Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy.

The effects of the number, precision and accuracy of interproton distance restraints, of direct refinement against nuclear Overhauser enhancement (NOE) intensities and of the description of the non-bonded contacts on the precision and accuracy of a nuclear magnetic resonance (NMR) protein structure determination have been investigated. The model system employed is the 56 residue immunoglobulin G binding domain of streptococcal protein G. This choice was based on the availability of a very high resolution NMR structure (atomic root-mean-square distribution of the ensemble of 60 calculated structures about the mean co-ordinate positions of 0.25 A for the backbone atoms, 0.65 A for all atoms and 0.39 A for all atoms excluding disordered surface side-chains). The experimental NMR data set for this structure determination comprised a total of 1058 experimental restraints of which 854 were approximate interproton distance restraints corresponding to all the structurally useful NOEs observable for this protein. The calculations presented in this paper reveal the following. (1) The number of interproton distance restraints constitutes the single most important determinant of both precision and accuracy. The ensemble precision and accuracy improves significantly as the number of interproton distance restraints is increased to an average of approximately 15 per residue, of which approximately 60% involve unique proton pairs; subsequent additions of interproton distance restraints, however, lead to less dramatic improvements as information redundancy sets in. (2) The ratio of ensemble precision to ensemble accuracy (which ranges from 0.5 to 0.7 for the backbone atoms) is approximately independent both of the number, precision and accuracy of the interproton distance restraints, and of whether the structures are refined against interproton distance restraints or directly against NOE intensities. (3) In an ensemble of structures generated from a large number of loose approximate interproton distance restraints (an average of approximately 15 restraints per residue with approximately 60% involving unique proton pairs), the interproton distance vectors corresponding to the restraints are very well defined with approximately 80% of vectors between unique proton pairs having a standard deviation of < or = 0.1 A. (4) The accuracy of the mean co-ordinates of an ensemble of structures is significantly higher than the average accuracy of the individual structures comprising the ensemble. For an average ensemble precision of > or = 0.6 A, the dependence of the accuracy of the mean co-ordinates on ensemble precision is approximately linear. (ABSTRACT TRUNCATED AT 400 WORDS)
Ichthyosporidium weissii n. sp. (Microsporidia) Infecting the Arrow Goby (Clevelandia ios)

Gonadal infections by a novel microsporidium were discovered in 34% (13/38) of arrow gobies, Clevelandia ios, sampled over a 3‐yr period from Morro Bay Marina in Morro Bay, California. Gonadal tumors had been reported in arrow gobies from this geographic area. The infected gonads, found primarily in females, typically appeared grossly as large, white‐gray firm and lobulated masses. Histological examination revealed large, multilobate xenomas within the ovaries and no evidence of neoplasia. Typical of the genus Ichthyosporidium, the large xenomas were filled with developmental stages and pleomorphic spores. Wet mount preparations showed two general spore types: microspores with mean length of 6.2 (7.0–4.9, SD = 0.6, N = 20) μm and mean width of 4.3 (5.3–2.9, SD = 0.8) μm; and less numerous macrospores with mean length of 8.5 (10.1–7.1, SD = 1.0, N = 10) μm and mean width of 5.5 (6.2–4.8, SD = 0.5) μm. Transmission electron microscopy demonstrated stages consistent with the genus and 35–50 turns of the polar filament. Small subunit rDNA gene sequence analysis revealed that the parasite from arrow gobies was most closely related to, but distinct from Ichthyosporidium sp. based on sequences available in GenBank. We conclude that this microsporidium represents a new species of Ichthyosporidium, the first species of this genus described from a member of the family Gobiidae and from the Pacific Ocean.
Distribution and quantification of beta1-, beta2-, and beta3-adrenergic receptor subtype transcripts in porcine tissues.

Distribution and concentration of beta-adrenergic receptor (betaAR) subtype transcripts (beta1AR, beta2AR, and beta3AR) were investigated in porcine and rat tissues. Reverse transcription (RT) coupled with PCR indicated the presence of beta1AR and beta2AR transcripts in porcine left ventricle, lung, longissimus muscle, and subcutaneous adipose tissue. The RT-PCR indicated that beta3AR transcripts were present in porcine subcutaneous adipose tissue, and transcripts were suggested in left ventricle and lung, but they were not detected in longissimus muscle. Quantitative ribonuclease protection assays indicated that the porcine beta1AR, beta2AR, and beta3AR transcript concentrations (amol/microg of total RNA) were, respectively as follows: heart left ventricle = 6.1, 2.4, and . 02; lung = 3.8, 1.9, and . 01; liver = 1.7, 2.1, and undetectable; skeletal muscle = 1.7, 1.1, . 02; subcutaneous adipose tissue = 1.3, . 4, . 14. The proportions of porcine betaAR subtypes (beta1AR:beta2AR:beta3AR) were as follows: heart left ventricle = 72:28:. 25; lung = 67:33:. 2; liver = 45:55:0; skeletal muscle = 60:39:. 7; and subcutaneous adipose = 73:20:7. Normalization of data to beta-actin transcript concentration did not change these relationships. Rat perigonadal adipose tissue beta1AR and beta3AR transcript concentrations were, respectively, . 59 and 1.84 amol/microg of total RNA. The rat perigonadal adipose tissue concentration of beta3AR transcript was tenfold that of porcine subcutaneous adipose tissue. The predominant betaAR transcript in rat adipose tissue was beta3AR, and the predominant betaAR transcript in pig adipose tissue was beta1AR.
Assessment of Rhodopseudomonas sphaeroides chromatophore membrane asymmetry through bilateral antiserum adsorption studies

The asymmetric structure of the Rhodopseudomonas sphaeroides chromatophore membrane was examined in detail by crossed immunoelectrophoresis techniques. Because these methods are quantitative and allow increased resolution and sensitivity, it was possible to analyze simultaneously the relative transmembrane distribution of a number of previously identified antigenic components. This was demonstrated by analysis of immunoglobulin samples that were adsorbed by preincubation with either isolated chromatophores or osmotically protected spheroplasts. The photochemical reaction center, the light-harvesting bacteriochlorophyll a-protein complex, the L-lactate dehydrogenase, and reduced nicotinamide adenine dinucleotide dehydrogenase (EC 1.6.99.3) were found to be exposed on the chromatophore surface (cytoplasmic aspect of the membrane within the cell). Other antigenic components were found to be exposed on the surface of spheroplasts (periplasmic aspect of the in vivo chromatophore membrane). Antigens with determinants expressed on both sides of the chromatophore membrane were also identified. Charge shift crossed immunoelectrophoresis confirmed the suggested amphiphilic character of the pigment-protein complexes and identified several additional amphiphilic membrane components.
Differences in Social Network Structure and Support Among Women in Violent Relationships

Social support is critical for women in abusive relationships. While social support may decrease the risk of getting into a violent relationship, it can also allow battered women to remain in violent relationships by reducing the negative impact of intimate partner violence (IPV). In addition to the social isolation that women in abusive relationships may experience, her social contacts appear to be important. The purpose of this study was to compare the size, structure, and composition of the social networks of women in abusive relationships with those of a matched cohort of nonabused women. The authors enrolled women from primary care clinics who reported abuse within the prior month, and a demographically matched comparison group of women in nonabusive relationships. Participants completed a social network analysis, and investigators compared social networks of abused with nonabused women. The networks of women in abusive relationships were smaller in size, but more efficient in their ability to reach their members, than those of nonabused women. Proportionally, networks of abused women had more women but fewer in-laws than those of comparison women. The women in these abusive relationships had higher measures of centrality, suggesting that they were more critical in holding their networks together. Yet, they had fewer social contacts, and provided more support than they received with fewer reciprocated ties. Thus, social networks of women in violent relationships are small and offer less support than those of comparison women. However, previous work on networks with weak ties and structural holes suggests that access to resources may be available through these networks.
The impact of high non-starch polysaccharide intake on serum micronutrient concentrations in a cohort of women

Abstract Objective: Many public health campaigns encourage increased fibre consumption, but short-term studies suggest that various components of dietary fibre inhibit the absorption of certain micronutrients including carotenoids. These do not take into account long-term adaptation to nutrient intake levels. We aimed to investigate the effect of non-starch polysaccharide (NSP) fibre on plasma micronutrient concentrations in a large free-living population consuming their usual diet. Design: Prospective cohort study. Semi-weighed 4-day food diaries were analysed for micronutrient and NSP fibre intakes. Blood samples were taken and analysed for carotenoids, vitamin A, vitamin E, thiamine, riboflavin, vitamin B6, vitamin B12, folic acid, vitamin C and trace metals. Setting: Participants in a large national cohort study who lived within 30 miles of Leeds. Subjects: Two hundred and eighty-three middle-aged women. Results: The association between NSP intake and plasma nutrient concentrations was assessed taking into account nutrient intakes and other dietary and lifestyle factors. Higher levels of NSP were not associated with lower plasma concentrations of the micronutrients measured, even allowing for the higher nutrient levels generally found in high-fibre foods. Conclusions: Amongst middle-aged women we have shown that current guidelines for increasing the population's NSP consumption can be safely applied. Such guidelines are unlikely to reduce serum micronutrient concentrations, although other, more vulnerable population groups may benefit from further investigation.
Joint Beamforming and Power-Splitting Control in Downlink Cooperative SWIPT NOMA Systems

This paper investigates the application of simultaneous wireless information and power transfer (SWIPT) to cooperative non-orthogonal multiple access (NOMA). A new cooperative multiple-input single-output (MISO) SWIPT NOMA protocol is proposed, where a user with a strong channel condition acts as an energy-harvesting (EH) relay by adopting power splitting (PS) scheme to help a user with a poor channel condition. By jointly optimizing the PS ratio and the beamforming vectors, we aim at maximizing the data rate of the “strong user” while satisfying the QoS requirement of the “weak user”. To resolve the formulated nonconvex problem, the semidefinite relaxation (SDR) technique is applied to reformulate the original problem, by proving the rank-one optimality. And then an iterative algorithm based on successive convex approximation (SCA) is proposed for complexity reduction, which can at least attain its stationary point efficiently. In view of the potential application scenarios, e.g., Internet of Things (IoT), the single-input single-output (SISO) case is also studied. The formulated problem is proved to be strictly unimodal with respect to the PS ratio. Hence, a golden section search (GSS) based algorithm with closed-form solution at each step is proposed to find the unique global optimal solution. It is worth pointing out that the SCA method can also converge to the optimal solution in SISO cases. In the numerical simulation, the proposed algorithm is numerically shown to converge within a few iterations, and the SWIPT-aided NOMA protocol outperforms the existing transmission protocols.
Cardiovascular Risk Factors Cause Cortical Thinning in Cognitively Impaired Patients: Relationships Among Cardiovascular Risk Factors, White Matter Hyperintensities, and Cortical Atrophy

Cardiovascular risk factors are associated with cognitive impairments. However, the effects of cardiovascular risk factors on the topography of cortical thinning have not yet been studied in patients with mild cognitive impairment (MCI) or dementia. Thus, we aimed to evaluate the topography of cortical thinning related to cardiovascular risk factors and the relationships among cardiovascular risk factors, white matter hyperintensities (WMH), and cortical atrophy. Participants included 226 patients with Alzheimer disease or subcortical vascular dementia and 135 patients with amnestic MCI or subcortical vascular MCI. We automatically measured the volume of WMH and cortical thickness. Hypertension was associated with cortical thinning in the frontal and perisylvian regions, and cortical thinning related to diabetes mellitus (DM) occurred in the frontal region. In path analyses, hypertension accounted for 0.04 of the frontal thinning with the mediation of WMH and 0.16 without the mediation of WMH. In case of DM, it accounted for 0.02 of the frontal thinning with the mediation of WMH and 0.13 without the mediation of WMH. Hypertension and DM predominantly affected frontal thinning both with and without the mediation of WMH, where the effects without the mediation of WMH were greater than those with the mediation of WMH.
A prediction rule for the development of arthritis in seropositive arthralgia patients

Objective To predict the development of arthritis in anticyclic citrullinated peptide antibodies and/or IgM rheumatoid factor positive (seropositive) arthralgia patients. Methods A prediction rule was developed using a prospective cohort of 374 seropositive arthralgia patients, followed for the development of arthritis. The model was created with backward stepwise Cox regression with 18 variables. Results 131 patients (35%) developed arthritis after a median of 12 months. The prediction model consisted of nine variables: Rheumatoid Arthritis in a first degree family member, alcohol non-use, duration of symptoms <12 months, presence of intermittent symptoms, arthralgia in upper and lower extremities, visual analogue scale pain ≥50, presence of morning stiffness ≥1 h, history of swollen joints as reported by the patient and antibody status. A simplified prediction rule was made ranging from 0 to 13 points. The area under the curve value (95% CI) of this prediction rule was 0.82 (0.75–0.89) after 5 years. Harrell's C (95% CI) was 0.78 (0.73–0.84). Patients could be categorised in three risk groups: low (0–4 points), intermediate (5–6 points) and high risk (7–13 points). With the low risk group as a reference, the intermediate risk group had a hazard ratio (HR; 95% CI) of 4.52 (2.42–8.77) and the high risk group had a HR of 14.86 (8.40–28.32). Conclusions In patients presenting with seropositive arthralgia, the risk of developing arthritis can be predicted. The prediction rule that was made in this patient group can help (1) to inform patients and (2) to select high-risk patients for intervention studies before clinical arthritis occurs.
Deficits in axon‐associated proteins in prefrontal white matter in bipolar disorder but not schizophrenia

Brain imaging studies have implicated white matter dysfunction in the pathophysiology of both bipolar disorder (BD) and schizophrenia (SCZ). However, the contribution of axons to white matter pathology in these disorders is not yet understood. Maintenance of neuronal function is dependent on the active transport of biological material, including synaptic proteins, along the axon. In this study, the expression of six proteins associated with axonal transport of synaptic cargoes was quantified in postmortem samples of prefrontal white matter in subjects with BD, those with SCZ, and matched controls, as a measure of axonal dysfunction in these disorders.
Suicide attempts associated with externalizing psychopathology in an epidemiological sample.

OBJECTIVE Borrowing from recent dimensional models of psychopathology, the authors conducted analyses that optimized the common variance shared by internalizing (depression, anxiety) and externalizing (antisocial personality, substance dependence) disorders in statistically predicting suicidal behaviors. These relationships were analyzed in a large epidemiological sample, thus allowing for the examination of gender differences in risk for suicide attempts associated with psychopathology. METHOD The data were obtained from the Colorado Social Health Survey. Participants (N=4,745) were a community sample recruited by household address. Structured clinical interviews were used to obtain lifetime diagnostic and symptom count information. Symptom counts were included in a factor analysis that yielded two main dimensions of psychopathology: internalizing and externalizing. These factors were used in hierarchical logistic regression analyses to predict history of suicide attempts associated with the presence of internalizing symptoms, externalizing symptoms, and comorbid internalizing and externalizing symptoms. RESULTS After the investigators controlled for the presence of internalizing symptoms and the comorbidity of internalizing and externalizing symptoms, externalizing symptoms were related to suicidal behavior in both men and women, although comorbidity was most predictive of suicide attempts among women, compared to men. CONCLUSIONS Suicidal behavior among individuals with externalizing symptoms is not necessarily a result of comorbid depressive or other internalizing disorder. Thus, persons exhibiting antisocial behaviors should receive rigorous assessment for suicidal ideation and behavior.
OpenFab

3D printing hardware is rapidly scaling up to output continuous mixtures of multiple materials at increasing resolution over ever larger print volumes. This poses an enormous computational challenge: large high-resolution prints comprise trillions of voxels and petabytes of data, and modeling and describing the input with spatially varying material mixtures at this scale are simply challenging. Existing 3D printing software is insufficient; in particular, most software is designed to support only a few million primitives, with discrete material choices per object. We present OpenFab, a programmable pipeline for synthesis of multimaterial 3D printed objects that is inspired by RenderMan and modern GPU pipelines. The pipeline supports procedural evaluation of geometric detail and material composition, using shader-like fablets, allowing models to be specified easily and efficiently. The pipeline is implemented in a streaming fashion: only a small fraction of the final volume is stored in memory, and output is fed to the printer with a little startup delay. We demonstrate it on a variety of multimaterial objects.
Effects of silver nanoparticles and silver nitrate in the earthworm reproduction test

The widespread use of silver nanoparticles (Ag‐NPs), for example, in textiles and cleaning products, means that they are likely to reach the environment via biosolids or the effluent from wastewater treatment plants. The aim of the present study was to determine the ecotoxicity of Ag‐NPs in the earthworm reproduction test using Eisenia andrei. In addition to the usual endpoints, the authors also investigated the uptake and accumulation of Ag by adult earthworms and the concentration of free Ag+ in soil pore water. Silver nanoparticles and Ag nitrate showed similar toxicities in the earthworm reproduction test. The uptake of Ag from Ag‐NPs in the earthworm was slightly higher than the uptake of Ag from Ag nitrate. Spiked soils showed a concentration‐dependent effect on reproduction, but there was no concentration‐dependent increase in the amount of Ag in earthworm tissues. The authors noted a concentration‐dependent increase in the levels of free Ag+ in the soil pore water regardless of the Ag source. The number of juveniles is a more suitable endpoint than biomass or mortality. The uptake of Ag does not appear to inhibit reproduction. Instead, inhibition seems to reflect Ag+ released into the soil pore water, which affects cocoons and juveniles in the soil. Analysis of transformed Ag‐NPs after purification in wastewater treatment plants would provide additional information. Environ. Toxicol. Chem. 2013;32:181–188. © 2012 SETAC
The role of functional status in discharge to assisted care facilities and in-hospital death among dialysis patients.

BACKGROUND Functional status is an important component in the assessment of hospitalized patients. We set out to determine the scope, severity, and prognostic significance of impaired functional status in acutely hospitalized dialysis patients. STUDY DESIGN Retrospective cohort study. SETTING & PARTICIPANTS 1,286 hospitalized dialysis patients admitted and discharged from 1 of 11 area hospitals in Manitoba, Canada, from September 2003 to September 2010 with an activity of daily living (ADL) assessment within 24 hours of admission. PREDICTOR The 12-point ADL score assesses 6 domains (bathing, toileting, dressing, incontinence, feeding, and transferring) and scores them as independent or supervision only (score, 0), partial assistance (1), and full assistance (2). Thus, higher score indicates worse functional status. Parametric and nonparametric tests were used as appropriate to determine differences in baseline characteristics. OUTCOMES Multivariable logistic regression and Cox proportional hazards assessed the association between functional status, in-hospital death, and discharge to an assisted care facility. RESULTS During the study period, 250 (19.4%) and 72 (5.6%) patients experienced the outcomes of in-hospital death or discharge to an assisted care facility. Abnormalities in functional status were present in >70% of the cohort. ADL score within 24 hours of admission combined with age differentiated risks of death and discharge to an assisted care facility home, ranging from 4.8%-46.6% and 0.6%-17.8%, respectively. After adjustment, ORs of death and discharge to an assisted care facility were 1.16 (95% CI, 1.11-1.22; P < 0.001; C statistic = 0.79) and 1.25 (95% CI, 1.14-1.36; P < 0.001; C statistic = 0.91) per 1-point increase in ADL score, respectively. Findings were consistent after accounting for the competing outcomes of in-hospital death or discharge to an assisted care facility versus discharge to home. LIMITATIONS A 1-time measurement of ADLs could not differentiate temporary from long-term deterioration in functional status. CONCLUSIONS Impaired functional status is common at the time of admission in the dialysis population. A single ADL score measurement at admission combined with age is highly predictive of poor outcomes in the hospitalized dialysis population.