Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV‐1 capsid protein

The cellular protein, cyclophilin A (CypA), is incorporated into the virion of the type 1 human immunodeficiency virus (HIV‐1) via a direct interaction with the capsid domain of the viral Gag polyprotein. We demonstrate that the capsid sequence 87His‐Ala‐Gly‐Pro‐Ile‐Ala92 (87HAGPIA92) encompasses the primary cyclophilin A binding site and present an X‐ray crystal structure of the CypA/HAGPIA complex. In contrast to the cis prolines observed in all previously reported structures of CypA complexed with model peptides, the proline in this peptide, Pro 90, binds the cyclophilin A active site in a trans conformation. We also report the crystal structure of a complex between CypA and the hexapeptide HVGPIA, which also maintains the trans conformation. Comparison with the recently determined structures of CypA in complexes with larger fragments of the HIV‐1 capsid protein demonstrates that CypA recognition of these hexapeptides involves contacts with peptide residues Ala(Val) 88, Gly 89, and Pro 90, and is independent of the context of longer sequences.
Intracistronic transcription termination in polysialyltransferase gene (siaD ) affects phase variation in Neisseria meningitidis

Expression of serogroup B meningococcal capsular polysaccharide is subject to frequent phase variation. A reversible +1/−1 frameshift mutation within a poly(dC) repeat altering the reading frame of the polysialyltransferase gene (siaD ), thereby causing premature arrest of translation, is responsible for loss of capsule expression. After analysis of transcription of the siaD gene from an encapsulated strain and from two unencapsulated derivatives, we have found that the siaD mRNA in the unencapsulated strains is reduced in size as a result of premature transcription termination at a cryptic Rho‐dependent site within the proximal region of the siaD cistron. Termination is sensitive to bicyclomycin, a natural inhibitor of Rho activity. Bicyclomycin decreased the rates of capsule re‐expression (off–on) without affecting the rates of loss of capsule expression (on–off). This finding suggested the existence of a novel mechanism linking transcription elongation termination and mutation frequency. A genetic system was therefore developed to measure phase variation of siaD–ermC′ gene fusions in wild type and Rho‐defective Escherichia coli strains. These studies demonstrated that in the Rho‐defective E. coli strain readthrough transcription of the mutated siaD gene caused a fourfold lower off–on phase variation rate than in the congenic Rho+ strain. Analysis of phase variation of siaD–ermC′ gene fusions in a DNA mismatch‐defective E. coli strain suggests that the effect of transcription on mutation rates required a functional mismatch repair system.
A physics based analytical model and numerical simulation for current-voltage characteristics of microwave power AlGaN/GaN HEMT

A simple analytical model which validates both intrinsic and extrinsic current-voltage characteristics of AlGaN/GaN HEMT is presented. The dependence of spontaneous and piezoelectric polarization effects at the heterointerface, applied gate bias and Al mole fraction of AlGaN layer have been taken into account for estimating the two-dimensional electron gas (2DEG) density and current characteristics. The polynomial approximation which relates EF and sheet carrier density simplifies the model for all regions of operation i.e., from subthreshold to strong inversion region. The effect of parasitic source and drain resistance are considered to predict the extrinsic HEMT characteristics. The results obtained from the analytical model are compared with experimental data and TCAD numerical simulation results, and shows good agreement, thereby proving the validity of the model.
Rapid estimation of cartilage T2 based on double echo at steady state (DESS) with 3 Tesla

The double‐echo‐steady‐state (DESS) sequence generates two signal echoes that are characterized by a different contrast behavior. Based on these two contrasts, the underlying T2 can be calculated. For a flip‐angle of 90°, the calculated T2 becomes independent of T1, but with very low signal‐to‐noise ratio. In the present study, the estimation of cartilage T2, based on DESS with a reduced flip‐angle, was investigated, with the goal of optimizing SNR, and simultaneously minimizing the error in T2. This approach was validated in phantoms and on volunteers. T2 estimations based on DESS at different flip‐angles were compared with standard multiecho, spin‐echo T2. Furthermore, DESS‐T2 estimations were used in a volunteer and in an initial study on patients after cartilage repair of the knee. A flip‐angle of 33° was the best compromise for the combination of DESS‐T2 mapping and morphological imaging. For this flip angle, the Pearson correlation was 0.993 in the phantom study (∼20% relative difference between SE‐T2 and DESS‐T2); and varied between 0.429 and 0.514 in the volunteer study. Measurements in patients showed comparable results for both techniques with regard to zonal assessment. This DESS‐T2 approach represents an opportunity to combine morphological and quantitative cartilage MRI in a rapid one‐step examination. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Alternate gram staining technique using a fluorescent lectin

Fluorescence-labeled wheat germ agglutinin binds specifically to N-acetylglucosamine in the outer peptidoglycan layer of gram-positive bacteria. The peptidoglycan layer of gram-negative bacteria is covered by a membrane and is not labeled by the lectin. By exploiting this phenomenon, an alternative Gram staining technique has been developed.
Exploring membrane protein structural features by oxidative labeling and mass spectrometry

Despite their biological importance, the structural characterization of integral membrane proteins (IMPs) by x-ray crystallography and NMR spectroscopy remains challenging. Hence, there is a need for complementary approaches that are capable of probing IMP conformational features in a robust fashion. Covalent labeling relies on the principle that solvent accessible regions can be modified by reactive species, whereas buried segments are protected. The readout of the labeling pattern is conducted by mass spectrometry. Hydroxyl radical (·OH) introduces oxidative modifications at amino acid side chains. In this article, the authors discuss the application of ·OH labeling for the structural interrogation of IMPs. Kyte-Doolittle hydropathy analyses are widely used for generating IMP topology models. The validation of these models by mutational techniques is labor intensive. ·OH labeling can readily distinguish transmembrane elements from solvent-exposed loops, thereby providing an alternative topology validation tool. For IMPs with published crystal structures, oxidative modifications can report on functionally relevant dynamic features that are invisible in the static x-ray data. The coupling of pulsed ·OH labeling with rapid mixing techniques represents a novel approach for studying IMP folding kinetics. In conclusion, ·OH labeling is a versatile tool that can provide insights into the structure and dynamics of IMPs.
Does self-reported sleep quality predict poor cognitive performance among elderly living in elderly homes?

Objectives: Sleep complaints are common among elderly, especially institutionalized elderly, as they experience poorer sleep quality and higher use of sedative hypnotics, when compared to community-dwelling elderly. Recent findings suggest that there may be a relationship between poor quality of sleep and cognitive deficits. This study aimed at studying the relation between sleep quality and cognitive performance in older adults living in elderly homes. Method: 100 elderly living in an elderly home in El Mansoura, Egypt, were recruited in this study, 50 cases with subjective poor quality of sleep and 50 controls with subjective good quality of sleep as assessed by Pittsburgh sleep quality index (PSQI). Each participant went through comprehensive geriatric assessment (CGA), including geriatric depression scale (GDS), assessment of cognitive function by mini mental state examination (MMSE). Results: 52% of poor sleepers showed impaired MMSE, while only 24% of good sleepers had impaired MMSE. Both orientation and (attention and calculation) were more affected (P = 0.027 and 0.035, respectively). Linear correlation coefficient between PSQI and different variables revealed significant negative correlation with total MMSE score, attention and calculation. Conclusion: Poor quality of sleep is related to cognitive impairment among elderly living in elderly homes and this problem should be taken in consideration among this group of elders.
Development and characterization of nine polymorphic microsatellite markers for Mexican spadefoot toads (Spea multiplicata) with cross‐amplification in Plains spadefoot toads (S. bombifrons)

We developed nine polymorphic microsatellite markers for the Mexican spadefoot toad, Spea multiplicata. Allele numbers range from five to 12, with observed heterozygosities from 0.48 to 0.87. Because two loci are in linkage disequilibrium, these nine loci provide eight independent markers. Three loci exhibit departure from Hardy–Weinberg equilibrium, possibly resulting from null alleles or population admixture. These markers will be useful for assessing population structure and relatedness in S. multiplicata. Based on our success at cross‐amplification in the Plains spadefoot toad (Spea bombifrons), these loci also may be useful in this species with additional optimization.
Association of dietary fiber intake with serum total cholesterol and low density lipoprotein cholesterol levels in Urban Asian-Indian adults with type 2 diabetes

Context: There is little data correlating dietary fibre (DF) intake and cardiovascular risk in Asian Indians with diabetes. Aim: To assess the DF intake and its association with lipid profile (total serum cholesterol and low density lipoprotein [LDL] - cholesterol levels) in urban Asian Indians with diabetes. Subjects and Methods: Dietary assessment using validated Food Frequency Questionnaire was conducted in 1191 free-living adults with known diabetes in the Chennai Urban Rural Epidemiology Study. Subjects taking medication for dyslipidemia, and those with cardiovascular disease and implausible energy intake (n = 262) were excluded, leaving 929 participants. Anthropometric and relevant biochemical parameters were measured using standardized techniques. Results: Diabetic individuals who consumed DF < median intake (29 g/day) had a higher prevalence of hypercholesterolemia (49.5% vs. 40.1% [P = 0.01]) and higher LDL cholesterol (46.2% vs. 35.5% [P = 0.001]) than those in the > median intake of DF group. The risk of hypercholesterolemia (odds ratio [OR] =1.38 [95% confidence interval [CI]: 1.02–1.85], P = 0.04), and high LDL cholesterol (OR: 1.43 [95% CI: 1.06–1.94], P = 0.02) was higher among those whose DF intake was less than the median. Serum triglycerides and high density lipoprotein cholesterol were not associated with DF intake. The main sources of DF were vegetables and legumes. Conclusion: In urban Asian Indians with diabetes, lower DF intake is positively related to total cholesterol and LDL cholesterol levels.
Frequency reconfigurable MIMO slot and UWB sensing antennas for CR applications

In this paper, an integrated annular slot based 2-element multiple-input-multiple-output (MIMO) antenna along with an ultra-wide-band (UWB) sensing antenna system is presented. The frequency reconfigurable slot based MIMO antenna system is tuned over a wide frequency band from 1.75 GHz to 2.48 GHz while the sensing antenna is resonating from 0.75 GHz to 7.65 GHz with an UWB operation. The frequency agile antenna covered several well known wireless standards. The proposed cognitive radio (CR) antenna system is suitable for wireless handheld devices and mobile terminals in CR applications. To analyze the MIMO performance metrics, envelop correlation coefficient values are computed to validate the MIMO operation.
Experience, Equity and Foreign Investment Risk: A PIC Perspective

We analyze foreign investment risk-mitigating effects of host-country policy stability, firm experience and equity stakes using an empirical context largely ignored by international business (IB) research: project investment companies (PICs). PICs permit cleaner separation of individual investment project risk from the parent firm, which may otherwise pool risk characteristics from managing multiple projects across different industries and countries. PICs also permit potentially unbiased, prospective risk assessment at the time of a project’s initial announcement based on the mix of debt and equity funding the project. Consistent with previous IB research, our analyses of 396 PICs announced in 53 countries from 1990–2006 indicate that investment risk measured as the percentage of equity-to-total capital funding a PIC decreases with greater host-country policy stability, lead-investor experience in the host country, and lead-investor equity stakes. But contrary to previous IB research, we find that lead-sponsor experience and equity stakes reduce investment risk less as host-country policy stability decreases. From a PIC perspective, investor experience and equity stakes are complements to (not substitutes for) host-country policy stability. Our PIC-based evidence re-invigorates research and related practice and policy debates about how investor experience and equity holdings affect foreign project decisions and suggests new avenues for future work.
Uteroglobin and transglutaminase modulate human sperm functions.

During the process of capacitation, spermatozoa undergo significant changes in membrane composition, including removal of decapacitating factors (DFs), which are present in seminal plasma, that lead to increased sensitivity to physiological stimuli of the acrosome reaction. In the present study we investigated the presence, localization, and effects on human spermatozoa of 2 proteins of seminal plasma origin, uteroglobin (UG) and transglutaminase (TG). These 2 proteins interact with one another because TG promotes covalent links of UG to sperm surface proteins. We found that UG is localized around the entire surface of ejaculated human sperm, whereas TG is predominantly localized in the neck. FACScan analysis confirmed the surface localization of both antigens and demonstrated that swim-up selection of spermatozoa was associated with a significant reduction in the contents of the 2 substances when compared with unselected samples. Western blot analysis of UG in total sperm lysates confirmed the lower content of the protein in swim-up-selected sperm. Swim-up-selected sperm were characterized by their ability to undergo a spontaneous, time-dependent increase of capacitation-characteristic chlortetracycline pattern of fluorescence and increase in responsiveness to progesterone. Such changes were not observed in unselected sperm. Exogenous addition of TG, together with recombinant rabbit UG, prevented the spontaneous increase in responsiveness to progesterone (acrosome reaction and intracellular calcium) at 24 hours in swim-up-selected sperm, suggesting the occurrence of a capacitation-inhibiting activity of the 2 substances. In addition, we found that endogenous UG and TG contents, as determined by FACScan analysis, were negatively correlated (P < .0001) with sperm motility and that exogenous addition of the 2 substances resulted in a substantial reduction of progressive motility (P < .01). Collectively, these data indicate that TG and UG represent 2 DFs, and contribute to understanding the biochemical mechanisms that characterize the process of capacitation.
A hybrid MAC protocol in data-collection-oriented underwater acoustic sensor networks

Due to the specific characteristics in terms of long propagation delay, high bit-error-rate and limited available bandwidth in the underwater environment, designing the medium access control (MAC) protocol in underwater acoustic sensor networks (UWASNs) is a challenging issue. Considering a UWASN for data collection, data generated at sensor nodes are transmitted to the sink node hop by hop. Since the traffic load in each hop is different, single-mode MAC protocol cannot satisfy the requirement of the data collection mission. In this paper, we propose a hybrid MAC protocol for two-tier data-collection-oriented UWASN. In the proposed hybrid MAC protocol, a contention-based MAC protocol is performed in the lightly loaded sub-network, and a reservation-based MAC protocol is carried out in the heavily loaded sub-network. Moreover, the proposed MAC protocol supports the access of mobile nodes, such as autonomous underwater vehicle (AUV). Simulation results show that the proposed hybrid MAC protocol achieves high throughput.
Solute Carrier Family 19, Member 1 (SLC19A1) Polymorphisms (−43T>C, 80G>A, and 696C>T), and Haplotypes in Idiopathic Recurrent Spontaneous Abortion in a Korean Population

The objective was to investigate the association between idiopathic recurrent spontaneous abortion (RSA) and 3 SLC19A1 polymorphisms (−43T>C, 80G>A, and 696C>T). DNA from 269 patients with RSA and 125 controls were genotyped for the 3 SLC19A1 single nucleotide polymorphisms (SNPs) by polymerase chain reaction–restriction fragment length polymorphism. Homocysteine and folate levels of 100 patients with RSA were available for analysis. The combination genotypes of SLC19A1 −43TC/80GG, −43TC/80AA, and −43CC/80GA; 80GA/696TT, 80AA/696CC; and −43TC/696CC were less frequent in patients with RSA compared to controls (P < .05 for each). The −43C/80A/696 T and −43T/80G/696C haplotypes were more frequent in patients than controls, whereas −43T/80A/696C, −43C/80A/696C, −43C/80G/696C, −43C/80G/696T, and −43T/80G/696T haplotypes were less frequent in patients (P < .05 for each). The −43T/80G and 80A/696T haplotypes were more frequent in patients, while −43T/80A, −43C/80G, 80A/696C, 80G/696T, and −43C/696C haplotypes occurred less frequently in patients (P < .05 for each). The associations between idiopathic RSA occurrence and SLC19A1 −43T>C/80G>A/696C>T polymorphisms were identified and can be developed as biomarkers for RSA risk.
The Luminal N‐Terminus of Yeast Nvj1 is an Inner Nuclear Membrane Anchor

The endoplasmic reticulum (ER) in Saccharomyces cerevisiae is largely divided between perinuclear and cortical compartments. Yeast Nvj1 localizes exclusively to small patches on the perinuclear ER where it interacts with Vac8 in the vacuole membrane to form nucleus–vacuole (NV) junctions. Three regions of Nvj1 mediate the biogenesis of NV junctions. A membrane‐spanning domain targets the protein to the ER. The C‐terminus binds Vac8 in the vacuole membrane, which induces the clustering of both proteins into NV junctions. The luminal N‐terminus is required for strict perinuclear localization. Three‐dimensional cryo‐electron tomography reveals that Nvj1 clamps the separation between the two nuclear membranes to half the width of bulk nuclear envelope. The N‐terminus contains a hydrophobic sequence bracketed by basic residues that resembles outer mitochondrial membrane signal‐anchors. The hydrophobic sequence can be scrambled or reversed without affecting function. Mutations that reduce the hydrophobicity of the core sequence or affect the distribution of basic residues cause mislocalization to the cortical ER. We conclude that the N‐terminus of Nvj1 is a retention sequence that bridges the perinuclear lumen and inserts into the inner nuclear membrane.
Effects of parenting style and parent-related weight and diet on adolescent weight status.

OBJECTIVE This study examined the interaction between parental limit setting of sedentary behaviors and health factors (weight status, physical activity [PA], fruit and vegetable [FV] intake) on standardized body mass index (zBMI) in African American adolescents. METHODS Data were from 67 parent-adolescent dyads. Parental limit setting, PA and FV intake were assessed via self-report, and objective height and weight measurements were collected. RESULTS Regressions examined the interaction between parental limit setting and BMI, PA, FV intake on adolescent zBMI. The model for parent BMI and FV intake accounted for 31% of the variance in adolescent zBMI. A significant interaction for parent BMI by limit setting showed that as parental BMI increased, higher (vs. lower) limit setting was associated with lower adolescent zBMI. Higher parent FV consumption was associated with lower adolescent zBMI. CONCLUSION Future interventions should integrate parent limit setting and target parent fruit and vegetable intake for obesity prevention in underserved adolescents.
Strategy for addressing sexual and domestic violence in universities: Prevention and response

This document summarises the essential elements of an effective strategic approach to preventing, and responding to, sexual and domestic violence against women and related forms of violence and abuse in university settings. In order to respond to their institutional responsibilities, universities should address: prevention; policy; monitoring and reporting; providing and signposting specialist response and support pathways; and fostering culture change – which is key to preventing violence against women. In addition to this institutional response, it is important for student unions and other student–led organisations to work in conjunction with universities particularly in regard to shaping culture change.
How Robust Are Hospital Ranks Based on Composite Performance Measures?

Background:Composite indices of healthcare performance are an aggregation of underlying individual performance measures. They are increasingly being used to rank healthcare organizations. Although composite indicators present the “big picture” in a way that is easy to interpret, misleading conclusions may be drawn if attention is not paid to key methodological issues in their construction. Objectives:We examine variability in performance measures in the context of the construction and use of composite measures. We illustrate how variability in the underlying data and the resulting composite may undermine the robustness of performance measures in health care. We also illustrate how variation in the methodological rules applied to aggregate the individual indicators can have an important impact on composite scores. Methods:We use data for 117 English acute hospitals to illustrate the generic methodological issues. The variance in performance measures is partitioned into “controllable” and “uncontrollable” elements. We create a composite index from the underlying performance indicators and use Monte Carlo simulations to examine the robustness of the composite. Results:Random variation beyond the control of organizations gives rise to considerable uncertainty in hospital scores. Composites are also sensitive to changes made to the weighting system and to the aggregation rules. Some hospitals can jump almost half of the league table as a result of subtle changes. Conclusions:Great care is warranted in interpreting the results of composite performance measures. Suggestions for their future development are made.