Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorescence Detection of Symmetric GroEL14(GroES7)2 Heterooligomers Involved in Protein Release during the Chaperonin Cycle*

The GroEL14 chaperonin from Escherichia coli was labeled with 5-((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid (I-AEDANS), a hydrophobic probe whose fluorescent emission is sensitive to structural changes within the protein. Increasing concentrations of ATP or adenylyl imidodiphosphate but not ADP caused two successive GroES7-dependent changes in the fluorescence intensity of AEDANS-GroEL14, corresponding to the sequential binding of two GroES7 heptamers and the formation of two types of chaperonin heterooligomers, GroEL14GroES7 and GroEL14(GroES7)2. The binding of thermally denatured malate dehydrogenase (MDH) caused a specific increase in fluorescence intensity of AEDANS-GroEL14 that allowed the direct measurement in solution at equilibrium of ATP- and GroES7-dependent protein release from the chaperonin. Structure/function analysis during the generation of ATP from ADP indicated the following sequence of events: 1) ADP-stabilized MDH-GroEL14GroES7 particles bind newly formed ATP. 2) MDH-GroEL14GroES7 particles bind a second GroES7. 3) MDH-GroEL14(GroES7)2 particles productively release MDH. 4) Released MDH completes folding. Therefore, the symmetrical GroEL14(GroES7)2 heterooligomer is an intermediate after the formation of which the protein substrate is productively released during the chaperonin-mediated protein folding cycle.
Effects of helium-oxygen on intrinsic positive end-expiratory pressure in intubated and mechanically ventilated patients with severe chronic obstructive pulmonary disease

ObjectiveTo test the hypothesis that replacing 70:30 nitrogen:oxygen (Air-O2) with 70:30 helium:oxygen (He-O2) can decrease dynamic hyperinflation (“intrinsic” positive end-expiratory pressure) in mechanically ventilated patients with chronic obstructive pulmonary disease (COPD), and to document the consequences of such an effect on arterial blood gases and hemodynamics. DesignProspective, interventional study. SettingMedical intensive care unit, university tertiary care center. PatientsTwenty-three intubated, sedated, paralyzed, and mechanically ventilated patients with COPD enrolled within 36 hrs after intubation. InterventionsMeasurements were taken at the following time points, all with the same ventilator settings: a) baseline; b) after 45 mins with He-O2; c) 45 mins after return to Air-O2. The results were then compared to those obtained in a test lung model using the same ventilator settings. Main Results (mean ± sd):Trapped lung volume and intrinsic positive end-expiratory pressure decreased during He-O2 ventilation (215 ± 125 mL vs. 99 ± 15 mL and 9 ± 2.5 cm H2O vs. 5 ± 2.7 cm H2O, respectively;p < .05). Likewise, peak and mean airway pressures declined with He-O2 (30 ± 5 cm H2O vs. 25 ± 6 cm H2O and 8 ± 2 cm H2O vs. 7 ± 2 cm H2O, respectively;p < .05). These parameters all rose to their baseline values on return to Air-O2 (p < .05 vs. values during He-O2). These results were in accordance with those obtained in the test lung model. There was no modification of arterial blood gases, heart rate, or mean systemic arterial blood pressure. In 12/23 patients, a pulmonary artery catheter was in place, allowing hemodynamic measurements and venous admixture calculations. Switching to He-O2 and back to Air-O2 had no effect on pulmonary artery pressures, right and left ventricular filling pressures, cardiac output, pulmonary and systemic vascular resistance, or venous admixture. ConclusionIn mechanically ventilated COPD patients with intrinsic positive end-expiratory pressure, the use of He-O2 can markedly reduce trapped lung volume, intrinsic positive end-expiratory pressure, and peak and mean airway pressures. No effect was noted on hemodynamics or arterial blood gases. He-O2 might prove beneficial in this setting to reduce the risk of barotrauma, as well as to improve hemodynamics and gas exchange in patients with very high levels of intrinsic positive end-expiratory pressure.
Aortic arch aneurysm: short- and mid-term results comparing open arch surgery and the hybrid procedure†.

OBJECTIVES Open arch surgery for aortic arch aneurysm was historically associated with a high risk of postoperative morbi-mortality. Improved operative techniques have now lowered the incidence of these complications but in parallel, hybrid arch procedures have emerged. Nowadays, very little data are available about their mid-term results compared with open surgery. METHODS From January 2002 to January 2014, 46 patients had treatment for an exclusive aortic arch aneurysm including 25 open arch surgeries and 21 type I hybrid arch procedures in our institution. All cases involved arch aneurysms involving at least one carotid artery (Zone 0 and Zone 1). Aneurysms of the distal arch and descending aorta were excluded (Zone 2 and beyond). Results from a retrospective database are reported. There were no patients lost to the follow-up. RESULTS There was no significant difference in preoperative comorbidities between the two groups. The incidence of in-hospital mortality was similar at 20% (5/25) for open surgery and 19% (4/21) for hybrid procedure (P = 0.830). The incidence of permanent cerebral neurological deficit was comparable at 17.4% (4/23) for open surgery and 21.1% (4/19) for hybrid procedure (P = 1). Median survival was 109.5 months for open surgery and 56.3 months for hybrid procedure. Freedom from all-cause mortality was 78, 63, 63 and 57% at 1, 3, 5 and 7 years, respectively in the open surgical group. Freedom from all-cause mortality was 74, 55, 46 and 28% at 1, 3, 5 and 7 years, respectively in the hybrid group. Survival rates and incidence of major adverse cardiac and cerebro-vascular event between open surgery and hybrid procedure were not statistically different (P = 0.530 and P = 0.325, respectively). However, incidence of reintervention was in favour of open surgery [14.5 vs 44.8% at 7 years, P = 0.045; 95% confidence interval: (0.06-0.97)]. CONCLUSIONS The type I hybrid arch procedure fails to demonstrate better results compared with open surgery, regarding morbi-mortality at the short- and mid-term follow-up. Moreover, it increases the risk of reintervention. Patients treated by this technique must undergo a closer follow-up because of this risk. Larger randomized studies are needed to better define the exact indications of this therapy.
Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid ecological speciation of an incipient species flock

The rapid rise of phenotypic and ecological diversity in independent lake‐dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260 000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species groups and to evaluate the relationships and genetic structure among five closely related, endemic, co‐occurring species (the Uruguay River species flock; URSF). Additionally, we evaluated ecological divergence of the URSF based on body and lower pharyngeal jaw (LPJ) shape and gut contents. Across the genus, we recovered novel relationships among the species groups. We found strong support for the monophyly of the URSF; however, relationships among these species remain problematic, likely because of the rapid and recent evolution of this clade. Clustered co‐ancestry analysis recovered most species as well delimited genetic groups. The URSF species exhibit species‐specific body and LPJ shapes associated with specialized trophic roles. Collectively, our results suggest that the URSF consists of incipient species that arose via ecological speciation associated with the exploration of novel trophic roles.
Genome size microscale divergence of Cyclamen persicum in Evolution Canyon, Israel

Using DAPI flow cytometry, we examined genome size divergence of the Persian violet, Cyclamen persicum (Primulaceae) (2n=48) on close opposite slopes of Evolution Canyon (EC), Mt. Carmel, Israel. The range of genome size variation detected among measured cyclamens was 6.41% in relation to the smallest measured DNA content. Our data on C. persicum at EC showed that local variability in the 2C-value exists. Significantly less DNA was recorded in plants growing in one station of the African savannah-like south-facing slope (AS) but not in the remaining two stations of the same slope. We were not able to reject the null hypothesis that there are no significant interslope differences in the genome size between the temperate European garrigue-like north-facing slope (ES) and the drier AS. In spite of the nonsignificant interslope trend for the higher genome size in C. persicum, the data-fusion (meta-analysis) test using correlations between C-values in C. persicum, and earlier studied carob tree (Ceratonia siliqua), trifoil (Lotus peregrinus) and a beetle (Oryzaephilus surinamensis) and their distribution along the aridity gradient indicates a positive relationship between drought and genome size at the microsite.
[Etiological study on viral diarrhea among children in Lanzhou, Gansu, from July 2004 through June 2005].

OBJECTIVE To study molecular epidemiology of four major etiological viruses among children with acute diarrhea in Lanzhou, Gansu province. METHODS Stool specimens were collected from all 400 inpatients less than 5 years old with acute diarrhea admitted in Department of Pediatrics, the First Hospital, Lanzhou University from Jul. 2004 through Jun. 2005. Dako IDEIA kits were used for detection of rotavirus, adenovirus and astrovirus. Calicivirus detection was done by both reverse transcription-polymerase chain reactions (RT-PCR) and ELISA. Further strain characterization of rotavirus and astrovirus was carried out with RT-PCR. RESULTS A total of 400 stool samples were collected and tested. Rotavirus was present in 47.3% of the cases: calicivirus in 15.5%, astrovirus in 9.5% and adenoviruses in 7.5%. Mixed infections with multiple enteric viruses were present in 13.5% of all samples. Among 189 rotavirus positive samples, serotype G2 (34.4%) was the predominant strain followed by G3 (32.8%), G1 (1.1%) and mixed-G infection (5.8%). 25.9% of strains remained to be non-typeable. P genotyping showed P [4] (45%) was most common followed by P [8] (22.1%), and non-typeable (32.9%). Strain P [4] G2 (43.6%) was the most common combination followed by P [8] G3 (25.6%), P [4] G3 (13.8%), and P [8] G2, P [4] G1 and P [8] G1. Among 38 astrovirus strains, serotypes 1 (57.8%) was the predominant. Serotype 3 and 8 were found only in one case respectively, 14 strains remained to be non-typeable. A peak admission of rotavirus diarrhea was observed from October through December. More than 95.0% of viral diarrhea patients under hospitalization occurred among children younger than 2 years. The incidence rates of rotavirus were highest in infants aged 6 - 23 months. CONCLUSION Rotavirus was the most important pathogen for viral diarrhea among children hospitalized in Lanzhou followed by calicivirus, astrovirus, and adenovirus. The predominant rotavirus strain circulated was P [4] G2, which was different from the finding in the previous years. The high rate of mixed infection with different viral agents was notable.
Root internalization, transport and in-planta survival of Salmonella enterica serovar Newport in sweet basil.

It is now acknowledged that food-borne pathogens present in the irrigation water or soil can become associated with crop plants in the field, penetrate internal plant tissues via the root, translocate and survive inside plants. Only little information is available concerning interaction between enteric pathogens and plants. The present study evaluated the potential for contamination of the aromatic plant, sweet basil during cultivation, by Salmonella enterica serovar Newport. Root internalization was plant-age-dependent, with the highest susceptibility occurring at the beginning of the rapid growth phase of the root. Higher incidence of internalization was detected in vegetative than reproductive plant organs, pointing at bacterial transport in the transpiration stream. Internalized Salmonella survived only < 30 h in the phyllosphere. In contrast, survival of Salmonella on the leaf surface was much pronounced (at least 8 days), and the initial decay rate was lower at the abaxial (lower) compared with the adaxial (upper) side of the leaf. Although the experiments were conducted with high concentration of Salmonella unlikely to happen in the field, internalization occurred at a low frequency and in-planta survival was limited to less than 30 h. These findings imply that leaf surface contamination, rather than root internalization, may pose higher risk for human infection following consumption of contaminated basil.
Current management of psoriasis in the United Kingdom: patterns of prescribing and resource use in primary care

The current management of psoriasis and its associated resource use in the United Kingdom (UK) was investigated in this retrospective analysis of 789,300 primary care patient records. Most patients with psoriasis (94%) were managed on topical psoriasis agents only, 4% were prescribed systemic psoriasis agents and 2% had no recorded psoriasis treatment at all during the 12‐month study period. Co‐medications to treat physical or psychological comorbidities were required by 22% of patients. Referral rates into secondary care were low, 5% of patients prescribed systemic psoriasis agents and 0.7% of patients prescribed topical psoriasis agents had secondary care appointments documented in their medical records. This study demonstrates that most patients with psoriasis in UK primary care are managed on topical agents even though there are surrogate markers, such as resource use and co‐medication prescriptions, which indicate that their psoriasis is not optimally controlled.
Molecular analysis of cyenopyrafen resistance in the two-spotted spider mite Tetranychus urticae.

BACKGROUND Cyenopyrafen is a recently developed acaricide with a new mode of action as a complex II inhibitor. However, it was recently shown that cross-resistance to cyenopyrafen can occur in resistant field strains of Tetranychus urticae, which might be linked to the previous use of classical METI acaricides. Here, we selected for cyenopyrafen resistance and studied the molecular mechanisms that underlie resistance. RESULTS Selection for cyenopyrafen resistance confers cross-resistance to the complex II inhibitor cyflumetofen, but also to pyridaben, a frequently used complex I inhibitor. Cyenopyrafen resistance is highly synergised by piperonyl butoxide, and a 15-fold higher P450 activity was detected in the resistant strain. Target-site resistance was not detected. Genome-wide gene expression data, followed by a meta-analysis of previously obtained gene expression data, revealed the overexpression specifically of CYP392A11 and CYP392A12. CONCLUSIONS Cyenopyrafen resistance is strongly linked to the overexpression of two P450s, which probably explains the observed cross-resistance. This information is highly valuable, as the novel complex II inhibitors cyenopyrafen and cyflumetofen are in the process of worldwide registration. The role of both CYP392A11 and CYP392A12 should be further supported by functional expression, but they are very promising candidates as molecular diagnostic markers for monitoring cyenopyrafen susceptibility in the field.
Microbial degradation, cytotoxicity and antibacterial activity of polyurethanes based on modified castor oil and polycaprolactone

Abstract The objective of this study was to assess the effects of type of polyol and concentration of polycaprolactone (PCL) in polyurethanes (PUs) on microbial degradability, cytotoxicity, biological properties and antibacterial activity to establish whether these materials may have biomedical applications. Chemically modified and unmodified castor oil, PCL and isophorone diisocyanate in a 1:1 ratio of NCO/OH were used. PUs were characterized by stress/strain fracture tests and hardness (ASTM D 676-59). Hydrophilic character was determined by contact angle trials and morphology was evaluated by scanning electron microscopy. Degradability with Escherichia coli and Pseudomonas aeruginosa was evaluated by measuring variations in the weight of the polymers. Cytotoxicity was evaluated using the ISO 10993-5 (MTT) method with mouse embryonic fibroblasts L-929 (ATCC® CCL-1) in direct contact with the PUs and with NIH/3T3 cells (ATCC® CRL-1658) in indirect contact with the PUs. Antimicrobial activity against E. coli and P. aeruginosa was determined. PUs derived from castor oil modified (P0 and P1) have higher mechanical properties than PUs obtained from castor oil unmodified (CO). The viability of L-929 mouse fibroblasts in contact with polymers was greater than 70%. An assessment of NIH/3T3 cells in indirect contact with PUs revealed no-toxic degradation products. Finally, the antibacterial effect of the PUs decreased by 77% for E. coli and 56% for P. aeruginosa after 24 h. These results indicate that PUs synthesized with PCL have biocidal activity against Gram-negative bacteria and do not induce cytotoxic responses, indicating the potential use of these materials in the biomedical field.
Presence of the cofactor speeds up folding of Desulfovibrio desulfuricans flavodoxin

Flavodoxin is an α/β protein with a noncovalently bound flavin‐mononucleotide (FMN) cofactor. The apo‐protein adopts a structure identical to that of the holo‐form, although there is more dynamics in the FMN‐binding loops. The equilibrium unfolding processes of Azotobacter vinelandii apo‐flavodoxin, and Desulfovibrio desulfuricans ATCC strain 27774 apo‐ and holo‐flavodoxins involve rather stable intermediates. In contrast, we here show that both holo‐ and apo‐forms of flavodoxin from D. desulfuricans ATCC strain 29577 (75% sequence similarity with the strain 27774 protein) unfold in two‐state equilibrium processes. Moreover, the FMN cofactor remains bound to the unfolded holo‐protein. The folding and unfolding kinetics for holo‐flavodoxin exhibit two‐state behavior, albeit an additional slower phase is present at very low denaturant concentrations. The extrapolated folding time in water for holo‐flavodoxin, ∼280 μsec, is in excellent agreement with that predicted from the protein's native‐state topology. Unlike the holo‐protein behavior, the folding and unfolding reactions for apo‐flavodoxin are best described by two kinetic phases, with rates differing ∼15‐fold, suggesting the presence of a kinetic intermediate. Both folding phases for apo‐flavodoxin are orders of magnitude slower (40‐ and 530‐fold, respectively) than that for the holo‐protein. We conclude that polypeptide–cofactor interactions in the unfolded state of D. desulfuricans strain 29577 flavodoxin alter the kinetic‐folding path towards two‐state and speed up the folding reaction.
In vitro vascular tube formation testing as a tool for treatment individualisation in patients with cervical cancer.

BACKGROUND/AIM Targeted tumour therapies are promising, but their results in unselected patient populations are modest and tumour growth and metastasis may be promoted rather than suppressed in some cases. The present study investigates the suitability of vascular in vitro tube formation as a tool for the identification of cervical neoplasms that will respond to bevacizumab therapy. PATIENTS AND METHODS Fifteen patients with recurrent cervical cancer selected from the ongoing cervical cancer monitoring database of the Charité University Hospital Berlin, Germany, were included. Information obtained from the database included tumour stage, malignancy grade, presence of nodal metastases, lymph vessel invasion, patient age and menopausal status and serum concentrations of vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), endostatin and vascular endothelial growth factor receptor 1 (VEGF-R1). Vascular tube formation was assessed with cultured human umbilical vein epithelial cells. RESULTS Five patients showed a positive, 5 an inverse and 5 no in vitro response to bevacizumab. Tube length showed a marked and significant dependency on bevacizumab response. Besides tube length, VEGF-R1 concentration was the only variable with some correlation to bevacizumab response, with high levels especially for inverse responders. CONCLUSION The identification of patients with a likely benefit from targeted therapies is crucial. Tube formation shows substantial potential, but its utility needs to be confirmed in studies on the clinical rather than in vitro response to bevacizumab.
MOXIBUSTION HAS A POSITIVE EFFECT ON PULMONARY FIBROSIS: AN ALTERNATIVE APPROACH

Background: An increasing number of people suffered idiopathic fibrosis (IPF) and the current treatment was far from clinical satisfaction. Moxibustion, another effective and safe unconventional therapy, had been introduced to treat this refractory disease. The study aimed to investigate the effect of moxibustion on a bleomycin A5-induced pulmonary fibrosis model. Materials and Methods: Sprague-dawley (SD) rats were randomly allocated to the blank group, model group, moxibustion group, and prednisone group, for which they received no treatment, modeling, moxibustion treatment and prednisone treatment. After four-week treatment, the rats were euthanized for Hematoxylin and Eosin (H.E.) staining, and TGF-β1 and IFN-γ protein and mRNA detection in lungs. Results: In the model group, TGF-β1 was significantly increased and IFN-γ was significantly decreased at both protein and mRNA levels in comparison to the blank group. In the moxibustion and prednisone group, however, TGF-β1 was decreased and IFN-γ was increased at both protein and mRNA levels in comparison to the model groups. Compared with prednisone, moxibustion showed comparable effect in lowing TGF-β1 (P>0.05) and better effect in up-regulating IFN-γ (P>0.05). Conclusion: The study concludes moxibustion protected pulmonary fibrosis by downregulating TGF-β1 and upregulating IFN-γ cytokines at both mRNA and protein levels, and the effect was comparable to prednisone. Moxibustion could be used as a therapeutic alternative treatment for pulmonary fibrosis.
A common polymorphism renders the luteinizing hormone receptor protein more active by improving signal peptide function and predicts adverse outcome in breast cancer patients.

CONTEXT Epidemiological and animal studies indicate a carcinogenic role of estrogens in breast tissue. The pituitary gonadotropin LH is an important regulator of estrogen production in premenopausal women, whereas even in women after menopause, 10-25% of ovarian steroid hormone production is LH dependent. OBJECTIVE We hypothesized that an LH receptor (LHR) gene variant may affect LHR function and thereby influence disease outcome in breast cancer patients. DESIGN The association of a polymorphic CTCCAG (Leu-Gln) insertion (insLQ), in the signal peptide encoded by exon 1 of the LHR gene with breast cancer risk, (disease-free) survival, and clinicopathological features was studied in a large cohort of 751 breast cancer patients with complete follow-up. Functional analysis of the insLQ-LHR and non-LQ-LHR (no LQ insertion) was carried out using transfection studies. RESULTS We found a significant association between the insLQ-LHR and a shorter disease-free survival (hazard ratio, 1.34; confidence interval, 1.11-1.63; P = 0.003). The mechanism of the effect of insLQ on LHR function involves increased receptor sensitivity (insLQ-LHR has a 1.9 times lower EC(50) than non-LQ-LHR; P = 0.02) and plasma membrane expression (insLQ-LHR has 1.4 times higher B(max); P = 0.0006) rendering the insLQ-LHR allele more active. CONCLUSIONS The insLQ polymorphism increases LHR activity, thereby shortening breast cancer disease-free survival, probably by increasing estrogen exposure in female carriers.