Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil respiration rates in coastal marshes subject to increasing watershed nitrogen loads in southern New England, USA

Mean soil respiration rates (carbon dioxide efflux from bare soils) among salt marshes in Narragansett Bay, RI ranged from 1.7–7.8 μmol m−2 s−1 inSpartina patens in high marsh zones and 1.7–6.0 μmol m−2 s−1 inS. alterniflora in low marsh zones. The soil respiration rates significantly increased along a gradient of increasing watershed nitrogen (N) loads (S. alterniflora, R2 = 0.95, P = 0.0008;S. patens, R2 = 0.70, P = 0.02). As the soil respiration increased, the percent carbon (C) and N in the soil surface layer decreased in theS. alterniflora, suggesting that in part, the increased soil respiration rates are contributing to the increased turnover of labile organic matter. In contrast, there were no apparent relationships between the soil respiration rates in the high marsh and the soil C and N contents of the surface layer. However, there was a broad-scale pattern and significant inverse relationship between the high marsh soil respiration rates and the landscape belowground biomass ofS. patens. As more and more salt marsh systems are subjected to increasing nutrient loads, decomposition rates of soil organic matter may increase in marsh soils leading to higher turnover rates of C and N.
Production of IgG antibodies to pneumococcal polysaccharides is associated with expansion of ICOS+ circulating memory T follicular-helper cells which is impaired by HIV infection

Dysfunction of T follicular-helper (TFH) cells is a possible cause of impaired germinal centre (GC) and IgG antibody responses in individuals with human immunodeficiency virus-1 (HIV-1) infection and might contribute to decreased magnitude and isotype diversification of IgG antibodies to pneumococcal polysaccharides (PcPs). We examined the production of IgG1 and IgG2 antibodies to PcPs 4, 6B, 9V and 14 by enumerating antibody secreting cells (ASCs) at day (D) 7 and determining fold-increase in serum antibody levels at D28 after vaccination with unconjugated PcPs in HIV seronegative subjects (n = 20) and in HIV patients who were receiving antiretroviral therapy (ART) (n = 28) or who were ART-naive (n = 11) and determined their association with ICOS+ and ICOS- circulating memory TFH (cmTFH) cells (CD4+CD45RA-CD27+CXCR5+PD-1+) and short lived plasmablasts (SPBs) at D7, and with PcP-specific and total IgM+ and IgG+ memory B cells at D0. In HIV seronegative subjects, production of IgG1+ and IgG2+ ASCs was consistently associated with the frequency of ICOS+ cmTFH cells but not ICOS- cmTFH cells or memory B cells. In contrast, post-vaccination ASCs in HIV patients, regardless of ART status, were lower than in HIV seronegative subjects and not associated with ICOS+ cmTFH cells, the expansion of which was absent (ART-naive patients) or much lower than in HIV seronegative subjects (ART-treated patients). Production of SPBs was also lower in ART-naive patients. Fold-increase in IgG2 antibodies at D28 also correlated with ICOS+ cmTFH cells at D7 in HIV seronegative subjects but not in HIV patients. These novel findings provide evidence that ICOS+ cmTFH cells contribute to the regulation of PcP-specific IgG antibody responses, including isotype diversification, and that TFH cell dysfunction may be a cause of impaired PcP-specific IgG antibody responses and increased susceptibility to pneumococcal disease in HIV patients.
C-Glucoside xanthone from the stem bark extract of Bersama engleriana

Background: The genus Bersama belongs to the Melianthaceae family and comprises of four species (B. swinnyi, B. yangambiensis, B. abyssinica, and B. engleriana) all of which are very high trees; the latter two detected species are found in Cameroon. Previous phytochemical investigation on B. yangambiensis, B. swinnyi, and B. abyssinica led to the isolation of triterpenes, saponins, flavonoids, and xanthones. Method: The stem bark of B. engleriana were collected in the village, Baham near Bafoussam city, Cameroon in August 2003 and identifi ed by Dr. Onana National Herbaruim, Yaoundι, Cameroon. The air dried and powdered stem bark of B. engleriana (1 kg) was extracted at room temperature with CH2Cl2-MeOH (1:1) 5 L for 48 hours. The mixture of the solvent was removed by evaporation to yield 200 g of crude extract. The latter was then dissolved in CH2Cl2 to give the CH2Cl2 soluble fraction of 5 g and a remaining gum of 195 g. Part of the remaining gum (22 g) was dissolved in water and extracted four times with butanol to give 12 g of red oil; which was then separated by paper chromatography, with butanol-acetic acid-water (4:1:5), to give 3 g of orange gum; purification was carried out on HPLC with MeOH (100%) to yield 2 g of mangiferin (1) as red oil. The CH2Cl2 soluble extract was eluted on silica gel n-hexane-CH2Cl2 gradient ratio and Sephadex LH-20 (n-hexane -CH2Cl2 -MeOH, (7:4:0.5) to afford compounds swinniol (2), Δ4-stigmaster-3β-ol (3), 4-methylstigmaster-5,23-dien-3β-ol(4). Results: Herein, we carried out a phytochemical study of the stem bark of B. engleriana, and we report herein the isolation and structural elucidation of mangiferin, in addition to three triterpenes, previously reported from other species of the genus. [35] The assignment of the signals of mangiferin was determined using 1H, 13C-NMR, and 2D-NMR spectral data (HMQC, COSY, HMBC). The terpenoids were identifi ed by comparison of their 1H and 13C-NMR spectra with the literature data. Fractionation of the CH2Cl2-MeOH (1:1) extract of the stem bark of B. engleriana Guike gave mangiferin (1), in addition to three previously reported triterpenes, swinniol (2), Δ4-stigmaster-3β-ol (3), and 4-methylstigmaster-5,23-dien-3-β-ol (4). Conclusions: A chemical investigation of the CH2Cl2-MeOH extract of the stem bark of Bersama engleriana afforded a xanthone C-glucoside (mangiferin) and fi rst isolation of three terpenoids from this species: swinniol (2), Δ4-stigmaster-3β-ol (3), and 4-methylstigmaster-5,23-dien-3-β-ol (4). The complete 1H and 13C chemical shift assignments of mangiferin were determined using 1D and 2D NMR spectroscopic data (COSY, HMQC, HMBC, DEPT). The structures of the terpenoids were determined from their 1H and 13C NMR data and compared with the literature data.
Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

ABSTRACT Pseudomonas aeruginosa 96 (PA96) was isolated during a multicenter surveillance study in Guangzhou, China, in 2000. Whole-genome sequencing of this outbreak strain facilitated analysis of its IncP-2 carbapenem-resistant plasmid, pOZ176. The plasmid had a length of 500,839 bp and an average percent G+C content of 57%. Of the 618 predicted open reading frames, 65% encode hypothetical proteins. The pOZ176 backbone is not closely related to any plasmids thus far sequenced, but some similarity to pQBR103 of Pseudomonas fluorescens SBW25 was observed. Two multiresistant class 1 integrons and several insertion sequences were identified. The blaIMP-9-carrying integron contained aacA4→blaIMP-9→aacA4, flanked upstream by Tn21 tnpMRA and downstream by a complete tni operon of Tn402 and a mer module, named Tn6016. The second integron carried aacA4→catB8a→blaOXA-10 and was flanked by Tn1403-like tnpRA and a sul1-type 3′ conserved sequence (3′-CS), named Tn6217. Other features include three resistance genes similar to those of Tn5, a tellurite resistance operon, and two pil operons. The replication and maintenance systems exhibit similarity to a genomic island of Ralstonia solanacearum GM1000. Codon usage analysis suggests the recent acquisition of blaIMP-9. The origins of the integrons on pOZ176 indicated separate horizontal gene transfer events driven by antibiotic selection. The novel mosaic structure of pOZ176 suggests that it is derived from environmental bacteria.
Legislative Professionalization and Membership Diversity in State Legislatures

Proponents of state legislative professionalization thought it would increase membership diversity. I assess whether this expectation has been met by examining the relationship between the level of professionalization and the numbers of blacks, women, and various occupational groups elected to the state legislature. I begin by proposing a new measurement of professionalization, one which uses the United States Congress as a baseline against which to measure the salary, staff, and time in session of all 50 state legislatures. Level of professionalization is found to be positively related to the percentage of blacks in a legislature but negatively related to the proportion of women serving. Occupational diversity also decreases as level of professionalization increases, because more members identify their occupation as full-time legislator.
Prevalence and prognostic factors for erectile dysfunction in renal transplant recipients.

INTRODUCTION The purpose of this study was to determine the prevalence of erectile dysfunction (ED) at our institution in the postrenal transplant population and to compare those patients who had ED with those who did not have ED, with respect to several patient characteristics. METHODS We conducted a cross-sectional study of male renal transplant recipients who were in attendance at the transplant clinic from April 1, 2004, to March 31, 2006. Erectile function was evaluated using the International Index of Erectile Function short form questionnaire. Patients were also screened for depression using the Beck Depression Inventory. We performed a chart review to obtain various patient characteristics. RESULTS This study involved 55 patients. Their average age was 50 years old and the mean duration of the current transplant was 7.9 years. ED was identified in 28 of the patients (51%). More patients with ED were over age 50 years (64% v. 26%, p = 0.004). There was a higher prevalence of diabetes mellitus (39% v. 11%, p = 0.02) in patients with ED compared with those patients without ED. More patients with ED were depressed compared with those patients who did not have ED (29% v. 7%, p = 0.04). These 3 factors were significantly associated with ED and this relationship was confirmed on multivariate analysis. CONCLUSION ED remains a common problem in the renal transplant population. The cause of ED is multifactorial, with increasing age and the presence of diabetes mellitus and depression increasing the risk of ED.
Experimental Multipath-Cluster Characteristics of 28-GHz Propagation Channel

In this paper, a channel measurement campaign is introduced, which utilizes direction-scan-sounding to capture the spatial characteristics of 28-GHz wave propagation channels with 500-MHz sounding bandwidth in office environments. Both line-of-sight and non-line-of-sight scenarios were considered. Measurements were performed by fixing a transmit pyramidal horn antenna, and rotating another one in the receiver site at 10° steps in azimuth. The antenna outputs are viewed as array signals, and a space-alternating generalized expectation-maximization (SAGE) algorithm is applied to estimate delay and angular parameters of multipath components. Benefiting from high resolution achieved by using the SAGE and deembedding of antenna radiation pattern and system responses, more multipath clusters with less spreads in delay and azimuth are found per channel compared with existing works on 28-GHz propagation. The statistics of channel parameters extracted here constitute a preliminary stochastic multipath-cluster spatial channel model.
Volume-dependent effect of perihaematomal oedema on outcome for spontaneous intracerebral haemorrhages

Introduction It is still unknown whether subsequent perihaematomal oedema (PHE) formation further increases the odds of an unfavourable outcome. Methods Demographic, clinical, radiographic and outcome data were prospectively collected in a single large academic centre. A multiple logistic regression model was then developed to determine the effect of admission oedema volume on outcome. Results 133 patients were analysed in this study. While there was no significant association between relative PHE volume and discharge outcome (p=0.713), a strong relationship was observed between absolute PHE volume and discharge outcome (p=0.009). In a multivariate model incorporating known predictors of outcome, as well as other factors found to be significant in our univariate analysis, absolute PHE volume remained a significant predictor of poor outcome only in patients with intracerebral haemorrhage (ICH) volumes ≤30 cm3 (OR 1.123, 95% CI 1.021 to 1.273, p=0.034). An increase in absolute PHE volume of 10 cm3 in these patients was found to increase the odds of poor outcome on discharge by a factor of 3.19. Conclusions Our findings suggest that the effect of absolute PHE volume on functional outcome following ICH is dependent on haematoma size, with only patients with smaller haemorrhages exhibiting poorer outcome with worse PHE. Further studies are needed to define the precise role of PHE in driving outcome following ICH.
In Vitro Analysis of Nuclear Transport Mediated by the C-terminal Shuttle Domain of Tap*

The Tap protein of higher eukaryotes is implicated in the nuclear export of type D retroviral mRNA and some cellular mRNAs. Here we have developed an in vitroassay to study nuclear export mediated by the C-terminal shuttle domain of Tap involving the rapamycin-induced attachment of this transport domain to a nuclear green fluorescent protein-containing reporter. We found that export by the Tap transport domain does not involve cytosolic transport factors including the GTPase Ran. The transport domain directly binds to several nucleoporins positioned in different regions of the nuclear pore complex. These results argue that a direct interaction of the Tap transport domain with nucleoporins is responsible for its nucleocytoplasmic translocation. We found that the karyopherin β-related export receptor CRM1 competes with the Tap transport domain for binding to Nup214 but not for binding to Nup62 or Nup153, suggesting that the Tap and CRM1 nuclear export pathways converge at the cytoplasmic periphery of the nuclear pore complex. Because the rates of in vitro nuclear import and export by the Tap transport domain are very similar, the directionality of mRNA export mediated by Tap probably is determined by mechanisms other than simple binding of the Tap transport domain to nucleoporins.
Deep neuromuscular block improves the surgical conditions for laryngeal microsurgery.

BACKGROUND Adequate neuromuscular block is required throughout laryngeal microsurgery. We hypothesized that the surgical conditions would improve under a deeper level of rocuronium-induced neuromuscular block. METHODS Seventy-two patients undergoing laryngeal microsurgery were randomly allocated to either the 'post-tetanic counts 1-2' (PTC1-2) group or the 'train-of-four counts 1-2' (TOFcount1-2) group according to the level of neuromuscular block used. Two different doses of rocuronium (1.2 or 0.5 mg kg(-1)) were used after anaesthetic induction, and two respective targets of neuromuscular block (post-tetanic counts ≤2 or train-of-four count of 1 or 2) were used. Surgical conditions were assessed by the surgeon using a five-point rating scale (extremely poor/poor/acceptable/good/optimal), and clinically acceptable surgical conditions were defined as those which were rated acceptable, good, or optimal. The occurrence of vocal cord movement and postoperative adverse events was assessed. RESULTS The surgical conditions were significantly different between the PTC1-2 and TOFcount1-2 groups (extremely poor/poor/acceptable/good/optimal: 0/2/1/7/26 and 3/10/2/14/7, respectively, P<0.001). The incidence of clinically acceptable surgical conditions was significantly higher in the PTC1-2 group than in the TOFcount1-2 group (94 vs 64%, P=0.003). The percentage of patients who exhibited vocal cord movement was significantly lower in the PTC1-2 group than in the TOFcount1-2 group (3 vs 39%, P<0.001). The incidence of postoperative adverse events was not significantly different except for the less frequent occurrence of mouth dryness in the PTC1-2 group (P=0.035). CONCLUSIONS Deep neuromuscular block (post-tetanic count of 1-2) surgical conditions in patients undergoing laryngeal microsurgery improves. CLINICAL TRIAL REGISTRATION NCT01980069.
Two Years of Broken Crypto: Debian's Dress Rehearsal for a Global PKI Compromise

A patch to the OpenSSL package maintained by Debian GNU/Linux (an operating system composed of free and open source software that can be used as a desktop or server OS) submitted in 2006 weakened its pseudo-random number generator (PRNG), a critical component for secure key generation. Putting both servers and users at risk, this vulnerability affected OpenSSH, Apache (mod_ssl), the onion router (TOR), OpenVPN, and other applications. In this article, the author examines these issue and its consequences. OpenSSL is an open source library implementing the SSL (Secure Socket Layer) and TLS (Transport Layer Security) protocols. Several widely deployed applications on many OSs rely on it for secure communications, particularly Linux and BSD-based systems. Where in use, it's a critical part of the OS's security subsystem.
DNA Damage Stimulates Human Cell Transformation by Integrative But Not Episomal Epstein‐Barr Virus‐Derived Plasmid

Previous work has demonstrated that ultraviolet (UV) irradiation of SV40‐based plasmids can strikingly enhance the frequency of stable transformation of human cells. In this study we compared the effect of UV‐induced DNA damage on transformation mediated by integrative versus autonomously replicating plasmids derived from human Epstein‐Barr virus (EBV). We report that transfection of human fibroblasts with UV‐irradiated integrative EBV‐based plasmid results in enhanced transformation. However, transfection of UV‐damaged episomal EBV‐based constructs into the same human cell line does not enhance transformation; in fact, the extrachromosomal status of the plasmid is maintained irrespective of the UV dose to the plasmid. We conclude that enhanced transformation of human cells by damaged DNA requires its chromosomal integration.
Cryptic tetracycline resistance determinant (class F) from Bacteroides fragilis mediates resistance in Escherichia coli by actively reducing tetracycline accumulation

Escherichia coli bearing a cryptic tetracycline resistance determinant from Bacteroides fragilis expressed low-level constitutive resistance to tetracycline under aerobic, but not anaerobic, growth conditions and accumulated less tetracycline aerobically than did isogenic susceptible cells. This decreased uptake was energy dependent and reversible by increased concentrations of tetracycline, suggesting a saturable carrier-mediated active efflux mechanism. Decreased uptake was not seen when the cells were grown and assayed anaerobically. Other tetracycline resistance determinants (classes A to E) isolated from gram-negative enteric bacteria expressed resistance and generated active efflux of tetracycline under anaerobic as well as aerobic conditions. When the Bacteroides determinant was placed in the same cell with any of the class A to E tetracycline resistance determinants, there was an increase in resistance under aerobic conditions of as much as 48% more than was projected by adding the resistances expressed by the determinants individually. In cells bearing the class A determinant together with the Bacteroides determinant, saturation of the active efflux system required over twofold more exogenous tetracycline than did cells bearing the class A determinant alone. We have designated this new tetracycline resistance determinant class F.
BREEDING SYSTEM, COLONY STRUCTURE, AND GENETIC DIFFERENTIATION IN THE CAMPONOTUS FESTINATUS SPECIES COMPLEX OF CARPENTER ANTS

Abstract All social insects live in highly organized societies. However, different social insect species display striking variation in social structure. This variation can significantly affect the genetic structure within populations and, consequently, the divergence between species. The purpose of this study was to determine if variation in social structure was associated with species diversification in the Camponotus festinatus desert carpenter ant species complex. We used polymorphic DNA microsatellite markers to dissect the breeding system of these ants and to determine if distinct C. festinatus forms hybridized in their natural range. Our analysis of single-queen colonies established in the laboratory revealed that queens typically mated with only a single male. The genotypes of workers sampled from a field population suggested that multiple, related queens occasionally reproduced within colonies and that colonies inhabited multiple nests. Camponotus festinatus workers derived from colonies of the same form originating at different locales were strongly differentiated, suggesting that gene flow was geographically restricted. Overall, our data indicate that C. festinatus populations are highly structured. Distinct C. festinatus forms possess similar social systems but are genetically isolated. Consequently, our data suggest that diversification in the C. festinatus species complex is not necessarily associated with a shift in social structure.
Thermophilic Adaptation of Proteins

Referee: Dr. Ruth Nussinov, Saic Frederick, Bldg. 469. 469, Room 151, Frederick, MD 21702-1201 Hyperthermophilic organisms optimally grow close to the boiling point of water. As a consequence, their macromolecules must be much more thermostable than those from mesophilic species. Here, proteins from hyperthermophiles and mesophiles are compared with respect to their thermodynamic and kinetic stabilities. The known differences in amino acid sequences and three-dimensional structures between intrinsically thermostable and thermolabile proteins will be summarized, and the crucial role of electrostatic interactions for protein stability at high temperatures will be highlighted. Successful attempts to increase the thermostability of proteins, which were either based on rational design or on directed evolution, are presented. The relationship between high thermo-stability of enzymes from hyperthermophiles and their low catalytic activity at room temperature is discussed. Not all proteins from hyperthermophiles are thermostable enough to retain their structures and functions at the high physiological temperatures. It will be shown how this shortcoming can be surpassed by extrinsic factors such as large molecular chaperones and small compatible solutes. Finally, the potential of thermostable enzymes for biotechnology is discussed.