Quasiatomic orbitals for ab initio tight-binding analysis

Wave functions obtained from plane-wave density-functional theory (DFT) calculations using norm-conserving pseudopotential, ultrasoft pseudopotential, or projector augmented-wave method are efficiently and robustly transformed into a set of spatially localized nonorthogonal quasiatomic orbitals (QOs) with pseudoangular momentum quantum numbers. We demonstrate that these minimal-basis orbitals can exactly reproduce all the electronic structure information below an energy threshold represented in the form of environment-dependent tight-binding Hamiltonian and overlap matrices. Band structure, density of states, and the Fermi surface are calculated from this real-space tight-binding representation for various extended systems (Si, SiC, Fe, and Mo) and compared with plane-wave DFT results. The Mulliken charge and bond order analyses are performed under QO basis set, which satisfy sum rules. The present work validates the general applicability of Slater and Koster\u27s scheme of linear combinations of atomic orbitals and points to future ab initio tight-binding parametrizations and linear-scaling DFT development

Population genomic analyses of protected incense trees Aquilaria sinensis reveal the existence of genetically distinct subpopulations

The incense tree Aquilaria sinensis (Thymelaeaceae) can produce agarwood with commercial values and is now under threat from illegal exploitation in Hong Kong, impairing the local population and biodiversity. Together with other species of Aquilaria, it is listed in the CITES Appendix II, which strictly regulates its international trade. To understand the population structure of A. sinensis and to make relevant conservation measures, we have sequenced 346 individuals collected in Hong Kong and southern mainland China. Population genomic analyses including principal component analysis, neighbor-joining tree construction, ADMIXTURE, and hierarchical pairwise-FST analyses suggested that genetically distinct populations are contained in certain areas. Genomic scan analyses further detected single-nucleotide polymorphism (SNP) outliers related to plant defense, including the CYP71BE gene cluster. In addition to the population analyses, we have developed a modified hexadecyltrimethyl-ammonium bromide (CTAB) DNA extraction protocol for obtaining DNA from agarwood samples in this study, and resequencing of DNA extracted from two agarwood samples using this method allows us to successfully map to the sample corresponding localities in the phylogenetic tree. To sum up, this study suggested that there is a genetically distinct subpopulation of incense tree in Hong Kong that would require special conservation measures and established a foundation for future conservation measures

Telephone-based behavioral activation intervention for dementia family caregivers: Outcomes and mediation effect of a randomized controlled trial

Objectives:  The study examined the effects of a telephone-administered psycho-education with behavioral activation intervention (TBA) for family caregivers of person’s with Alzheimer’s dementia to reduce levels of depressive symptoms and burden and to enhance relationship satisfaction with the care-recipient Methods:  A double-blinded randomized trial compared TBA with telephone-based psycho-education with general monitoring (TGM). Ninety-six dementia caregivers were randomized. Both conditions received four weekly psycho-education sessions led by a social worker. TBA participants then received eight bi-weekly behavioral activation practice sessions delivered by paraprofessionals. TGM participants received eight bi-weekly monitoring sessions by paraprofessionals. Results:  As compared to TGM, TBA participants reported significantly larger reductions in depressive symptoms and burden and larger improvement in relationship satisfaction. Self-efficacy for controlling upsetting thoughts was found to have a partial meditation effect between TBA and the reduction of depressive symptoms. Qualitative feedback suggested that TBA participants expressed unique gains in awareness and developing new ways of reappraising the caregiving situation. Conclusion:  TBA was an effective intervention to reduce depressive symptoms and burden as well as to enhance relationship satisfaction in dementia caregivers

Comparison of two surgical techniques for reconstructing posterolateral corner of the knee: a cadaveric study evaluated by navigation system

Purpose: This study aimed to evaluate the immediate effect on knee kinematics by 2 different techniques of posterolateral corner (PLC) reconstruction. Methods: Five intact formalin-preserved cadaveric knees were used in this study. A navigation system was used to measure knee kinematics (posterior translation, varus angulation, and external rotation) after application of a constant force and torque to the tibia. Four different conditions of the knee were evaluated during the biomechanical test: intact knee and PLC-sectioned knee and PLC-reconstructed knee by the doublefemoral tunnel technique and singlefemoral tunnel technique. Results: Sectioning of the PLC structures resulted in significant increases in external rotation at 30° of flexion from 11.2° (SD, 2.6) to 24.6° (SD, 6.2), posterior translation at 30° of flexion from 3.4 mm (SD, 1.5) to 7.4 mm (SD, 3.8), and varus angulation at 0° of flexion from 2.3° (SD, 2.1) to 7.9° (SD, 5.1). Both reconstruction techniques significantly restored the varus stability. The external rotation and posterior translation at 30° of flexion after reconstruction with the doublefemoral tunnel technique were 10.2° (SD, 1.3) and 3.4° (SD, 2.7), respectively, which were significantly better than those of the singlefemoral tunnel technique. Conclusions: Both techniques of reconstruction showed improved stability compared with PLC-sectioned knees. The doublefemoral tunnel technique in PLC reconstruction showed better rotational stability and resistance to posterior translation than the singlefemoral tunnel technique without compromising varus stability. Clinical Relevance: PLC reconstruction by a doublefemoral tunnel technique achieves better rotational control and resistance to posterior translation

Germline breast cancer susceptibility genes, tumor characteristics, and survival.

BACKGROUND: Mutations in certain genes are known to increase breast cancer risk. We study the relevance of rare protein-truncating variants (PTVs) that may result in loss-of-function in breast cancer susceptibility genes on tumor characteristics and survival in 8852 breast cancer patients of Asian descent. METHODS: Gene panel sequencing was performed for 34 known or suspected breast cancer predisposition genes, of which nine genes (ATM, BRCA1, BRCA2, CHEK2, PALB2, BARD1, RAD51C, RAD51D, and TP53) were associated with breast cancer risk. Associations between PTV carriership in one or more genes and tumor characteristics were examined using multinomial logistic regression. Ten-year overall survival was estimated using Cox regression models in 6477 breast cancer patients after excluding older patients (≥75years) and stage 0 and IV disease. RESULTS: PTV9genes carriership (n = 690) was significantly associated (p < 0.001) with more aggressive tumor characteristics including high grade (poorly vs well-differentiated, odds ratio [95% confidence interval] 3.48 [2.35-5.17], moderately vs well-differentiated 2.33 [1.56-3.49]), as well as luminal B [HER-] and triple-negative subtypes (vs luminal A 2.15 [1.58-2.92] and 2.85 [2.17-3.73], respectively), adjusted for age at diagnosis, study, and ethnicity. Associations with grade and luminal B [HER2-] subtype remained significant after excluding BRCA1/2 carriers. PTV25genes carriership (n = 289, excluding carriers of the nine genes associated with breast cancer) was not associated with tumor characteristics. However, PTV25genes carriership, but not PTV9genes carriership, was suggested to be associated with worse 10-year overall survival (hazard ratio [CI] 1.63 [1.16-2.28]). CONCLUSIONS: PTV9genes carriership is associated with more aggressive tumors. Variants in other genes might be associated with the survival of breast cancer patients. The finding that PTV carriership is not just associated with higher breast cancer risk, but also more severe and fatal forms of the disease, suggests that genetic testing has the potential to provide additional health information and help healthy individuals make screening decisions

Characterisation of protein-truncating and missense variants in PALB2 in 15 768 women from Malaysia and Singapore

Funder: National University Cancer Institute, Singapore; FundRef: http://dx.doi.org/10.13039/501100011105Background: Rare protein-truncating variants (PTVs) in partner and localiser of BRCA2 (PALB2) confer increased risk to breast cancer, but relatively few studies have reported the prevalence in South-East Asian populations. Here, we describe the prevalence of rare variants in PALB2 in a population-based study of 7840 breast cancer cases and 7928 healthy Chinese, Malay and Indian women from Malaysia and Singapore, and describe the functional impact of germline missense variants identified in this population. Methods: Mutation testing was performed on germline DNA (n=15 768) using targeted sequencing panels. The functional impact of missense variants was tested in mouse embryonic stem cell based functional assays. Results: PTVs in PALB2 were found in 0.73% of breast cancer patients and 0.14% of healthy individuals (OR=5.44; 95% CI 2.85 to 10.39, p<0.0001). In contrast, rare missense variants in PALB2 were not associated with increased risk of breast cancer. Whereas PTVs were associated with later stage of presentation and higher-grade tumours, no significant association was observed with missense variants in PALB2. However, two novel rare missense variants (p.L1027R and p.G1043V) produced unstable proteins and resulted in a decrease in homologous recombination-mediated repair of DNA double-strand breaks. Conclusion: Despite genetic and lifestyle differences between Asian and other populations, the population prevalence of PALB2 PTVs and associated relative risk of breast cancer, are similar to those reported in European populations

The effects of a mindfulness-based family psychoeducation intervention for the caregivers of young adults with first-episode psychosis: A randomized controlled trial

Objective: In this study, we investigated the effects of a mindfulness-based family psychoeducation (MBFPE) program on the mental-health outcomes of both caregivers and young adults with first-episode psychosis with an onset in the past three years through a multi-site randomized controlled trial. We also studied the outcomes of three potential mediating effects of interpersonal mindfulness, expressed emotions, and non-attachment on the program. Method: We randomly assigned 65 caregivers of young adults with psychosis to MBFPE (n = 33) or an ordinary family psychoeducation (FPE) program (n = 32); among them, 18 young adults in recovery also participated in the evaluation of outcomes. Results: Intent-to-treat analyses were conducted. No significant time × group interaction effects of MBFPE and FPE programs were found in any of the caregivers’ outcomes. However, the young adults with psychosis reported higher levels of recovery after the MBFPE program than after the ordinary FPE program (F = 8.268, p = 0.012, d = 1.484). They also reported a larger reduction in over-involvement of their caregivers (F = 4.846, p = 0.044, d = 1.136), showing that MBFPE had a superior effect to FPE in promoting recovery and reducing over-involvement. Conclusions: A brief psychoeducation program may not reduce the burden on or improve the mental-health outcome of caregivers of individuals with recent-onset psychosis. However, integrating mindfulness into a conventional family psychoeducation program may reduce the expressed emotions of caregivers, especially over-involvement. Further studies should explore how psychoeducation programs can reduce the impact of psychosis on family through sustainable effects in terms of reducing their burden and expressed emotions, using a rigorous study and adequate sample size