Miracle-dz/UniFAR-FTUs huggingface dataset:
Ligand Responses of Vfr, the Virulence Factor Regulator from Pseudomonas aeruginosa

ABSTRACT Vfr, a transcription factor homologous to the Escherichia coli cyclic AMP (cAMP) receptor protein (CRP), regulates many aspects of virulence in Pseudomonas aeruginosa. Vfr, like CRP, binds to cAMP and then recognizes its target DNA and activates transcription. Here we report that Vfr has important functional differences from CRP in terms of ligand sensing and response. First, Vfr has a significantly higher cAMP affinity than does CRP, which might explain the mysteriously unidirectional functional complementation between the two proteins (S. E. H. West et al., J. Bacteriol. 176:7532–7542, 1994). Second, Vfr is activated by both cAMP and cGMP, while CRP is specific to cAMP. Mutagenic analyses show that Thr133 (analogous to Ser128 of CRP) is the key residue for both of these distinct Vfr properties. On the other hand, substitutions that cause cAMP-independent activity in Vfr are similar to those seen in CRP, suggesting that a common cAMP activation mechanism is present. In the course of these analyses, we found a remarkable class of Vfr variants that have completely reversed the regulatory logic of the protein: they are active in DNA binding without cAMP and are strongly inhibited by cAMP. The physiological impact of Vfr's ligand sensing and response is discussed, as is a plausible basis for the fundamental change in protein allostery in the novel group of Vfr variants.
Genetic Divergence of Campylobacter fetus Strains of Mammal and Reptile Origins

ABSTRACT Campylobacter fetus is a gram-negative bacterial pathogen of both humans and animals. Two subspecies have been identified, Campylobacter fetus subsp. fetus and Campylobacter fetus subsp. venerealis, and there are two serotypes, A and B. To further investigate the genetic diversity among C. fetus strains of different origins, subspecies, and serotypes, we performed multiple genetic analyses by utilizing random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE), and DNA-DNA hybridization. All 10 primers used for the RAPD analyses can distinguish C. fetus strains of reptile and mammal origin, five can differentiate between C. fetus subsp. fetus and C. fetus subsp. venerealis strains, and four showed differences between type A and type B isolates from mammals. PFGE with SmaI and SalI digestion showed varied genome patterns among different C. fetus strains, but for mammalian C. fetus isolates, genome size was well conserved (mean, 1.52 ± 0.06 Mb for SmaI and 1.52 ± 0.05 Mb for SalI). DNA-DNA hybridization demonstrated substantial genomic-homology differences between strains of mammal and reptile origin. In total, these data suggest that C. fetus subsp fetus strains of reptile and mammal origin have genetic divergence more extensive than that between the two subspecies and that between the type A and type B strains. Combining these studies with sequence data, we conclude that there has been substantial genetic divergence between Campylobacter fetus of reptile and mammal origin. Diagnostic tools have been developed to differentiate among C. fetus isolates for taxonomic and epidemiologic uses.
Role of Iron in Nramp1-Mediated Inhibition of Mycobacterial Growth

ABSTRACT Innate resistance to mycobacterial growth is mediated by a gene,Nramp1. We have previously reported that Nramp1mRNA from macrophages of Mycobacterium bovis BCG-resistant (Bcgr) mice is more stable thanNramp1 mRNA from macrophages of BCG-susceptible (Bcgs) mice. Based on these observations and on reports that show that the closely related Nramp2 gene is a metal ion transporter, we evaluated the effect of iron on the growth ofMycobacterium avium within macrophages as well as on the stability of Nramp1 mRNA. The addition of iron to macrophages from Bcgs mice resulted in a stimulation of mycobacterial growth. In contrast, iron increased the capacity of macrophages from Bcgr mice to control the growth of M. avium. When we treated recombinant gamma interferon (IFN-γ)-activated macrophages with iron, we found that iron abrogated the growth inhibitory effect of IFN-γ-activated macrophages from Bcgs mice but that it did not affect the capacity of macrophages from Bcgrmice to control microbial growth. A more detailed examination of the effect of iron on microbial growth showed that the addition of small quantities of iron to resident macrophages fromBcgr mice stimulated antimicrobial activity within a very narrow dose range. The effect of iron on the growth inhibitory activity of macrophages from Bcgrmice was abrogated by the addition of catalase or mannitol to the culture medium. These results are consistent with an Fe(II)-mediated stimulation of the Fenton/Haber-Weiss reaction and hydroxyl radical-mediated inhibition of mycobacterial growth.
Reversal of Capillary Stasis and Prevention of Necrosis in Burns

It has been suggested that the ultimate depth of burn necrosis might be minimized by prevention or reversal of the progressive capillary stasis which occurs in the early postburn hours. To study the role of wound dehydration in determining burn depth, 5% body surface area, 75 C, 10 second burns (in which the zone of stasis included the full thickness of skin) were inflicted on the backs of guinea pigs and subsequent mechanical trauma was prevented. At various times postburn, water content, (and after India ink perfusion) depth of capillary stasis and histological structure of burn were studied in the following groups: 1) blister intact; 2) blister removed; and 3) blister replaced by several different types of dressing. Reversal of capillary stasis was least and necrosis full-thickness in depth in undressed wounds with blister removed. Reversal of capillary stasis was complete and necrosis absent with blister replaced by fresh split-thickness porcine skin and correlated with prevention of wound dehydration. Similar, though less complete, prevention of necrosis occurred with blister intact or replaced by sialastic film. Other dressings were associated with deep necrosis or gross infection. These and other data suggest that in the zone of stasis, capillary stasis may be reversed and necrosis avoided by appropriate prevention of wound dehydration. Clinical correlations are suggested.
Genetic association of HLA‐DRB1 multiple polymorphisms with dermatomyositis in Chinese population

Genetic variation in HLA plays an important role in the pathogenesis of dermatomyositis (DM). The aim of this study was to investigate the association of HLA class II with DM in China. Two hundred and twenty‐four DM patients and 300 healthy controls were randomly enrolled at China‐Japan Friendship Hospital. High‐resolution typing of HLA‐DRB1 alleles was performed by sequencing based typing. The HLA‐DQA1 and HLA‐DQB1 alleles were determined by polymerase chain reaction sequence‐specific primers. The frequencies of HLA‐DRB1*09:01 (28.6% vs 11.3%, P < .0001, odds ratio, OR = 3.14, 95% confidence interval, CI = 2.47‐3.99) and HLA‐DRB1*12:01 (29.0% vs 11.0%, P < .0001, OR = 3.30, 95% CI = 2.59‐4.20) in DM patients were significantly higher than that in healthy controls. No significant difference was found in HLA‐DQA1 or DQB1 alleles between DM patients and healthy controls. Furthermore, DM patients with anti‐melanoma differentiation‐associated gene 5 antibody (anti‐MDA5) had a significantly higher frequency of HLA‐DRB1*12:01 compared to that for patients without anti‐MDA5 (P < .0001, OR = 4.77, 95% CI: 2.29‐9.93). Multivariate binary logistic regression analysis was performed to identify the risk factors for interstitial lung disease. The HLA‐DRB1*09:01 allele was a poor prognostic factor (P = .01, OR = 9.21, 95% CI: 1.47‐57.50) for DM patients with anti‐MDA5 autoantibody. In summary, our findings indicate that HLA‐DRB1*09:01 and HLA‐DRB1*12:01 alleles may contribute to susceptibility of adult DM in Han Chinese population. In addition, the DRB1*12:01 genotype is significantly associated with the presence of anti‐MDA5 antibody in DM patients.
Retrospective analysis of clinical findings and outcome of cats with suspected rattlesnake envenomation in Southern California: 18 cases (2007-2010).

OBJECTIVE To evaluate treatment and survival rates of cats with suspected rattlesnake envenomation. DESIGN Retrospective study. SETTING Veterinary emergency referral hospital in Southern California. ANIMALS Client-owned animals. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Eighteen cats were treated for suspected rattlesnake envenomation between January 2007 and August 2010. There were 3 fatalities and 15 cats survived (16% mortality rate). Two cases developed pelvic limb paresis 3-4 days post envenomation. There were no apparent adverse reactions to treatment with antivenom. CONCLUSIONS Cats are presented infrequently for treatment of envenomation compared to dogs. Envenomation in cats should be treated according to guidelines established for people and dogs and administration of antivenom does not appear to be associated with adverse events. The mortality rate in this study was found to be 16%, which is higher than the mortality rate reported for dogs suspected of rattlesnake envenomation in a similar region (4.1%). Pelvic limb paresis may develop 3-4 days post envenomation but can resolve within 24 hours.
Distribution of hepatitis C virus genotypes among intravenous drug users in the Çukurova region of Turkey.

BACKGROUND/AIM The most common hepatitis C virus (HCV) genotype in Turkey is genotype 1. However, there has not been a study about the distribution of HCV genotypes among intravenous drug users (IVDUs) in the Çukurova region of Turkey. This study was planned to understand if there is a difference between IVDUs and the normal population. MATERIALS AND METHODS Between May 2010 and May 2014, anti-HCV positive IVDUs who applied to the 6 hospitals in the Çukurova region of Turkey were included in this study. Their HCV genotypes were studied. RESULTS Ninety-seven anti-HCV positive IVDUs were screened in terms of HCV RNA and genotype. Ten were excluded from the study because their HCV RNA results were negative. Fifty-one of the 87 patients (58.6%) had genotype 3. Genotype 2 was detected in 26 (29.9%) and genotype 1 was detected in 10 (11.5%) patients. CONCLUSION HCV genotypes seem to be different between the normal population and IVDUs according to studies worldwide. Among IVDUs, we detected a dominance of genotype 3 and genotype 2, which is apparently different from the normal population. The reason for this difference can be simply explained by infection through shared needles. However, there may still be a different immunological response in IVDUs, the investigation of which may lead to further studies.
Bilateral Empyema Caused by Adult-Onset Still’s Disease

Empyemas are usually of infectious origin. Noninfectious causes of empyema may be a considerable diagnostic challenge, as exemplified in the present case report. A 21-year-old male presented with high fever, sore throat and myalgias of 1 week duration. In the following days, bilateral pleural effusions developed, with cellular counts in the pleural fluid up to 117 × 109/liter (98% neutrophils). Despite institution of empiric antibiotic therapy, spiking fever continued. All culture studies resulted in being negative. Following the report of a serum ferritin concentration of 6,975 µg/l, adult-onset Still’s disease was diagnosed and successfully treated with anti-inflammatory drugs. This case adds adult-onset Still’s disease to the list of noninfectious causes of empyema and underlies the value of measuring serum ferritin as a diagnostic tool.
Distinct Neuronal Interactions in Anterior Inferotemporal Areas of Macaque Monkeys during Retrieval of Object Association Memory

In macaque monkeys, the anterior inferotemporal cortex, a region crucial for object memory processing, is composed of two adjacent, hierarchically distinct areas, TE and 36, for which different functional roles and neuronal responses in object memory tasks have been characterized. However, it remains unknown how the neuronal interactions differ between these areas during memory retrieval. Here, we conducted simultaneous recordings from multiple single-units in each of these areas while monkeys performed an object association memory task and examined the inter-area differences in neuronal interactions during the delay period. Although memory neurons showing sustained activity for the presented cue stimulus, cue-holding (CH) neurons, interacted with each other in both areas, only those neurons in area 36 interacted with another type of memory neurons coding for the to-be-recalled paired associate (pair-recall neurons) during memory retrieval. Furthermore, pairs of CH neurons in area TE showed functional coupling in response to each individual object during memory retention, whereas the same class of neuron pairs in area 36 exhibited a comparable strength of coupling in response to both associated objects. These results suggest predominant neuronal interactions in area 36 during the mnemonic processing, which may underlie the pivotal role of this brain area in both storage and retrieval of object association memory.
Decreased physical function in juvenile rheumatoid arthritis.

OBJECTIVE To assess the extent of physical disability in juvenile rheumatoid arthritis (JRA), classified according to subtype, and whether synovitis or flexion contractures are present on examination. METHODS This retrospective study included 88 JRA patients and 50 controls without musculoskeletal disease. The outcome measure was the disability index (DI) derived from the Childhood Health Assessment Questionnaire (CHAQ). RESULTS DI scores for JRA patients with synovitis (mean 0.49, range 0-1.88) and without synovitis (mean 0.37, range 0-1.75) were significantly higher (P < 0.001 for both groups) than for controls (mean 0.06, range 0-0.75, P < 0.001), but not significantly different from one another. Similarly, DI scores for JRA patients with and without any flexion contractures were higher than for controls, but not significantly different from one another. DI scores for JRA patients with both synovitis and flexion contractures were significantly higher than DI scores for JRA patients with neither, but were not distinguishable from JRA patients with synovitis only or flexion contractures only. Likewise, DI scores for JRA patients lacking synovitis and flexion contractures were not significantly different than those for JRA patients with one or the other. DI scores for systemic and polyarticular patients were higher than for pauciarticular patients, and DI scores for all 3 subtypes were higher than for controls. CONCLUSION Our findings suggest that many JRA patients, including those with pauciarticular JRA, have problems with physical function, even when synovitis and flexion contractures are not present. Further attention and research is needed to elucidate the causes or origins of disability in JRA patients with seemingly well-controlled disease. We recommend that health status instruments like the CHAQ be more widely used for JRA patients to complement other assessments, especially in planning occupational and physical therapy.
Determinants of performance in the isocitrate dehydrogenase of Escherichia coli

The substrate specificity of the NADP‐dependent isocitrate dehydrogenase of Escherichia coli was investigated by combining site‐directed mutagenesis and utilization of alternative substrates. A comparison of the kinetics of the wild‐type enzyme with 2R‐malate reveals that the γ‐carboxylate of 2R, 3S‐isocitrate contributes a factor of 12, 000, 000 to enzyme performance. Analysis of kinetic data compiled for 10 enzymes and nine different substrates reveals that a factor of 1, 650 can be ascribed to the hydrogen bond formed between S113 and the γ‐carboxylate of bound isocitrate, a factor of 150 to the negative charge of the γ‐carboxylate, and a factor of 50 for the γ‐methyl. These results are entirely consistent with X‐ray structures of Michaelis complexes that show a hydrogen bond positions the γ‐carboxylate of isocitrate so that a salt bridge can form to the nicotinamide ring of NADP.
Comparison of the reactivity of human and rabbit blood towards pyrogenic stimuli.

A comparison between humans and rabbits was performed based on stimulation of whole blood with well-known pyrogens from Gram-negative and Gram-positive bacteria, such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), respectively. The reactivity was measured as release of IL-1 beta and IL-8 by ELISA. The reactivity of the two species towards LPS was found to be similar, whereas their reactivity towards LTA differed considerably. Differences between the levels of IL-1 beta and IL-8 release were observed in both species. This finding suggests that the In vitro Pyrogen Test (IPT) which uses human blood to detect contaminations, e.g. of injectable drugs, might predict the human reaction to the contamination better than the "gold standard" rabbit pyrogen test.
Unique and interactive effects of depression, age, socioeconomic advantage, and gender on cognitive performance of normal healthy older people.

A sample of 4,243 residents of Manchester, England and Newcastle-upon-Tyne, England, aged 50 to 93 years, completed the Beck Depression Scale (A.T. Beck, C.H. Ward, M. Mendelson, J. Mock, & J. Erbaugh, 1961) and a battery of 6 different cognitive tests. Beck scores were low, indicating gradations of dysphoria rather than clinical depression. Beck scores did not vary with age but were significantly higher for women than for men and for disadvantaged than for advantaged socioeconomic groups. Measures of fluid, but not of crystallized, ability declined as age increased. Socioeconomic disadvantage was associated with poorer performance on all cognitive tests. Men scored higher on a test of spatial reasoning, and women scored higher on a test of word definition and on 2 tests of verbal memory and learning. However, after variance associated with all these demographic and individual-difference variables was considered, and within a range indicative of dysphoria rather than clinical depression, higher Beck scores were associated with significantly poorer performance on both crystallized and fluid measures of cognitive ability. This association was less marked in women than in men, but age, socioeconomic advantage, and estimated lifetime intellectual ability did not act as protective or risk factors for vulnerability of cognitive processes to dysphoria.
Intravenous cyclophosphamide and plasmapheresis in dialysis-dependent ANCA-associated vasculitis.

BACKGROUND AND OBJECTIVES Induction therapy with oral cyclophosphamide (CYP) has been a mainstay of treatment in patients with severe renal failure secondary to ANCA-associated vasculitis (AAV). Recent evidence proposes using pulsed intravenous CYP in less severe disease to minimize adverse events. It is unclear if this can be translated to those with dialysis-dependent renal insufficiency. DESIGN, SETTING, PARTICIPANTS, & METHODS All AAV patients presenting between 2005 and 2010 requiring dialysis at presentation were retrospectively analyzed. Patients were treated with plasma exchange, corticosteroids, and intravenous CYP. Rate of dialysis independence at 3 and 12 months and adverse effects were assessed and compared with the outcome of the plasmapheresis, prednisolone, and oral CYP arm of the randomized MEPEX (methylprednisolone versus plasma exchange) trial. RESULTS Forty-one patients were included. At 3 months, 3 (7.3%) patients had died on dialysis, 12 (29.3%) remained dialysis dependent, and 26 (63.4%) were dialysis independent (creatinine, 2.5 mg/dl; GFR, 26 ml/min per 1.73 m(2)). Four patients subsequently reached ESRD at a median time of 83 days. Thirty-seven (90%) patients reached 1 year follow-up, 13 (35%) remained dialysis dependent, and 24 (65%) had independent renal function. Eleven patients (27%) had episodes of leukopenia (white cell count <4×10(9)/L) during CYP therapy and 17 (41%) experienced infectious complications. This compares favorably with the dialysis-dependent cohort treated with plasmapheresis in the MEPEX study in which 51% were alive with independent renal function at 1 year. CONCLUSIONS Intravenous CYP used with corticosteroids and plasmapheresis may be an effective alternative to oral CYP in patients with dialysis-dependent AAV.
The effect of gastric bypass on the pharmacokinetics of serotonin reuptake inhibitors.

OBJECTIVE Morbidly obese patients frequently present with mood and anxiety disorders, which are often treated with serotonin reuptake inhibitors (SRIs). Having observed that patients treated with SRIs frequently relapse after Roux-en-Y gastric bypass surgery, the authors sought to assess whether SRI bioavailability is reduced postoperatively. METHOD Twelve gastric bypass candidates treated with an SRI for primary mood or anxiety disorders were studied prospectively. Timed blood samples for SRI plasma levels were drawn for pharmacokinetic studies before surgery and 1, 6, and 12 months afterward. Maximum concentration, time to maximum concentration, and area under the concentration/time curve (AUC) were determined. RESULTS In eight of the 12 patients, AUC values 1 month after surgery dropped to an average of 54% (SD=18) of preoperative levels (range=36%-80%); in six of these patients, AUC values returned to baseline levels (or greater) by 6 months. Four patients had an exacerbation of depressive symptoms, which resolved by 12 months in three of them. Three of the four patients had a reduced AUC level at 1 month and either gained weight or failed to lose weight between 6 and 12 months. Normalization of the AUC was associated with improvement in symptom scores. CONCLUSIONS Patients taking SRIs in this study were at risk for reduced drug bioavailability 1 month after Roux-en-Y gastric bypass. The authors recommend close psychiatric monitoring after surgery.
Characterization of the Proliferation State in Canine Mammary Tumors by the Standardized AgNOR Method with Postfixation and Immunohistologic Detection of Ki-67 and PCNA

Paraffin-embedded tissue sections of 96 surgically removed mammary tumors from female dogs were analyzed for their proliferation state using three different methods. The AgNOR method, originally developed by Ploton and coworkers in 1986,34 modified and standardized by the AgNOR committee, is an easy, inexpensive silver-staining procedure used to determine cell proliferation and prognosis of various tumors. Due to the standardized staining protocol of the AgNOR method and a postfixation step, results obtained were of excellent quality for image analysis processing. The growth fraction was evaluated by counting of immuno-histologically positive-stained cells for Ki-67 or proliferating-cell nuclear antigen (PCNA). The values determined were, in general, lower with Ki-67 (MIB1) than with PCNA (PC10). Nevertheless, the labeling indices of these antigens correlated significantly (P < 0.001). Though the differences of the means between the tumor groups according to the classification system of the World Health Organization were significant for all three investigated methods (P < 0.001), there was a considerable overlap between the tumor groups concerning all investigated parameters. An exploratory data analysis (multivariate analysis) was performed to evaluate the prognostic relevance of the three methods including further anamnestic, clinical, gross, and histopathologic variables. Besides the histopathologic diagnosis (survival P < 0.001; survival time P < 0.05; reappearance of tumor growth P < 0.05), only the PCNA-labeling index (time until reappearance of tumor growth P < 0.001) was of prognostic significance.