Miracle-dz/UniFAR-FTUs huggingface dataset:
C-H...pi Interactions in Proteins: A Structural Bioinformatics Study

A non-redundant set of 1154 protein structures from the Protein Data Bank was examined with respect to close interactions between C-H-donor and pi-acceptor groups. A total of 31,087 interactions were found to satisfy our selection criteria. Their geometric parameters suggest that these interactions can be classified as weak hydrogen bonds.A set of 12 interaction classes were defined based on the division of the donors into three groups and the acceptors into four groups. These classes were examined separately, and the respective interactions described in detail in each class. Most prominent were interactions between aliphatic C-H donors and aromatic pi-acceptors and interactions between aromatic C-H donors and aromatic pi-acceptors. About three-quarters of the Trp-rings, half of all Phe and Tyr-rings and a quarter of all His-rings were found to be involved as acceptors in C-H.pi-interactions. On the donor side, a preference for aromatic C-H groups was observed, but also for the aliphatic side-chains of the long, extended amino acid residues Lys, Arg and Met, and the Pro ring. The average distance between the C-donor and the center-of-mass of the pi-acceptor was observed to be significantly longer in the 174 protein structures determined at >2.5 A resolution. Also, the distribution is significantly wider. This resolution dependence suggests that the force fields commonly used for the refinement of protein structures may not be adequate. C-H.pi-interactions involving aromatic groups either as donor or as acceptor groups are found mostly in the interior of the protein. The more hydrophilic the participating groups are, the closer to the surface are the interactions located. About 40 % of all C-H.pi-interactions occur between amino acid residue side-chains that are separated by nine or less residues in sequence. Dependent on the interaction class, different preferences for secondary structure, residue type and side-chain conformation were observed. It is likely that the C-H.pi-interactions contribute significantly to the overall stability of a protein.
Sleep quality and diurnal preference in a sample of young adults: Associations with 5HTTLPR, PER3, and CLOCK 3111

Research investigating associations between specific genes and individual differences with regards to the quality and timing of sleep has primarily focussed on serotonin‐related and clock genes. However, there are only a few studies of this type and most of those to date have not considered the possibility of gene–environment interaction. Here, we describe associations between sleep quality and diurnal preference and three functional polymorphisms: 5HTTLPR, PERIOD3, and CLOCK 3111. Furthermore, we assessed whether associations between genotypes and sleep phenotypes were moderated by negative life events—a test of gene–environment interaction. DNA from buccal swabs was collected from 947 individuals [mean age = 20.3 years (SD = 1.77), age range = 18–27 years; 61.8% female] and genotyped for the three polymorphisms. Participants completed the Pittsburgh Sleep Quality Index and the Morningness‐Eveningness Questionnaire. There was a significant main effect of 5HTTLPR on sleep quality, indicating that “long–long” homozygotes experienced significantly poorer sleep quality (mean = 6.35, SD = 3.36) than carriers of at least one “short” allele (mean = 5.67, SD = 2.96; β = −0.34, P = 0.005). There were no main effects of 5HTTLPR on diurnal preference; no main effects of PERIOD3 or CLOCK on sleep quality or diurnal preference; and no significant interactions with negative life events. The main effect of the “long” 5HTTLPR allele contradicts previous research, suggesting that perhaps the effects of this gene are heterogeneous in different populations. Failure to replicate previous research in relation to PERIOD3 and CLOCK concurs with previous research suggesting that the effects of these genes are small and may be related to population composition. © 2011 Wiley‐Liss, Inc.
Chemical Peels: Indications and Special Considerations for the Male Patient

BACKGROUND Chemical peels are a mainstay of aesthetic medicine and an increasingly popular cosmetic procedure performed in men. OBJECTIVE To review the indications for chemical peels with an emphasis on performing this procedure in male patients. MATERIALS AND METHODS Review of the English PubMed/MEDLINE literature and specialty texts in cosmetic dermatology, oculoplastic, and facial aesthetic surgery regarding sex-specific use of chemical peels in men. RESULTS Conditions treated successfully with chemical peels in men include acne vulgaris, acne scarring, rosacea, keratosis pilaris, melasma, actinic keratosis, photodamage, resurfacing of surgical reconstruction scars, and periorbital rejuvenation. Chemical peels are commonly combined with other nonsurgical cosmetic procedures to optimize results. Male patients may require a greater number of treatments or higher concentration of peeling agent due to increased sebaceous quality of skin and hair follicle density. CONCLUSION Chemical peels are a cost-effective and reliable treatment for a variety of aesthetic and medical skin conditions. Given the increasing demand for noninvasive cosmetic procedures among men, dermatologists should have an understanding of chemical peel applications and techniques to address the concerns of male patients.
Spatial distribution of FMISO in head and neck squamous cell carcinomas during radio-chemotherapy and its correlation to pattern of failure

ABSTRACT Background. Tumour hypoxia can be measured by FMISO-PET and negatively impacts local tumour control in patients with head and neck squamous cell carcinoma (HNSCC) undergoing radiotherapy. The aim of this post hoc analysis of a prospective clinical trial was to investigate the spatial variability of FMISO hypoxic subvolumes during radio-chemotherapy and the co-localisation of these volumes with later recurrences as a basis for individualised dose prescription trials with dose escalation defined by FMISO-PET. Methods. Sequential FMISO scans of 12 (of 25) patients presenting residual hypoxia taken before (FMISOpre) and during (FMISOw1–FMISOw5) radio-chemotherapy were analysed regarding the stability of the FMISO subvolumes and, in case of local failure, their correlation to local relapse. Results. Consecutive FMISO-PET positive volumes could be classified as moderately stable with Dice conformity indices of 62% and 58% up to the second week of treatment. Substantial volumetric variation during treatment was observed, with more than 20% geographic miss in all patients and more than 40% in half of the patients. The localisation of the maximum standardised uptake value (SUVmax) differed with a mean distance of 7.0 mm and 13.5 mm between the pre-therapeutic and first or second FMISO-PET during treatment. A stable hypoxic consensual volume (i.e. overlap of pre-therapeutic FMISO and intra-treatment FMISO subvolumes up to week two, generated by different contouring methods) was determined for six patients with imaging information of local recurrence. Three of these six local recurrences were located within this consensual volume. Conclusions. Our data suggest that selective dose painting to hypoxic tumour subvolumes requires adaptation during treatment and sufficient margins. An alternative strategy is to escalate the dose to the gross tumour volume, accepting lesser escalation of dose outside hypoxic areas if indicated by constraints for organs at risk.
Developmental segregation of spinal networks driving axial‐ and hindlimb‐based locomotion in metamorphosing Xenopus laevis

Amphibian metamorphosis includes a complete reorganization of an organism's locomotory system from axial‐based swimming in larvae to limbed propulsion in the young adult. At critical stages during this behavioural switch, larval and adult motor systems operate in the same animal, commensurate with a gradual and dynamic reconfiguration of spinal locomotor circuitry. To study this plasticity, we have developed isolated preparations of the spinal cord and brainstem from pre‐ to post‐metamorphic stages of the amphibian Xenopus laevis, in which spinal motor output patterns expressed spontaneously or in the presence of NMDA correlate with locomotor behaviour in the freely swimming animal. Extracellular ventral root recordings along the spinal cord of pre‐metamorphic tadpoles revealed motor output corresponding to larval axial swimming, whereas postmetamorphic animals expressed motor patterns appropriate for bilaterally synchronous hindlimb flexion–extension kicks. However, in vitro recordings from metamorphic climax stages, with the tail and the limbs both functional, revealed two distinct motor patterns that could occur either independently or simultaneously, albeit at very different frequencies. Activity at 0.5–1 Hz in lumbar ventral roots corresponded to bipedal extension–flexion cycles, while the second, faster pattern (2–5 Hz) recorded from tail ventral roots corresponded to larval‐like swimming. These data indicate that at intermediate stages during metamorphosis separate networks, one responsible for segmentally organized axial locomotion and another for more localized appendicular rhythm generation, coexist in the spinal cord and remain functional after isolation in vitro. These preparations now afford the opportunity to explore the cellular basis of locomotor network plasticity and reconfiguration necessary for behavioural changes during development.
Stable expression of meningococcal class 1 protein in an antigenically reactive form in outer membranes of Escherichia coli

The entire gene encoding the class 1 outer membrane protein of Neisseria meningitidis is located on a 2.2 kb fragment, obtained on digestion of chromosomal DNA with Xbal. This Xbal fragment from strain MC50 (subtype P1‐16), which had previously been cloned in bacteriophage M13, has been transferred to the plasmid vector pMTL20. The resulting plasmid (pPORA100) was propagated in Escherichia coli (JM109) and cell lysates were subjected to SDS‐PAGE. Western blotting with anti‐class 1 protein antibodies revealed constitutive expression of a protein of 41kD, corresponding to the class 1 protein of the parent meningococcal strain, which was absent in the E. coli control Fractionation of E. coli cells carrying the recombinant plasmid revealed that the protein was exclusively located in the outer membrane, and N‐terminal amino acid analysis of the expressed protein revealed that normal processing of the signal peptide had occurred. Immuno‐gold electron microscopy showed that the protective epitope recognized by a P1‐16 subtype‐specific monoclonal antibody was exposed in an antigenically reactive form on the surface of E. coli cells carrying plasmid pPORA100. In contrast, expression in E. coli of a second plasmid (pPORA104) lacking the coding sequence for the first 15 amino acids of the signal peptide resulted in accumulation of recombinant class 1 protein only in the cytoplasm of the cells.
The impact of age, BMI and sex hormone on aging males’ symptoms and the international index of erectile function scores

Abstract Objective: To analyze the impact of age, BMI and sex hormone on aging males’ symptoms (AMS) and the 5-item version of the international index of erectile function (IIEF-5) scores in middle-aged and elderly Chinese men. Methods: A population-based cross-sectional study was conducted in Jiashan County. A total of 969 men, aged between 40 and 80 years old, were admitted. Physical examination and the sex hormones were measured, and AMS and IIEF-5 scores were assessed. Results: The oneway ANOVA analysis indicated older age groups had higher AMS total-scores, somatic and sexual sub-scores, and lower IIEF5 scores (all p < .01). Pairwise correlation (rpairwise) analyses showed the significant associations between AMS and age or sex hormone (cFT, Bio-T, SHBG, and LH) levels, and similar for IIEF5. However, when age was adjusted, the correlation coefficients (rpartial) weakened, and correlation significance disappeared, except LH (for AMS: rpartial = 0.096, p = .009; for IIEF-5: rpartial = −0.140, p = .001). Multiple linear regressions confirmed the influence of increased age and LH on the AMS and IIEF5 scores. Conclusion: CFT, Bio-T and SHBG failed to yield any additional predicting information when age was adjusted. To improve the male reproductive health, future research should pay more attention on aging-related comorbidities and how to improve general wellness.
Investigating lake-area dynamics across a permafrost-thaw spectrum using airborne electromagnetic surveys and remote sensing time-series data in Yukon Flats, Alaska

Lakes in boreal lowlands cycle carbon and supply an important source of freshwater for wildlife and migratory waterfowl. The abundance and distribution of these lakes are supported, in part, by permafrost distribution, which is subject to change. Relationships between permafrost thaw and lake dynamics remain poorly known in most boreal regions. Here, new airborne electromagnetic (AEM) data collected during June 2010 and February 2016 were used to constrain deep permafrost distribution. AEM data were coupled with Landsat-derived lake surface-area data from 1979 through 2011 to inform temporal lake behavior changes in the 35 500- km2 Yukon Flats ecoregion of Alaska. Together, over 1500 km of AEM data, and roughly 30 years of Landsat data were used to explore processes that drive lake dynamics across a variety of permafrost thaw states not possible in studies conducted with satellite imagery or field measurements alone. Clustered time-series data identified lakes with similar temporal dynamics. Clusters possessed similarities in lake permanence (i.e. ephemeral versus perennial), subsurface permafrost distribution, and proximity to rivers and streams. Of the clustered lakes, ∼66% are inferred to have at least intermittent connectivity with other surface-water features, ∼19% are inferred to have shallow subsurface connectivity to other surface water features that served as a low-pass filter for hydroclimatic fluctuations, and ∼15% appear to be isolated by surrounding permafrost (i.e. no connectivity). Integrated analysis of AEM and Landsat data reveals a progression from relatively synchronous lake dynamics among disconnected lakes in the most spatially continuous, thick permafrost to quite high spatiotemporal heterogeneity in lake behavior among variably-connected lakes in regions with notably less continuous permafrost. Variability can be explained by the preferential development of thawed permeable gravel pathways for lateral water redistribution in this area. The general spatial progression in permafrost thaw state and lake area behavior may be extended to the temporal dimension. However, extensive permafrost thaw, beyond what is currently observed, is expected to promote ubiquitous subsurface connectivity, eventually evolving to a state of increased lake synchronicity.
Utility of the NeuroTrax Computerized Battery for Cognitive Screening in Parkinson's Disease: Comparison with the MMSE and the MoCA

ABSTRACT To determine the utility of a computerized assessment in Parkinson's disease (PD), we compared the cognitive performance of 50 PD patients on the NeuroTrax computerized battery relative to the mini-mental state examination (MMSE) and the Montreal Cognitive Assessment (MoCA). The results revealed fair agreement between impairment on the NeuroTrax and the MMSE (κ=.291, p=.031) but only slight agreement between the NeuroTrax and the MoCA (κ=.138, p = .054) and between the MoCA and the MMSE (κ = .168, p = .069). The NeuroTrax identified 52% of the sample as average or above, 40% as below average, and 8% as impaired. The MoCA identified 54% of the sample as impaired (28% average or above and 18% below average), while the MMSE identified 66% as average or above (20% below average and 14% impaired). Several stepwise regressions revealed that executive and verbal functions were the best predictors of cognitive functioning on the NeuroTrax, while memory recall, serial sevens, naming, and abstraction were the best predictors on the MoCA. These results suggest that although the NeuroTrax may be useful in identifying executive cognitive deficits in PD, similar to the MMSE the NeuroTrax may lack optimal sensitivity. While the MoCA is sensitive, it may be too stringent in overclassifying PD patients as impaired.
Assessing Transient Measurement Errors for High-Efficiency Silicon Solar Cells and Modules

High-efficiency silicon solar cells are well known to have high “capacitance,” in the sense of having a slow time response to changes in voltage or current. This is often seen during power measurements of cells or modules. This issue is increasingly important as high-efficiency cells such as p-type passivated-emitter rear contact (PERC) and n-type heterojunction cells become more common within the industry. A fundamental understanding of solar cell device physics is essential to evaluate the various test methods used to accurately measure device power output under transient conditions during flash testing. This paper offers a simple device physics framework that is sufficient to understand a wide variety of test conditions and evaluate test solutions for cell or module output power measurements.
Red Blood Cell Fatty Acids and Incident Diabetes Mellitus in the Women’s Health Initiative Memory Study

The relations between dietary and/or circulating levels of fatty acids and the development of type 2 diabetes is unclear. Protective associations with the marine omega‐3 fatty acids and linoleic acid, and with a marker of fatty acid desaturase activity delta‐5 desaturase (D5D ratio) have been reported, as have adverse relations with saturated fatty acids and D6D ratio.
Testicular Lectinhistochemistry in the Sertoli‐Cell‐Only‐Syndrome/Testikuläre Lectinhistochemie beim Sertolizell‐Syndrom

Summary: Glycoconjugate expression was studied in tissue specimens of the Sertoli‐cell‐only‐syndrome by lectinhistochemistry. Both ConA and WGA marked the cell surface of Sertoli cells fainty. UEA I labelled their nucleoli. PNA and RCA failed to stain Sertoli cells. These staining patterns resembled those of normal human testis. The thickened tubular walls in the Sertoli‐cell‐only‐syndrome were abundant in binding sites for WGA, PNA, UEA I, and RCA. ConA stained the outer part of the wall heavily, but failed to react with the adluminal part. It is suggested, that the Sertoli‐cell‐only‐syndrome is accompanied by a selective loss of mannosyl residues in the adluminal part of thickened tubular walls.
Hybrid cardiac imaging with MR‐CAT scan: A feasibility study

We demonstrate the feasibility of a new versatile hybrid imaging concept, the combined acquisition technique (CAT), for cardiac imaging. The cardiac CAT approach, which combines new methodology with existing technology, essentially integrates fast low‐angle shot (FLASH) and echoplanar imaging (EPI) modules in a sequential fashion, whereby each acquisition module is employed with independently optimized imaging parameters. One important CAT sequence optimization feature is the ability to use different bandwidths for different acquisition modules. Twelve healthy subjects were imaged using three cardiac CAT acquisition strategies: a) CAT was used to reduce breath‐hold duration times while maintaining constant spatial resolution; b) CAT was used to increase spatial resolution in a given breath‐hold time; and c) single‐heart beat CAT imaging was performed. The results obtained demonstrate the feasibility of cardiac imaging using the CAT approach and the potential of this technique to accelerate the imaging process with almost conserved image quality. J. Magn. Reson. Imaging 2000;11:711–716. © 2000 Wiley‐Liss, Inc.
Egyptian Farmers' Attitudes and Behaviors Regarding Agricultural Pesticides: Implications for Pesticide Risk Communication

The need to boost pre‐ and postharvest agricultural productivity serves as a powerful driving force for developing countries to promote the use of agricultural pesticides. Pesticides are, however, “poisons by design” and poisonings resulting from unsafe use of these chemicals are the most prevalent and serious occupational hazards faced by agricultural workers in developing countries. This article provides the results of a study designed to investigate the extent of unsafe use of pesticides by farmers in one of the largest agricultural areas in Egypt, the farmers' knowledge about pesticides, and their preferred sources of receiving risk information on pesticides. The results of this study show a high level of unsafe use of pesticides and inappropriate methods of disposal of empty pesticide containers. Also, knowledge about pesticides is scant. Notwithstanding that more than half of the farmers obtain regular drinking water from wells, most of the respondents were “not sure” as to whether or not pesticides may contaminate groundwater. The low level of knowledge about pesticides can be attributed to relatively low levels of education and that almost all the respondents have never participated in a pesticide education program. This article concludes with a recommendation for pesticide and pesticide use education programs, especially through “ministry officials” who most of the respondents seem to trust regarding receiving pesticide information.
The Influence of Functional Knee Bracing on the Anterior Cruciate Ligament Strain Biomechanics in Weightbearing and Nonweightbearing Knees

Functional knee braces are commonly prescribed after anterior cruciate ligament injury or reconstruction; however, their ability to protect the ligament, or graft, remains unclear. Our objective was to evaluate the anterior cruciate ligament strain response in braced and unbraced knees during weightbearing and nonweightbearing in combination with three externally applied loads: 1) anterior-posterior shear forces, 2) internal-external torques, and 3) varus-valgus moments. The Legend brace was tested. All external loads were applied to the tibia with the knee flexed to 20°. Reproducible data were obtained from 11 subjects. For anterior shear loads up to 130 N, the brace significantly reduced strain values compared with the unbraced knee during nonweightbearing and weightbearing conditions. For internal torques of the tibia (up to 9 N m), strain in the braced knee was significantly less than in the unbraced knee when the knee was nonweightbearing only. The brace did not reduce strain values when the knee was subjected to external torques (9 N m) or varus-valgus moments (10 N m) in weightbearing and nonweightbearing knees. These data indicate that a functional knee brace can protect the anterior cruciate ligament during anterior-posterior shear loading in the nonweightbearing and weightbearing knee and during internal torques in the nonweightbearing knee.
Secure V2V Communications via Relays: Resource Allocation and Performance Analysis

In this letter, we will investigate the joint relay selection and subcarrier allocation problem for decode-and-forward relay assisted secure vehicle-to-vehicle (V2V) communications, where the eavesdroppers could be any illegal receivers or non-intending information destinations. The joint relay selection and subcarrier allocation scheme will be proposed to minimize the secure outage probability of each <inline-formula> <tex-math notation="LaTeX">${V_{\text {Tx}}}$ </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">${V_{\text {Rx}}}$ </tex-math></inline-formula> pair while guaranteeing fairness. Specifically, the joint relay selection and subcarrier allocation problem in secure V2V communications is formulated into a random bipartite graph (RBG) model. The considered problem is then equivalent to generate the maximum matching on every sample of the RBG, thus it can be solved by R<sup>2</sup>HK algorithm with low complexity. By analyzing the properties of the RBG model-based maximum matching, the closed-form approximation formula of the secure outage probability is then obtained. Simulation results will not only verify the accuracy of theoretical derivations, but also show the performance improvement of the proposed approach.