass 72.7 ± 7.8 kg) were monitored during 8 training sessions (80 individual training sessions) over 10 d. The Edwards summated heart-rate-zone method was used as a reference measure of ITL; the session-RPE rating was obtained using CR-10 scale modified by Foster. The Pearson product-moment was applied to regress the Edwards heart-rate-zone method against CR-10 session RPE for each training session and individual data. RESULTS Analyses reported overall high (r = .88, R(2) = . 78) and significant (P < .001) correlations between the Edwards heart-rate and session-RPE methods. Significant correlations were also shown for each training session (r range .69-.92, R(2) range . 48-. 85, P < . 05) and individual data (r range .76-.98, R(2) range . 58-. 97, P < . 05). DISCUSSION The results confirmed that the session-RPE method as an easy and reliable tool to evaluate ITL in youth water polo, allowing coaches to efficiently monitor their training plans.
Decrease in muscle glucose transporter number in chronic physical inactivity in rats.

In this study, whole body insulin action on glucose uptake and muscle glucose transporter number of rats subjected to 14 days of physical inactivity conditions was examined. Unlike other suspension and denervation models of muscle disuse, this physical inactivity model allows voluntary contractile activity with minimal stress. Minimal depression of body weight gain and significant depression of gastrocnemius muscle growth were observed compared with that of control rats after 14 days of physical inactivity. The whole body insulin sensitivity and responsiveness were determined by the euglycemic clamp technique, with 1.4, 3.6, and 14 mU insulin.kg-1.min-1 perfusion and 2-deoxy-D-[3H]glucose incorporation. The rates of glucose disposal were the same in the restrained rats as in the controls with the 1.4 and 3.6 mU insulin perfusion; however, glucose disposal significantly decreased with 14 mU insulin perfusion. 2-Deoxy-D-[3H]glucose uptake into the gastrocnemius muscle was higher in the control rats than in the physically inactive rats. Glucose transporters in the gastrocnemius and quadriceps muscles, measured by means of the D-glucose-inhibitable cytochalasin B binding assay, were significantly decreased in number in the physically inactive rats. These findings suggest that the decrease in whole body glucose uptake might in part be explained by the decreases in the total glucose transporter number in muscles.
Assessment of the Kinetics of Treponema pallidum Dissemination into Blood and Tissues in Experimental Syphilis by Real-Time Quantitative PCR

ABSTRACT Little is known about the size and kinetics of treponemal burdens in blood and tissues during acquired or experimental syphilitic infection. We used real-time quantitative PCR to measure Treponema pallidum DNA levels in rabbits infected intratesticularly with the prototype Nichols strain. At the outset, we performed a series of in vitro blood spiking experiments to determine the effect of blood processing procedures on the distribution of treponemes in various blood components. T. pallidum DNA levels in plasma and whole blood were approximately 10-fold higher than those in serum and more than 200-fold greater than those in peripheral blood mononuclear cells (PBMCs). Ten rabbits were inoculated intratesticularly with doses of treponemes ranging from 4 × 107 to 2 × 108 organisms. In five rabbits, T. pallidum DNA levels were measured sequentially in serum, plasma, whole blood, and PBMCs until sacrifice at peak orchitis, at which time brain, kidney, liver, spleen, and testicles were harvested; blood and organs were also harvested at orchitis from the other five rabbits. T. pallidum DNA was detected in plasma within 24 h postinfection. Treponeme levels in whole blood and blood components increased significantly with the development of peak orchitis. Overall, levels in serum and PBMCs were lower than those in plasma and whole blood; this disparity was particularly marked at early time points. Significantly greater numbers of spirochetes were found in the spleen than in liver, kidney, or brain tissue at the time of sacrifice. Our findings highlight the remarkable capacity of T. pallidum to disseminate from the site of infection to blood and tissues, and they identify the spleen as a prime target for treponemal invasion.
Response acceleration with mirtazapine augmentation of citalopram in obsessive-compulsive disorder patients without comorbid depression: a pilot study.

BACKGROUND Therapeutic action of selective serotonin reuptake inhibitors (SSRIs) is delayed from 8 to 12 weeks in patients with obsessive-compulsive disorder (OCD). Several different agents have been tested to reduce the SSRI therapeutic latency time. Mirtazapine, an antagonist at alpha2-adrenoceptors, does not enhance serotonin (5-HT) neurotransmission directly but disinhibits the norepinephrine activation of 5-HT neurons and thereby increases 5-HT neurotransmission by a mechanism that may not require a time-dependent desensitization of receptors. The present study was undertaken to determine whether the mirtazapine-citalopram combination could induce an earlier and/or greater effect on the 5-HT system in OCD subjects than citalopram alone. METHOD Forty-nine patients with OCD (DSM-IV) without comorbid depression were randomly assigned to a 2-tailed, single-blind, 12-week clinical trial with citalopram (20-80 mg/day) plus placebo or citalopram plus mirtazapine (15-30 mg/day). Assessments were performed weekly with the Yale-Brown Obsessive Compulsive Scale (YBOCS), the Hamilton Rating Scale for Depression, and the Clinical Global Impressions scale. Data were collected from November 2001 to July 2003. RESULTS The citalopram plus mirtazapine group achieved a reduction of at least 35% in YBOCS score and a "much improved" or "very much improved" rating on the Clinical Global Impressions-Improvement scale from the fourth week, while the citalopram plus placebo group obtained these results only from the eighth week. The number of responders was higher in the citalopram plus mirtazapine group at the fourth week of treatment, while no difference between groups in the response rate was noted at the eighth and twelfth weeks of treatment. CONCLUSIONS We found an earlier onset of response action in OCD symptoms and reduced undesired side effects when mirtazapine was added to citalopram. This augmentation strategy deserves clinical and research consideration through further double-blind, placebo-controlled studies.
Risk factors for invasive aspergillosis in living donor liver transplant recipients

Invasive aspergillosis (IA) is a severe complication of liver transplantation. Risk factors for IA after deceased donor liver transplantation (DDLT) have been presented in several reports, but are not well established for living donor liver transplant recipients. Here, a retrospective case‐control study was performed. Five cases with IA were investigated after living donor liver transplantation (LDLT) between January 1999 and December 2002 at Kyoto University Hospital. For comparison, living donor liver transplant recipients without IA were taken as controls. These patients had undergone LDLT 1 month before or after each IA case and had the same survival times as the latter. We evaluated the clinical and laboratory findings for both groups up until their demise. Patients with IA after LDLT had a very poor prognosis. By univariate analysis, risk factors for IA were preoperative intensive care unit stay (P = 0.02) and preoperative steroid administration (P = 0.02). Preoperative steroid administration for fulminant hepatitis possibly predisposed to the development of IA after LDLT. Liver Transpl 13:566–570, 2007. © 2007 AASLD.
TWO MODIFIED RNA EXTRACTION METHODS COMPATIBLE WITH TRANSCRIPT PROFILING AND GENE EXPRESSION ANALYSIS FOR COTTON ROOTS

Efficient isolation of high-quality RNA is of prime importance for optimal transcript profiling results and further gene expression analysis. However, it is difficult for cotton roots because of lower-than-average RNA content and high content of polysaccharides, polyphenols, and other secondary metabolites. To develop simple and reliable protocols for high-quality RNA extraction from cotton roots for transcript profiling and gene expression analysis, some modifications were introduced to a reported plant RNA isolation protocol and a reagent kit method. Using method A, we successfully extracted high-quality RNA for transcript profiling from cotton roots. Gel electrophoresis analysis and polymerase chain reaction (PCR) assay indicated that RNA had good integrity without protein and genomic DNA contamination. Furthermore, the A260/280 (1.9) and A260/230 (1.6) ratios indicated that the isolated RNA was of high purity. Using method B, about 7 µg total RNA of high quality could be obtained from 0.1 g samples from cotton roots, which can be used for reverse-transcription (RT)-PCR and quantitative real-time RT-PCR. The two RNA extraction methods were used to investigate different gene expression of cotton roots (Gossypium hirsutum) infected by weak pathogenic Verticillium dahliae and the results showed they can satisfy the transcript profiling and quantitative real-time RT-PCR requirements for RNA. Supplemental materials are available for this article. Go to the publisher's online edition of Preparative Biochemistry and Biotechnology to view the supplemental file.
Randomized clinical trial of lifestyle interventions in Pima Indians: a pilot study

A pilot trial was conducted to test adherence to specific lifestyle interventions among Pima Indians of Arizona, and to compare them for changes in risk factors for diabetes mellitus. Ninety‐five obese, normoglycaemic men and women, aged 25–54 years, were randomized to treatments named ‘Pima Action’ (Action) and ‘Pima Pride’ (Pride), which were tested for 12 months. Action involved structured activity and nutrition interventions, and Pride included unstructured activities emphasizing Pima history and culture. Adherence to interventions, changes in self‐reported activity and diet, and changes in weight, glucose concentrations, and other risk factors were assessed regularly. Thirty‐five eligible subjects who had declined randomization were also followed as an ‘observational’ group and 22 members of this group were examined once at a median of 25 months for changes in weight and glucose concentration. After 12 months of intervention, members of both intervention groups reported increased levels of physical activity (median: Action 7.3 h month−1, Pride 6.3 h month−1, p < 0.001 for each), and Pride members reported decreased starch intake (28 g, p = 0.008). Body mass index, systolic and diastolic blood pressures, weight, 2‐h glucose and 2‐h insulin had all increased in Action members (p < 0.003 for each), and waist circumference had decreased in Pride members (p = 0.05). Action members gained more weight than Pride members (2.5 kg vs 0.8 kg, p = 0.06), and had a greater increase in 2‐h glucose than Pride members (1.33 mM vs 0.03 mM, p = 0.007). Members of the observational group gained an average of 1.9 kg year−1 in weight and had an increase of 0.36 mM year−1 in 2‐h glucose. Sustaining adherence in behavioural interventions over a long term was challenging. Pimas may find a less direct, less structured, and more participative intervention more acceptable than a direct and highly structured approach. © 1998 John Wiley & Sons, Ltd.
Experimental Osteomyelitis: What Have We Learned from Animal Studies about the Systemic Treatment of Osteomyelitis?

Abstract Clinical trials of systemic antibiotic treatment of osteomyelitis are difficult to perform for many reasons, such as low incidence rate of osteomyelitis, variety of anatomic locations, stage and etiologic agents. In this article, we reviewed the experimental studies on osteomyelitis available in the English medical literature since 1968, to ascertain their actual and potential impact on the treatment of human osteomyelitis. Major results are summarized and topics of major interest, such as reproducibility of animal models, predictive value of animal models, correlation of pharmacokinetics between different animals and humans, and the correlation of outcome between animal and clinical studies are discussed. Most of the reviewed animal models are reproducible and dependable. However, establishing the right dose regimen in animals appeared a critical factor, which might undermine the predictive value of the experimental study. Due to difficulties in comparing results of animal and human studies, the predictive value of animal studies about osteomyelitis is still unclear. However, animal models gave valuable information to the clinician for choosing the minimal duration of antibiotic treatment. Even though the use of antibiotic combinations was associated with better outcome in the majority of animal studies, such a finding seems to have limited impact on clinical practice.
Design of an MTJ-based nonvolatile lookup table circuit using an energy-efficient single-ended logic-in-memory structure

A 6-input nonvolatile lookup table (LUT) circuit is proposed using an energy-efficient single-ended logic-in-memory (LIM) structure in conjunction with a magnetic tunnel junction (MTJ) device. While the use of a conventional single-ended LIM structure makes the multi-input LUT circuit compact, a long delay due to the small difference in the MTJ resistance and a large amount of dynamic power consumption due to a DC current path are unavoidable. To overcome the problem, a PMOS feedback transistor which makes it possible to accelerate the logic operation is utilized in the proposed LUT circuit. The use of the PMOS feedback transistor also makes it possible to reduce dynamic power consumption by automatically cutting off the DC current just after logic value `0' is read. In fact, the power-delay product of the proposed 6-input LUT circuit is reduced by 66% in comparison with that of the conventional single-ended one under a 90-nm CMOS technology.