Miracle-dz/UniFAR-FTUs huggingface dataset:
An efficient grid‐based scheme to compute QTAIM atomic properties without explicit calculation of zero‐flux surfaces

We introduce a method to compute atomic properties according to the “quantum theory of atoms in molecules. ” An integration grid in real space is partitioned into subsets, ωi. The subset, ωi, is composed of all grid points contained in the atomic basin, Ωi, so that integration over Ωi is reduced to simple quadrature over the points in ωi. The partition is constructed from deMon2k's atomic center grids by following the steepest ascent path of the density starting from each point in the grid. We also introduce a technique that exploits the cellular nature of the grid to make the algorithm faster. The performance of the method is tested by computing properties of atoms and nonnuclear attractors (energies, charges, dipole, and quadrupole moments) for a set of representative molecules. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009
Comparative Study of Adipose-Derived Stem Cells From Abdomen and Breast

Background Abdominal tissue enriched with adipose-derived stem cells (ASCs) is often used in cell-assisted lipotransfer procedures for breast reconstruction. However, as the tissue microenvironment and stem cell niche play important roles in defining the characteristics of the resident cells, it is hypothesized that the stem cell population present in the donor abdominal tissue has dissimilar properties as compared with the cells in the recipient breast tissue, which may ultimately affect the long-term success of the graft. Methods Adipose-derived stem cells were isolated from breast and abdominal fat tissues and characterized for mesenchymal-specific cell surface markers, and their population doubling, colony-forming capabilities, and proliferative properties were compared. The multilineage potential of both cell populations was also investigated. Results Adipose-derived stem cells from both tissue sites were found to possess similar marker expression and multilineage differentiation potential. However, breast fat–derived ASCs were observed to have a higher self-renewal capability and an unstable population doubling as compared with abdominal fat-derived ASCs. Gene expression studies revealed that the breast fat–derived ASCs were predisposed to the osteogenic lineage and the abdominal fat–derived ASCs to the adipogenic lineage. Conclusions Cells derived from both fat tissues possess different characteristics in terms of their growth kinetics and predisposition to the osteolineages and adipolineages. In particular, ASCs from the abdominal tissue appear to contribute to adipose tissue turnover, whereas ASCs from breast tissue, if used for cell-assisted fat grafting, may potentially be responsible for complications in fat grafting, such as oil cysts, calcifications, fat necrosis, and tumors.
Clinical performance of access flap in the treatment of class II furcation defects. A systematic review and meta-analysis of randomized clinical trials.

OBJECTIVES To systematically review the performance of access flap (OFD) in the treatment of class II furcation defects (FD). METHODS RCTs evaluating surgical treatment of class II FD with OFD, minimum 6 months follow-up were identified. Screening, data extraction, and quality assessment were conducted independently by three reviewers. The primary outcomes were tooth survival and change in the horizontal clinical attachment level (HCAL). Changes in vertical clinical attachment level (VCAL), reduction of pocket probing depth (PPD), recession increase (REC), horizontal (HBL), and vertical bone level (VBL) were also collected. RESULTS The search identified 1571 studies out of which 11 articles met the inclusion criteria. Data analysis was performed on 199 patients and 251 FD. Tooth survival was seldom reported. Altogether with inflammatory amelioration, the weighted mean differences were for HCAL 0.96 mm [CI: (0.60, 1.32), p < 0.001], 0.55 mm [CI: (0.00, 1.10), p = 0.05] for VCAL gain. PPD reduction over 6 months was 1.38 mm [CI: (0.91, 1.85), p < 0.01]. Potential risk of bias was identified. CONCLUSIONS Teeth with mandibular class II furcation involvement treated with OFD show significant clinical improvements 6 months after surgery. Nevertheless, in order to better understand the magnitude of these changes and their clinical relevance, prospective long-term trials are needed.
Replication of the association of GLT6D1 with aggressive periodontitis in a Sudanese population.

BACKGROUND Susceptibility to aggressive periodontitis (AgP) is influenced by genetic as well as environmental factors. Studies linking gene variants to AgP have been mainly centred in developed countries with limited data from Africa. AIM To investigate whether previously reported candidate gene associations with AgP could be replicated in a population from Sudan. METHODS The investigation was a case-control design. Cases with AgP (n = 132) and controls (n = 136) were identified from patients attending the Periodontal Department in Khartoum Dental Hospital. Genotyping was performed using the Sequenom MassARRAY iPLEX platform. Analysis focused on gene variants with a minor allele frequency (MAF) > 25% in the Sudanese subjects that had previously been reported to be associated with AgP. RESULTS One candidate gene rs1537415 (GLT6D1) was significantly associated with AgP, OR = 1.50 (95% CI 1.04-2.17), p = 0.0295 (increasing to p = 0.09 after correction for multiple testing). The association strengthened to OR = 1.56 (95% CI 1.15-2.16), p = 0.0042 when the controls were supplemented with data from the Hap map for the Yoruba in Ibadan (n = 147) and remained significant (p = 0.013) after correction for multiple testing. CONCLUSION The study independently replicated the finding that rs1537415, a variant in glycosyl transferase gene GLT6D1, is associated with AgP and provided the first report of genetic associations with AgP in a Sudanese population.
Tuning independently the Fermi energy and spin splitting in Rashba systems: ternary surface alloys on Ag(111)

By detailed first-principles calculations we show that the Fermi energy and the Rashba splitting in disordered ternary surface alloys BixPbySb1 − x − y/Ag(111) can be independently tuned by choosing the concentrations x and y of Bi and Pb, respectively. The findings are explained by three fundamental mechanisms, namely the relaxation of the adatoms, the strength of the atomic spin–orbit coupling, and band filling. By mapping the Rashba characteristics, i.e. the splitting kR and the Rashba energy ER, and the Fermi energy of the surface states in the complete range of concentrations, we find that these quantities depend monotonically on x and y, with a very few exceptions. Our results suggest that we should investigate experimentally effects which rely on the Rashba spin–orbit coupling depending on spin–orbit splitting and band filling.
Lateral Crural Reinforcement in Secondary Cleft Lip Nasal Deformity Through a Combined Lateral Crural Turn-over Flap and Strut Graft

Background Secondary cleft lip nasal deformity is a complex deformity, and the variety of recommended techniques used to correct this deformity attests to it. Much of the nasal deformity can be attributed to an abnormal lower lateral cartilage. This study presents our experience with applying a lateral crural turnover flap with a sandwiched strut graft in adjunct with other procedures to correct unilateral secondary cleft lip nasal deformity. Methods A retrospective review was conducted of 20 cases of unilateral cleft lip patients undergoing secondary rhinoplasty with lateral crural turnover flap with strut graft. Nostril base augmentation, columellar strut, suture techniques, and alar base reduction were performed as needed. Anthropometric analysis and subjective grading of the postoperative results were performed to evaluate the effect of the procedure on nostril symmetry. Results At long-term follow-up of 1 year, the symmetry for cleft side and noncleft side nostril height, width, and angulation of long axis of nostril improved after surgery. Subjective evaluation revealed improved results for all patients. Conclusions The lateral crural turnover flap with sandwiched strut graft is a useful technique for reinforcing, repositioning, and reshaping the lower lateral cartilage in cleft lip patients with hyperconcave lateral crus and hypoplastic pyriform margin. Combined with other techniques, the nostril is increased in height, decreased in width, and thus satisfactory symmetry is obtained.
Marathon Des Sables: A Scientific Case Study

The Marathon des Sables is an ultra-endurance foot race across the Sahara Desert. The event lasts 6 days, and competitors are susceptible to a variety of specific injuries, including dehydration, heat stress, and ultimately poor performance. This study involved the monitoring of a highly trained 42-year-old male competitor through a 6-month training program and immediately after the event. The monitoring sessions assessed maximal oxygen uptake (VO2 Max), pulmonary function, anthropometric characteristics, body composition, resting metabolic rate, training, and nutritional status. The subject also completed a period of acclimation during the taper phase of the training program in an environmental chamber. The last pre-race VO2max of 4.5 1–min showed a decrease of 0.5 1–min. The subject's diet successfully maintained body weight during the training period, and the subject's weight increased from 67.7kg at 12.2% body fat to 71kg at 13.2% body fat during the taper. The subject sustained no chronic injuries during the training or race periods. We concluded that the intervention strategies adopted were successful in preparing the subject to successfully complete the Marathon des Sables. The athlete covered the 229km in 29hr 21min 21sec, finishing in 75th place.
Accurate estimation of solvation free energy using polynomial fitting techniques

This report details an approach to improve the accuracy of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable λ) and its application to calculating solvation free energy. The central idea is to utilize polynomial fitting schemes to approximate the thermodynamic integration data to improve the accuracy of the free energy difference estimates. Previously, we introduced the use of polynomial regression technique to fit thermodynamic integration data (Shyu and Ytreberg, J Comput Chem, 2009, 30, 2297). In this report we introduce polynomial and spline interpolation techniques. Two systems with analytically solvable relative free energies are used to test the accuracy of the interpolation approach. We also use both interpolation and regression methods to determine a small molecule solvation free energy. Our simulations show that, using such polynomial techniques and nonequidistant λ values, the solvation free energy can be estimated with high accuracy without using soft‐core scaling and separate simulations for Lennard‐Jones and partial charges. The results from our study suggest that these polynomial techniques, especially with use of nonequidistant λ values, improve the accuracy for ΔF estimates without demanding additional simulations. We also provide general guidelines for use of polynomial fitting to estimate free energy. To allow researchers to immediately utilize these methods, free software and documentation is provided via http://www.phys.uidaho.edu/ytreberg/software. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Efficacy of adjunctive anti-plaque chemical agents: a systematic review and network meta-analyses of the Turesky modification of the Quigley and Hein plaque index.

AIM The aim of this systematic review and network meta-analysis (NMA) was to compare the efficacy of different anti-plaque chemical agents, in 6-month, home-use, randomized clinical trials (RCTs), in terms of plaque index (PlI) changes. MATERIAL AND METHODS RCTs assessing PlI were identified, screened, and evaluated for inclusion. Relevant information was extracted, and quality and risk of bias were assessed. Mean differences between baseline-end were calculated to obtain weighted mean differences and 95% confidence intervals. NMA protocols were applied to assess direct and indirect comparisons among products using Turesky PlI. RESULTS Eighty-three papers were included: 49 examined dentifrices, 32 mouthrinses and 2 both. The NMA analysed 51 studies including data from 4242 and 4180 subjects for dentifrices and mouthrinses respectively. For dentifrices, triclosan-copolymer and chlorhexidine showed the greatest effect, with significant differences when compared with stannous fluoride. For mouthrinses, essential oils and chlorhexidine showed the greatest effect, with significant differences when compared with delmopinol, alexidine and cetylpyridinium chloride. CONCLUSION Within the limitations of this study (including the severe imbalance in the amount of evidence), dentifrices containing triclosan-copolymer or chlorhexidine and mouthrinses containing essential oils or chlorhexidine showed the greatest effect on PlI scores as assessed with NMA.
PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints

PaDEL‐Descriptor is a software for calculating molecular descriptors and fingerprints. The software currently calculates 797 descriptors (663 1D, 2D descriptors, and 134 3D descriptors) and 10 types of fingerprints. These descriptors and fingerprints are calculated mainly using The Chemistry Development Kit. Some additional descriptors and fingerprints were added, which include atom type electrotopological state descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.
Lipopolysaccharide, a possible molecular mediator between periodontitis and coronary artery disease

AIM We aimed to study how lipopolysaccharide (LPS) in saliva and serum associates with each other, periodontal microbial burden, periodontitis and coronary artery disease (CAD). MATERIALS AND METHODS The used Parogene cohort comprised N = 505 Finnish adults. Coronary diagnosis was acquired by coronary angiography, and the main outcomes were as follows: no significant CAD (n = 123), stable CAD (n = 184) and acute coronary syndrome (n = 169). Periodontitis was defined according to clinical and radiographic examinations. Levels for 75 strains of subgingival bacteria were determined by checkerboard DNA-DNA hybridization. Saliva and serum LPS activity was analysed by Limulus amebocyte lysate assay. RESULTS The level of 11 bacterial strains, which were mainly oral and respiratory Gram-negative species, associated with salivary LPS levels in an age- and gender-adjusted linear regression. A total of 4.9% of the serum LPS, that is endotoxemia, variation was explainable by saliva LPS among patients with periodontitis (n = 247, R2 = .049, Pearson's r = .222, p < .001). Endotoxemia associated with stable CAD in a confounder adjusted multinomial logistic regression model (OR 1.99, 95% CI 1.04-3.81, p = .039, 3rd tertile). CONCLUSIONS In particular in periodontitis patients, subgingival microbial burden contributes to endotoxemia. LPS is a possible molecular mediator between periodontitis and CAD.
Double-blind comparison of pramipexole and bromocriptine treatment with placebo in advanced Parkinson's disease

Pramipexole is a new, selective, nonergoline dopamine agonist that acts on D2 and preferentially on D3 dopamine receptors. Phase II and III clinical trials have shown this drug to be useful in treating both early and advanced Parkinson's disease (PD) patients. A double-blind, randomized, multicenter study was performed to compare the safety, tolerance, and efficacy of pramipexole versus placebo in patients with advanced PD with motor fluctuations. A bromocriptine treatment group was included to enable comparisons between bromocriptine and placebo groups, but the study was not powered to show statistical differences between the active treatment groups. The study included 247 patients with "wearing off. " Patients were Hoehn and Yahr stages II to IV during "on" times. The trial included three phases: dose escalation, 6 months' maintenance, and dose reduction. The primary end points were the Unified Parkinson's Disease Rating Scale (UPDRS) parts II and III. Up to 4.5 mg per day of pramipexole and 30 mg per day of bromocriptine were used. The results of the study showed that the UPDRS part II improved by 26.7% for pramipexole (p = 0.0002) and 14% for bromocriptine(p = 0.02) versus 4.8% for placebo. The UPDRS part III showed improvements of 34% for pramipexole (p = 0.0006) and 23.8% for bromocriptine (p = 0.01) versus 5.7% for placebo. There were no major differences in safety data. In the active treatment groups there were more reports of dyskinesia and nausea compared with placebo. In regard to comparison of the Global Clinical Assessment of Efficacy between active treatment groups, there was a trend to significance (p = 0.056) in favor of pramipexole. We conclude that pramipexole-treated patients with advanced PD improved significantly more than placebo for both primary end points.
Patient‐reported outcomes and health‐related quality of life in effectiveness studies: pros and cons

The importance of patient perspectives on disease impact and response to therapy is increasingly recognized. Patient‐reported outcomes (PROs), including health‐related quality of life (HRQL), provide information on the effectiveness of medical interventions that cannot be obtained using objective clinical measures. For drug development, PROs such as symptom questionnaires are accepted by the European Medicines Agency (EMEA) and US Food and Drug Administration (FDA) in the approval process. HRQL assessments can help to establish the niche for a new product to support marketing efforts. Utilities can also be derived from health outcomes measures for cost‐effectiveness analyses required by health plans for granting drug reimbursement. Because they more closely reflect routine clinical care, effectiveness studies are often a superior setting than traditional randomized controlled trials (RCTs) for conducting comprehensive PRO assessments to determine the real‐world impact of therapy on symptoms and other aspects of everyday life. Screening, quality of care, self‐reported adherence to treatment, and patient monitoring are important potential applications of PROs in effectiveness studies. However, well‐known limitations of effectiveness studies also apply to PROs; these sometimes include a lack of randomization, controls, and blinding. It may be difficult to obtain patient compliance and clinician assistance with PRO assessments in a real‐world setting. PRO data may be biased by nonrandom patient dropout, errors in timing of PRO assessments, and the environment in which questionnaires are administered. Additionally, the drug development schedule often requires outcomes results before effectiveness studies can be conducted. Addressing these difficulties during study design and the use of short and targeted questionnaires will improve the usefulness and feasibility of PRO measures in effectiveness studies. Drug Dev. Res. 67:193–201, 2006. © 2006 Wiley‐Liss, Inc.
The effect of horizontal and vertical furcation involvement on molar survival: A retrospective study

BACKGROUND Periodontal involvement of the furcation area (furcation involvement, FI) has been reported to confer molars a higher risk of tooth loss. AIMS The aim of this retrospective analysis was to assess the effect of FI on disease progression and tooth loss in molars of patients with chronic periodontitis undergoing supportive periodontal therapy (SPT) in a UK private practice setting. MATERIALS AND METHODS Six-hundred and thirty-three molars were analysed in 100 chronic periodontitis patients treated with active periodontal therapy (APT) and followed up in SPT for at least 5 years. Molars were treated with a combination of resective, regenerative or conservative approaches, according to the different clinical needs. RESULTS Twenty-three molars were extracted during APT and a further 23 were lost during SPT. Multivariable analysis showed that both horizontal FI and vertical furcation component were associated with increased risk of tooth loss during SPT (OR 5.26, 95% CI: 1.46-19.03, p = .012 and OR 9.83, 95% CI: 1.83-50.11, p = .006, respectively). CONCLUSION Attention should be placed on both horizontal and vertical FI in molars, owing to their association with tooth loss during SPT.
Reproductive Knowledge and Preferences of Adolescents and Adults with Cystic Fibrosis: A Web-Based Assessment

ABSTRACT The reproductive consequences of cystic fibrosis (CF) have increased in relevance as individuals with CF now live well into their reproductive years. This article describes the first Internet-based study of sexual and reproductive health (SRH) knowledge, experiences, and preferences of adolescents and adults with CF participating in an online discussion board. Although broad SRH knowledge was demonstrated, CF-specific SRH knowledge was incomplete. Respondents reported wanting providers to initiate reproductive health discussions and offer more CF-specific SRH information. Respondents also reported experiencing a variety of disease-specific reproductive health issues (e.g., shortness of breath with sexual activity, vaginal dryness due to viscous mucous, etc.). Future research should explore how to enhance access to disease-specific SRH information.
Annual Research Review: Positive adjustment to adversity--trajectories of minimal-impact resilience and emergent resilience.

BACKGROUND Research on resilience in the aftermath of potentially traumatic life events (PTE) is still evolving. For decades, researchers have documented resilience in children exposed to corrosive early environments, such as poverty or chronic maltreatment. Relatively more recently, the study of resilience has migrated to the investigation of isolated PTE in adults. METHODS In this article, we first consider some of the key differences in the conceptualization of resilience following chronic adversity versus resilience following single-incident traumas, and then describe some of the misunderstandings that have developed about these constructs. To organize our discussion, we introduce the terms emergent resilience and minimal-impact resilience to represent trajectories of positive adjustment in these two domains, respectively. RESULTS We focused in particular on minimal-impact resilience, and reviewed recent advances in statistical modeling of latent trajectories that have informed the most recent research on minimal-impact resilience in both children and adults and the variables that predict it, including demographic variables, exposure, past and current stressors, resources, personality, positive emotion, coping and appraisal, and flexibility in coping and emotion regulation. CONCLUSIONS The research on minimal-impact resilience is nascent. Further research is warranted with implications for a multiple levels of analysis approach to elucidate the processes that may mitigate or modify the impact of a PTE at different developmental stages.