Quantifying Charge Extraction and Recombination Using the Rise and Decay of the Transient Photovoltage of Perovskite Solar Cells.

The extraction of photogenerated charge carriers and the generation of a photovoltage belong to the fundamental functionalities of any solar cell. These processes happen not instantaneously but rather come with finite time constants, e.g., a time constant related to the rise of the externally measured open circuit voltage following a short light pulse. Herein, a new method to analyze transient photovoltage measurements at different bias light intensities combining rise and decay times of the photovoltage. The approach uses a linearized version of a system of two coupled differential equations that are solved analytically by determining the eigenvalues of a 2 × 2 matrix. By comparison between the eigenvalues and the measured rise and decay times during a transient photovoltage measurement, the rates of carrier recombination and extraction as a function of bias voltage are determined, and establish a simple link between their ratio and the efficiency losses in the perovskite solar cell.

Toward the Integration of a Silicon/Graphite Anode-Based Lithium-Ion Battery in Photovoltaic Charging Battery Systems.

Solar photovoltaic (PV) energy generation is highly dependent on weather conditions and only applicable when the sun is shining during the daytime, leading to a mismatch between demand and supply. Merging PVs with battery storage is the straightforward route to counteract the intermittent nature of solar generation. Capacity (or energy density), overall efficiency, and stability at elevated temperatures are among key battery performance metrics for an integrated PV-battery system. The performance of high-capacity silicon (Si)/graphite (Gr) anode and LiNi0.6Mn0.2Co0.2O2 (NMC622) cathode cells at room temperature, 45, and 60 °C working temperatures for PV modules are explored. The electrochemical performance of both half and full cells are tested using a specially formulated electrolyte, 1 M LiPF6 in ethylene carbonate: diethyl carbonate, with 5 wt % fluoroethylene carbonate, 2 wt % vinylene carbonate, and 1 wt % (2-cyanoethyl)triethoxysilane. To demonstrate solar charging, perovskite solar cells (PSCs) are coupled to the developed batteries, following the evaluation of each device. An overall efficiency of 8.74% under standard PV test conditions is obtained for the PSC charged lithium-ion battery via the direct-current-direct-current converter, showing the promising applicability of silicon/graphite-based anodes in the PV-battery integrated system.

Trait-environment relationships differ between mixed-species flocking and nonflocking bird assemblages.

Hypotheses about the mechanisms of community assembly suggest that biotic and abiotic filters constrain species establishment through selection on their functional traits. It is unclear how differences in traits influence the niche dimensions of closely related bird species when they coexist in spatiotemporally heterogeneous environments. Further, it is necessary to take into account their participation in mixed-species flocks, social systems that can include both competition and facilitation. For 6 yr, we conducted counts of forest bird species and took measurements of environmental variables along an elevational gradient in the Nanling Mountains, China. To disentangle different deterministic and historical/stochastic processes between flocking and nonflocking bird assemblages, we first compared phylogenetic and functional structure, and community-weighted mean trait values (CWM). We further assessed elevational variations in trait-environment relationships. We found that the flocking and nonflocking bird assemblages were structured by environmental gradients in contrasting ways. The nonflocking assemblage showed a strong change from over-dispersed to clustered community structure with increasing elevations, consistent with the strong selective pressures of a harsh environment (i.e., environmental filtering). The nonflocking assemblage also displayed significant trait-environment relationships in bivariate correlations and multivariate ordination space, including specific morphological and foraging traits that are linked to vegetation characteristics (e.g., short trees at high elevations). By contrast, flocking birds were more resilient to habitat change with elevation, with relatively consistent community membership, and showed fewer trait-environment associations. CWM of traits that are known to be associated with species' propensity to join mixed-species flocks, including small body size and broad habitat specificity, were linked to the flocking assemblage consistently across the elevational gradient. Collectively, our trait-based analyses provide strong evidence that trait-environment relationships differ between flocking and nonflocking bird assemblages. Besides serving as bellwethers of changing environments, emergent properties of flock systems may increase the resilience of animal communities undergoing environmental change. Mixed-species flocks present an ideal model with which to explore cooccurrence of closely related species, because habitat filtering may be buffered, and the patterns observed are therefore the outcomes of species interactions including both competition and facilitation.

LncRNA HOXA-AS2 and its molecular mechanisms in human cancer.

Long non-coding RNAs (lncRNAs), a novel class of noncoding RNAs, are commonly defined as RNA molecules more than 200 nucleotides in length. Emerging research indicated that lncRNA played a vital role in human tumorigenesis and progression by serving as tumor oncogenes or suppressors. LncRNA has been shown to get involved in participate various biological processes, such as cell growth, anti-apoptosis, migration and invasion. LncRNA HOXA cluster antisense RNA2 (HOXA-AS2) is a novel cancer-related lncRNA. It was recently found to exhibit aberrant expression in a variety of malignancies, including breast cancer, gastric cancer, gallbladder carcinoma, hepatocellular carcinoma and pancreatic cancer. The oncogenicity of lncRNA HOXA-AS2 mainly inhibits or promotes the expression of related genes through direct or indirect pathways, suggesting that HOXA-AS2 likely represents a feasible biomarker or therapeutic target in human cancers. In this review, we summarize current evidences concerning the biological functions and mechanisms of HOXA-AS2 during tumor development.

Diagnosis and management of primary hepatic pregnancy: literature review of 31 cases.

PURPOSE: To summarize the appropriate diagnostic methods and therapeutic options for primary hepatic pregnancy (PHP). METHODS: Literature searches were performed in Pubmed, Web of Science, Cochrane Library and Embase databases (1956-2017), using the following search terms: primary hepatic pregnancy, hepatic pregnancy, liver pregnancy, hepatic ectopic pregnancy and intrahepatic pregnancy. Further literature was confirmed through cross-referencing. RESULTS: Thirty-one cases were reviewed and collected. The site mostly described in literatures is the right lobe of liver (93.5%). Main symptoms of PHP included abdominal pain (77.4%), amenorrhea (45.2%), acuteperitonism (32.3%), shock (25.8%) and vomit (16.1%). Majority of patients (83.9%) were treated by laparotomy. Less-invasive approaches (16.1%) such as laparoscopy or combination of postoperative injection of methotrexate were used less frequently. The outcome was acceptable at the end of the follow-up period in ten cases (1-72 months) and the recovery rate was 96.7%. One patient died and other complications were noted in three patients during the postoperative period. CONCLUSIONS: The clinical diagnosis of PHP can be settled up by comprehensive analysis of serum HCG levels, ultrasound and imaging. The analysis should be assessed carefully before therapeutic procedure. Invasive methods should be preferential. Less-invasive approaches can be selected when the patients have stable hemodynamics and non-acute abdomen.

Prognostic Significance of Major Histocompatibility Complex Class II Expression in Pediatric Adrenocortical Tumors: A St. Jude and Children's Oncology Group Study.

PURPOSE: Histologic markers that differentiate benign and malignant pediatric adrenocortical tumors are lacking. Previous studies have implicated an association of MHC class II expression with adrenocortical tumor prognosis. Here, we determined the expression of MHC class II as well as the cell of origin of these immunologic markers in pediatric adrenocortical tumor. The impact of MHC class II gene expression on outcome was determined in a cohort of uniformly treated children with adrenocortical carcinomas. EXPERIMENTAL DESIGN: We analyzed the expression of MHC class II and a selected cluster of differentiation genes in 63 pediatric adrenocortical tumors by Affymetrix Human U133 Plus 2.0 or HT HG-U133+PM gene chip analyses. Cells expressing MHC class II were identified by morphologic and immunohistochemical assays. RESULTS: MHC class II expression was significantly greater in adrenocortical adenomas than in carcinomas (P = 4.8 ×10-6) and was associated with a higher progression-free survival (PFS) estimate (P = 0.003). Specifically, HLA-DPA1 expression was most significantly associated with PFS after adjustment for tumor weight and stage. HLA-DPA1 was predominantly expressed by hematopoietic infiltrating cells and undetectable in tumor cells in 23 of 26 cases (88%). CONCLUSIONS: MHC class II expression, which is produced by tumor-infiltrating immune cells, is an indicator of disease aggressiveness in pediatric adrenocortical tumor. Our results suggest that immune responses modulate adrenocortical tumorigenesis and may allow the refinement of risk stratification and treatment for this disease. Clin Cancer Res; 22(24); 6247-55. ©2016 AACR.

Partial Geometric Frustration in Inorganic Supramolecular Spin Systems with One-Dimensional Trigonally Aligned Magnetic Chains ∞1(MCl4)2- (M = Fe2+, Co2+).

Exploration of new spin systems with low-dimensional subunits have been of great interest in the past decades due to their interesting physical properties and potential applications in molecular spintronics. Two inorganic supramolecular complexes, (Hg3S2)(FeCl4) and (Hg3S2)(CoCl4), with trigonally aligned 1-D infinite magnetic ∞(1)(FeCl4)(2-) or ∞(1)(CoCl4)(2-) chains have been prepared by solid-state reactions. They exhibit 3-D long-range spin order with strong field dependence and field induced metamagnetic behavior. The intrachain and interchain magnetic coupling constants were estimated by DFT+U and DFT+U+SOC calculations and the both complexes can be regarded as partially frustrated spin systems. The spin Hamiltonian was constructed, the ground state is proposed to be incommensurate spiral spin order, which differs from the commensurate 120° spin structure ground state of fully frustrated trigonal case by a little canted angle. This study shows that cooperative magnetic ordering induced by geometric frustration can be realized in inorganic supramolecular systems assembled by weak van der Waals' interactions.

Color tunable and near white-light emission of two solvent-induced 2D lead(II) coordination networks based on a rigid ligand 1-tetrazole-4-imidazole-benzene.

Two new lead(II) coordination polymers, [Pb(NO3)(tzib)]n (1) and [Pb(tzib)2]n (2), were successfully synthesized from the reaction of a rigid ligand 1-tetrazole-4-imidazole-benzene (Htzib) and lead(II) nitrate in different solvents. The obtained polymers have been characterized by single-crystal X-ray diffraction analyses, which show that both polymers feature 2D layer structures. The inorganic anion nitrate in 1 shows a µ2-κO3:κO3 bridging mode to connect adjacent lead ions into a zigzag chain, and then the organic ligands tzib(-) join the neighboring chains into a 2D layer by a µ3-κN1:κN2:κN6 connection mode. In 2, there are two different bridging modes of the tzib(-) ligand: µ3-κN1:κN2:κN6 and µ3-κN1:κN6 to coordinate the lead ions into a 2D layer structure. Interestingly, both polymers displayed broadband emissions covering the entire visible spectra, which could be tunable to near white-light emission by varying excitation wavelengths.

SVSI: fast and powerful set-valued system identification approach to identifying rare variants in sequencing studies for ordered categorical traits.

In genetic association studies of an ordered categorical phenotype, it is usual to either regroup multiple categories of the phenotype into two categories and then apply the logistic regression (LG), or apply ordered logistic (oLG), or ordered probit (oPRB) regression, which accounts for the ordinal nature of the phenotype. However, they may lose statistical power or may not control type I error due to their model assumption and/or instable parameter estimation algorithm when the genetic variant is rare or sample size is limited. To solve this problem, we propose a set-valued (SV) system model to identify genetic variants associated with an ordinal categorical phenotype. We couple this model with a SV system identification algorithm to identify all the key system parameters. Simulations and two real data analyses show that SV and LG accurately controlled the Type I error rate even at a significance level of 10(-6) but not oLG and oPRB in some cases. LG had significantly less power than the other three methods due to disregarding of the ordinal nature of the phenotype, and SV had similar or greater power than oLG and oPRB. We argue that SV should be employed in genetic association studies for ordered categorical phenotype.

Genomic landscape of paediatric adrenocortical tumours.

Paediatric adrenocortical carcinoma is a rare malignancy with poor prognosis. Here we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing. Most cases (91%) show loss of heterozygosity (LOH) of chromosome 11p, with uniform selection against the maternal chromosome. IGF2 on chromosome 11p is overexpressed in 100% of the tumours. TP53 mutations and chromosome 17 LOH with selection against wild-type TP53 are observed in 28 ACTs (76%). Chromosomes 11p and 17 undergo copy-neutral LOH early during tumorigenesis, suggesting tumour-driver events. Additional genetic alterations include recurrent somatic mutations in ATRX and CTNNB1 and integration of human herpesvirus-6 in chromosome 11p. A dismal outcome is predicted by concomitant TP53 and ATRX mutations and associated genomic abnormalities, including massive structural variations and frequent background mutations. Collectively, these findings demonstrate the nature, timing and potential prognostic significance of key genetic alterations in paediatric ACT and outline a hypothetical model of paediatric adrenocortical tumorigenesis.

Intense photo- and tribo-luminescence of three tetrahedral manganese(II) dihalides with chelating bidentate phosphine oxide ligand.

Three air-stable tetrahedral manganese(ii) dihalide complexes [MnX2(DPEPO)] (DPEPO = bis[2-(diphenylphosphino)phenyl]ether oxide; X = Cl, Br and I) were prepared. All of the obtained compounds were structurally characterized by single-crystal X-ray diffraction analyses, which reveal that they crystallize in centrosymmetric space groups and feature an isolated mononuclear structure with Mn(2+) in a tetrahedral environment. Interestingly, these complexes show excellent photoluminescent performance in neat solid form, with the highest total quantum yield (Φtotal) of up to 70% recorded for the dibromide complex. Intense green flashes of light could be observed by the naked eye when rubbing the manganese(ii) complexes.

The genomic landscape of childhood and adolescent melanoma.

Despite remarkable advances in the genomic characterization of adult melanoma, the molecular pathogenesis of pediatric melanoma remains largely unknown. We analyzed 15 conventional melanomas (CMs), 3 melanomas arising in congenital nevi (CNMs), and 5 spitzoid melanomas (SMs), using various platforms, including whole genome or exome sequencing, the molecular inversion probe assay, and/or targeted sequencing. CMs demonstrated a high burden of somatic single-nucleotide variations (SNVs), with each case containing a TERT promoter (TERT-p) mutation, 13/15 containing an activating BRAF V600 mutation, and >80% of the identified SNVs consistent with UV damage. In contrast, the three CNMs contained an activating NRAS Q61 mutation and no TERT-p mutations. SMs were characterized by chromosomal rearrangements resulting in activated kinase signaling in 40%, and an absence of TERT-p mutations, except for the one SM that succumbed to hematogenous metastasis. We conclude that pediatric CM has a very similar UV-induced mutational spectrum to that found in the adult counterpart, emphasizing the need to promote sun protection practices in early life and to improve access to therapeutic agents being explored in adults in young patients. In contrast, the pathogenesis of CNM appears to be distinct. TERT-p mutations may identify the rare subset of spitzoid melanocytic lesions prone to disseminate.

An R package that automatically collects and archives details for reproducible computing.

BACKGROUND: It is scientifically and ethically imperative that the results of statistical analysis of biomedical research data be computationally reproducible in the sense that the reported results can be easily recapitulated from the study data. Some statistical analyses are computationally a function of many data files, program files, and other details that are updated or corrected over time. In many applications, it is infeasible to manually maintain an accurate and complete record of all these details about a particular analysis. RESULTS: Therefore, we developed the rctrack package that automatically collects and archives read only copies of program files, data files, and other details needed to computationally reproduce an analysis. CONCLUSIONS: The rctrack package uses the trace function to temporarily embed detail collection procedures into functions that read files, write files, or generate random numbers so that no special modifications of the primary R program are necessary. At the conclusion of the analysis, rctrack uses these details to automatically generate a read only archive of data files, program files, result files, and other details needed to recapitulate the analysis results. Information about this archive may be included as an appendix of a report generated by Sweave or knitR. Here, we describe the usage, implementation, and other features of the rctrack package. The rctrack package is freely available from http://www.stjuderesearch.org/site/depts/biostats/rctrack under the GPL license.

The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression.

SUMMARY: Several outlier and subgroup identification statistics (OASIS) have been proposed to discover transcriptomic features with outliers or multiple modes in expression that are indicative of distinct biological processes or subgroups. Here, we borrow ideas from the OASIS methods in the bioinformatics and statistics literature to develop the 'most informative spacing test' (MIST) for unsupervised detection of such transcriptomic features. In an example application involving 14 cases of pediatric acute megakaryoblastic leukemia, MIST more robustly identified features that perfectly discriminate subjects according to gender or the presence of a prognostically relevant fusion-gene than did seven other OASIS methods in the analysis of RNA-seq exon expression, RNA-seq exon junction expression and micorarray exon expression data. MIST was also effective at identifying features related to gender or molecular subtype in an example application involving 157 adult cases of acute myeloid leukemia. AVAILABILITY: MIST will be freely available in the OASIS R package at http://www.stjuderesearch.org/site/depts/biostats CONTACT: stanley.pounds@stjude.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Homochiral zinc(II) coordination compounds based on in-situ-generated chiral amino acid-tetrazole ligands: circular dichroism, excitation light-induced tunable photoluminescence, and energetic performance.

We employed two pairs of new in-situ-generated chiral amino acid-tetrazole ligands in constructing homochiral Zn(II) coordination compounds: [Zn(tzet)]n (1a for (S)-tzet and 1b for (R)-tzet, H2tzet = N-[2-(1H-tetrazol-5-yl)ethyl]tryptophan) and [Zn(tzep)(H2O)2]·H2O (2a for (S)-tzep and 2b for (R)-tzep, H2tzep = N-[2-(1H-tetrazol-5-yl)ethyl]proline), which were hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. Structural analysis reveals that 1 features a 2D homochiral framework generated by both tetrazolate and carboxylate bridges in tzet(2-) ligands. The isolated structure of 2 is stabilized by extensive hydrogen bonds, which leads to formation of a supramolecular 2D architecture. The absolute configuration induced at the nitrogen atoms of 1 and 2 is strictly related to the neighboring chiral carbon atoms by hydrogen-bond interactions. To further investigate their chirality, the combined experimental and theoretical analyses of circular dichroism spectra reveal the absolute configurations and nature of the Cotton effects. Solid-state excitation and emission spectra for 1 and 2 at room temperature were investigated with relevant density of states calculation, and tunable photoluminescence emission of 1 under different excitation wavelengths was discussed. As nitrogen-rich tetrazolate compounds, 1 and 2 possess higher enthalpies of combustion and may serve as a new family of promising energetic materials.

Large mid-IR second-order nonlinear-optical effects designed by the supramolecular assembly of different bond types without IR absorption.

Two new different-bond-type hybrid compounds, (Hg6P4Cl3)(PbCl3) (1) and (Hg23P12)(ZnCl4)6 (2), with supramolecular interactions between host and guest moieties, which based on metal-pnicogen, pnicogen-pnicogen, and metal-halogen bonds were obtained by solid-state reactions. Compounds 1 and 2 show large second-harmonic-generation (SHG) activity and are transparent in the wide mid-IR region, providing an effective route for searching new IR nonlinear-optical material systems by combining two or more different bond types with no IR absorption within a single compound through supramolecular assembly. Theory predications based on first-principles calculations are also performed on the SHG properties of 1 and 2.

A genomic random interval model for statistical analysis of genomic lesion data.

MOTIVATION: Tumors exhibit numerous genomic lesions such as copy number variations, structural variations and sequence variations. It is difficult to determine whether a specific constellation of lesions observed across a cohort of multiple tumors provides statistically significant evidence that the lesions target a set of genes that may be located across different chromosomes but yet are all involved in a single specific biological process or function. RESULTS: We introduce the genomic random interval (GRIN) statistical model and analysis method that evaluates the statistical significance of the abundance of genomic lesions that overlap a specific locus or a pre-defined set of biologically related loci. The GRIN model retains certain biologically important properties of genomic lesions that are ignored by other methods. In a simulation study and two example analyses of leukemia genomic lesion data, GRIN more effectively identified important loci as significant than did three methods based on a permutation-of-markers model. GRIN also identified biologically relevant pathways with a significant abundance of lesions in both examples. AVAILABILITY: An R package will be freely available at CRAN and www.stjuderesearch.org/site/depts/biostats/software.

NCK2 is significantly associated with opiates addiction in African-origin men.

Substance dependence is a complex environmental and genetic disorder with significant social and medical concerns. Understanding the etiology of substance dependence is imperative to the development of effective treatment and prevention strategies. To this end, substantial effort has been made to identify genes underlying substance dependence, and in recent years, genome-wide association studies (GWASs) have led to discoveries of numerous genetic variants for complex diseases including substance dependence. Most of the GWAS discoveries were only based on single nucleotide polymorphisms (SNPs) and a single dichotomized outcome. By employing both SNP- and gene-based methods of analysis, we identified a strong (odds ratio = 13.87) and significant (P value = 1.33E - 11) association of an SNP in the NCK2 gene on chromosome 2 with opiates addiction in African-origin men. Codependence analysis also identified a genome-wide significant association between NCK2 and comorbidity of substance dependence (P value = 3.65E - 08) in African-origin men. Furthermore, we observed that the association between the NCK2 gene (P value = 3.12E - 10) and opiates addiction reached the gene-based genome-wide significant level. In summary, our findings provided the first evidence for the involvement of NCK2 in the susceptibility to opiates addiction and further revealed the racial and gender specificities of its impact.

Genetic association test for multiple traits at gene level.

Genome-wide association studies (GWASs) at the gene level are commonly used to understand biological mechanisms underlying complex diseases. In general, one response or outcome is used to present a disease of interest in such studies. In this study, we consider a multiple traits association test from the gene level. We propose and examine a class of test statistics that summarizes the association information between single nucleotide polymorphisms (SNPs) and each of the traits. Our simulation studies demonstrate the advantage of gene-based multiple traits association tests when multiple traits share common genes. Using our proposed tests, we reanalyze the dataset from the Study of Addiction: Genetics and Environment (SAGE). Our result validates previous findings while presenting stronger evidence for consideration of multiple traits.

Empirical evaluation of scoring functions for Bayesian network model selection.

In this work, we empirically evaluate the capability of various scoring functions of Bayesian networks for recovering true underlying structures. Similar investigations have been carried out before, but they typically relied on approximate learning algorithms to learn the network structures. The suboptimal structures found by the approximation methods have unknown quality and may affect the reliability of their conclusions. Our study uses an optimal algorithm to learn Bayesian network structures from datasets generated from a set of gold standard Bayesian networks. Because all optimal algorithms always learn equivalent networks, this ensures that only the choice of scoring function affects the learned networks. Another shortcoming of the previous studies stems from their use of random synthetic networks as test cases. There is no guarantee that these networks reflect real-world data. We use real-world data to generate our gold-standard structures, so our experimental design more closely approximates real-world situations. A major finding of our study suggests that, in contrast to results reported by several prior works, the Minimum Description Length (MDL) (or equivalently, Bayesian information criterion (BIC)) consistently outperforms other scoring functions such as Akaike's information criterion (AIC), Bayesian Dirichlet equivalence score (BDeu), and factorized normalized maximum likelihood (fNML) in recovering the underlying Bayesian network structures. We believe this finding is a result of using both datasets generated from real-world applications rather than from random processes used in previous studies and learning algorithms to select high-scoring structures rather than selecting random models. Other findings of our study support existing work, e.g., large sample sizes result in learning structures closer to the true underlying structure; the BDeu score is sensitive to the parameter settings; and the fNML performs pretty well on small datasets. We also tested a greedy hill climbing algorithm and observed similar results as the optimal algorithm.