bluuebunny/crossref_metadata_2025_split huggingface dataset:
POPSIM: a general population simulation program.
Authors: Hampe J , Wienker T , Schreiber S , N√ºrnberg P 
Published: July 2002

Abstract
MOTIVATION: The investigation of common disorders of polygenic inheritance using both population-based association designs and non-parametric linkage analysis within families is gaining increasing importance. We have created a program that allows for the flexible simulation of populations as a tool to investigate the properties of population-based mapping approaches. RESULTS: We have created a population simulation program, POPSIM, that (i) creates a virtual representation of every individual, (ii) makes no prior assumptions but the Mendelian rules and (iii) allows populations of several million individuals in size to be generated and to be followed over hundreds of generations. The parameters of the disease model, population structure and population expansion rate can be specified. Flexible sampling options exist that allow samples of families and individuals to be drawn at any given point during the population history. The program may be a useful tool in the study of the influence of genetic drift, recombination and admixture on the generation and maintenance of linkage disequilibrium in populations, as well as the evaluation of stochastic sampling characteristics of families and individuals conditional on a complex genetic phenotype from homogeneous and heterogeneous populations. AVAILABILITY: The source code as well as Sun and Windows NT4.0 console executables of the program are available under http://www.ukrv. de/ch/medgen/html/benutzer/j.hampe/popsim. html. CONTACT: J. Hampe@mucosa.de
Protein domain decomposition using a graph-theoretic approach
Authors: Xu Ying , Xu Dong , Gabow Harold N. 
Published: July 2002

Abstract
Motivation: Automatic decomposition of a multi-domain protein into individual domains represents a highly interesting and unsolved problem. As the number of protein structures in PDB is growing at an exponential rate, there is clearly a need for more reliable and efficient methods for protein domain decomposition simply to keep the domain databases up-to-date.
Results: We present a new algorithm for solving the domain decomposition problem, using a graph-theoretic approach. We have formulated the problem as a network flow problem, in which each residue of a protein is represented as a node of the network and each residue–residue contact is represented as an edge with a particular capacity , depending on the type of the contact. A two-domain decomposition problem is solved by finding a bottleneck (or a minimum cut) of the network, which minimizes the total cross-edge capacity, using the classical Ford–Fulkerson algorithm. A multi-domain decomposition problem is solved through repeatedly solving a series of two-domain problems. The algorithm has been implemented as a computer program, called DomainParser. We have tested the program on a commonly used test set consisting of 55 proteins. The decomposition results are 78.2% in agreement with the literature on both the number of decomposed domains and the assignments of residues to each domain, which compares favorably to existing programs. On the subset of two-domain proteins (20 in number), the program assigned 96.7% of the residues correctly when we require that the number of decomposed domains is two.
Availability: The executable of DomainParser and its web server are available at http://compbio.ornl.gov/structure/domainparser/.
Contact: xyn@ornl.gov
* To whom correspondence should be addressed.
Insights into 2D/2D MXene Heterostructures for Improved Synergy in Structure toward Next‐Generation Supercapacitors: A Review
Authors: Nasrin Kabeer , Sudharshan Vasudevan , Subramani Kaipannan , Sathish Marappan 
Published: February 2022

Abstract2D interfacial heterostructures have found an unassailable status in energy storage systems, particularly in supercapacitors citing the intriguing structural and electrochemical characteristics. Exactly a decade ago, MXene, a promising 2D transition metal carbide/nitride/carbonitride was found to possess excellent conductivity, hydrophilicity, laudable charge storage opportunities, and enriched surface functionalities conducive for supercapacitors with inherent challenging shortcomings. To substantially improve, assembled 2D/2D MXene heterostructures exhibit commendable performance backed by the fact of swift increase in research interest. In this review, state‐of‐the‐art research progress in material design and electrochemical performance of 2D/2D MXene heterostructures for supercapacitors are investigated. Discussion is initially on MXene fundamentals including synthesis and energy storage governing properties. Particularly, different preparation including electrostatic assembly, in situ growth, hydrothermal treatment, and objective specific strategies and its implications are elaborated. Especially, the electrochemical interface science, electrode–electrolyte interaction and ion/electron dynamics and synergistic enhancement of MXene/rGO, MXene/LDH, MXene/metal sulfides and timely investigations on other 2D MXene architectures are provided for its compatibility from solid‐state to microsupercapacitors for commerciality. To conclude, a well‐comprehended outlook, key challenges, and prospective research guidelines stretching from fundamental mechanism investigations to material and electrolyte optimizations are presented to encourage advanced 2D MXene architectures for future generation supercapacitors.
Grain‐Boundaries‐Engineering via Laser Manufactured La‐Doped BaSnO3 Nanocrystals with Tailored Surface States Enabling Perovskite Solar Cells with Efficiency of 23.74%
Authors: Yang Xiaokun , Zhao Wenhao , Li Mingjie , Ye Linfeng , Guo Pengfei , Xu Youxun , Guo Hang , Yu Huiwu , Ye Qian , Wang Hongyue , Harvey Daniel , Shchukin Dmitry , Feng Minjun , Sum Tze Chien , Wang Hongqiang 
Published: February 2022

AbstractGrain boundaries (GBs) engineering of hybrid perovskite films is of significance for accessing high performance perovskite solar cells (PSCs), owing to the abundant defect states existed therein originating from the low temperature film processing. Nanocrystals embedding at GBs has shown profound advantages in carrier dynamics modulation, while the surface defects on nanocrystals in turn lead usually to the trapping of carriers at GBs. The authors herein demonstrate the efficient GBs engineering via laser generated nanocrystals with tailored surface states for improved carriers dynamics and environmental stability of PSCs. The embedding of La doped BaSnO3 (LBSO) nanocrystals with bare surfaces in perovskite provides an additional channel to facilitate the effective carrier extraction and reduce the carrier recombination, leading to a maximum power conversion efficiency (PCE) of 21.11% with negligible hysteresis for the mixed‐cation PSCs. To clarify the influence of surface defect states of the laser generated nanocrystals on the performance of PSCs, 1H,1H‐perfluorooctylamine is grafted on LBSO nanocrystals during the laser irradiation, resulting in improved champion PCE up to 21.65% and pronounced environmental stability. The universal embedding of the LBSO nanocrystals with tailored surface states in different perovskite by fabricating FAPbI3 PSCs with a champion PCE of 23.74% is further demonstrated.
Dual Modification Engineering via Lanthanide‐Based Halide Quantum Dots and Black Phosphorus Enabled Efficient Perovskite Solar Cells with High Open‐Voltage of 1.235 V
Authors: Liu Shuainan , Lyu Jiekai , Zhou Donglei , Zhuang Xinmeng , Shi Zhichong , Sun Rui , Liu Le , Wu Yanjie , Liu Bin , Liu Dali , Song Hongwei 
Published: February 2022

AbstractInterfacial engineering is one of the most effective means to improve the photoelectric conversion efficiency (PCE) and stability of perovskite solar cells (PSCs). In this work, Ln3+‐based halide Cs3TbCl6 quantum dots (QDs) are synthesized through a modified hot‐injection method, which displays an excitonic emission centered at 431 nm and the characteristic emission peaks of Tb3+ ions. Then, the Ln3+‐based halide Cs3TbCl6 QDs are introduced to the interface of Cs0.05(FA0.83MA0.17)0.95Pb(I0.83Br0.17)3 perovskite films in the PSCs, which can regulate the energy levels, fill the grain boundaries and remove the ionic defects. Surprisingly, the Cs3TbCl6 QDs modified devices achieve a champion PCE of 22.89% with a super high open‐voltage of 1.235 V. The high open‐voltage can be mainly attributed to the better bandgap alignment, enhanced interface, and reduced defects density. Afterward, the hole transport layer (HTL) is modified by the black phosphorus QDs (BPQDs), yielding a champion PCE of 23.49% and a filling factor of 80.32%. The Cs3TbCl6 QDs modified unencapsulated device possesses well environmental stability and humidity stability. This work demonstrates a new kind of Ln3+‐based metal QDs and explores a new approach to fabricate the PSCs with high open‐voltage, high efficiency, and good stability through the QD‐based passivation techniques.
Nano‐in‐Microparticles for Aerosol Delivery of Antibiotic‐Loaded, Fucose‐Derivatized, and Macrophage‐Targeted Liposomes to Combat Mycobacterial Infections: In Vitro Deposition, Pulmonary Barrier Interactions, and Targeted Delivery
Authors: Huck Benedikt C. , Thiyagarajan Durairaj , Bali Aghiad , Boese Annette , Besecke Karen F. W. , Hozsa Constantin , Gieseler Robert K. , Furch Marcus , Carvalho‐Wodarz Cristiane , Waldow Franziska , Schwudke Dominik , Metelkina Olga , Titz Alexander , Huwer Hanno , Schwarzkopf Konrad , Hoppstädter Jessica , Kiemer Alexandra K. , Koch Marcus , Loretz Brigitta , Lehr Claus‐Michael 
Published: February 2022

AbstractNontuberculous mycobacterial infections rapidly emerge and demand potent medications to cope with resistance. In this context, targeted loco‐regional delivery of aerosol medicines to the lungs is an advantage. However, sufficient antibiotic delivery requires engineered aerosols for optimized deposition. Here, the effect of bedaquiline‐encapsulating fucosylated versus nonfucosylated liposomes on cellular uptake and delivery is investigated. Notably, this comparison includes critical parameters for pulmonary delivery, i.e., aerosol deposition and the noncellular barriers of pulmonary surfactant (PS) and mucus. Targeting increases liposomal uptake into THP‐1 cells as well as peripheral blood monocyte‐ and lung‐tissue derived macrophages. Aerosol deposition in the presence of PS, however, masks the effect of active targeting. PS alters antibiotic release that depends on the drug's hydrophobicity, while mucus reduces the mobility of nontargeted more than fucosylated liposomes. Dry‐powder microparticles of spray‐dried bedaquiline‐loaded liposomes display a high fine particle fraction of >70%, as well as preserved liposomal integrity and targeting function. The antibiotic effect is maintained when deposited as powder aerosol on cultured Mycobacterium abscessus. When treating M. abscessus infected THP‐1 cells, the fucosylated variant enabled enhanced bacterial killing, thus opening up a clear perspective for the improved treatment of nontuberculous mycobacterial infections.
Organoids at the PUB: The Porcine Urinary Bladder Serves as a Pancreatic Niche for Advanced Cancer Modeling
Authors: Melzer Michael Karl , Breunig Markus , Arnold Frank , Wezel Felix , Azoitei Anca , Roger Elodie , Krüger Jana , Merkle Jessica , Schütte Lena , Resheq Yazid , Hänle Mark , Zehe Viktor , Zengerling Friedemann , Azoitei Ninel , Klein Lukas , Penz Frederike , Singh Shiv K. , Seufferlein Thomas , Hohwieler Meike , Bolenz Christian , Günes Cagatay , Gout Johann , Kleger Alexander 
Published: February 2022

AbstractDespite intensive research and progress in personalized medicine, pancreatic ductal adenocarcinoma remains one of the deadliest cancer entities. Pancreatic duct‐like organoids (PDLOs) derived from human pluripotent stem cells (PSCs) or pancreatic cancer patient‐derived organoids (PDOs) provide unique tools to study early and late stage dysplasia and to foster personalized medicine. However, such advanced systems are neither rapidly nor easily accessible and require an in vivo niche to study tumor formation and interaction with the stroma. Here, the establishment of the porcine urinary bladder (PUB) is revealed as an advanced organ culture model for shaping an ex vivo pancreatic niche. This model allows pancreatic progenitor cells to enter the ductal and endocrine lineages, while PDLOs further mature into duct‐like tissue. Accordingly, the PUB offers an ex vivo platform for earliest pancreatic dysplasia and cancer if PDLOs feature KRASG12D mutations. Finally, it is demonstrated that PDOs‐on‐PUB i) resemble primary pancreatic cancer, ii) preserve cancer subtypes, iii) enable the study of niche epithelial crosstalk by spiking in pancreatic stellate and immune cells into the grafts, and finally iv) allow drug testing. In summary, the PUB advances the existing pancreatic cancer models by adding feasibility, complexity, and customization at low cost and high flexibility.
Interpretation of Rubidium‐Based Perovskite Recipes toward Electronic Passivation and Ion‐Diffusion Mitigation
Authors: Xu Chenzhe , Chen Xiwen , Ma Shuangfei , Shi Mingyue , Zhang Suicai , Xiong Zhaozhao , Fan Wenqiang , Si Haonan , Wu Hualin , Zhang Zheng , Liao Qingliang , Yin Wanjian , Kang Zhuo , Zhang Yue 
Published: February 2022

AbstractRubidium cation (Rb+) addition is witnessed to play a pivotal role in boosting the comprehensive performance of organic–inorganic hybrid perovskite solar cells. However, the origin of such success derived from irreplaceable superiorities brought by Rb+ remains ambiguous. Herein, grain‐boundary‐including atomic models are adopted for the accurate theoretical analysis of practical Rb+ distribution in perovskite structures. The spatial distribution, covering both the grain interiors and boundaries, is thoroughly identified by virtue of synchrotron‐based grazing‐incidence X‐ray diffraction. On this basis, the prominent elevation of the halogen vacancy formation energy, improved charge‐carrier dynamics, and the electronic passivation mechanism in the grain interior are expounded. As evidenced by the increased energy barrier and suppressed microcurrent, the critical role of Rb+ addition in blocking the diffusion pathway along grain boundaries, inhibiting halide phase segregation, and eventually enhancing intrinsic stability is elucidated. Hence, the linkage avalanche effect of occupied location dominated by subtle changes in Rb+ concentration on electronic defects, ion migration, and phase stability is completely investigated in detail, shedding a new light on the advancement of high‐efficiency cascade‐incorporating strategies and perovskite compositional engineering.
Quasi Solid–Liquid Reaction Strategy to In Situ Synthesize the Conductive MOF Film with Ordered Submicron Macropores for Gas Sensing
Authors: Miao Meng , Wang Zhipeng , Guo Zhiming , Xing Jinfeng 
Published: February 2022

AbstractA quasi solid–liquid reaction strategy is proposed that is based on the instantaneous transformation of structured solid ligand aggregation into insoluble Cu3(HITP)2 metal–organic framework (MOF) aggregation without morphologic change (HITP = 2,3,6,7,10,11‐hexaiminotriphenylene). The initial 3D ordered submicron macropores (TOM) in ligand aggregation can be maintained during the transformation due to the extremely rapid rate of coordination reaction. In this case, the in situ synthesis of the Cu3(HITP)2 MOF film with large‐scale TOM structure (TOM‐Cu3(HITP)2 film) on ceramic‐based gold interdigital electrode (IDE) is achieved. Scanning electron microscope is used to confirm the morphology in each stage of synthetic process. Spectroscopic characterizations prove that there is no essential difference between TOM‐Cu3(HITP)2 film and ordinary Cu3(HITP)2 MOF, except for slight differences in the contents of individual surface functional group and integral crystallinities, respectively. Notably, TOM structure endows the TOM‐Cu3(HITP)2 film with a dramatic promotion in sensitivity to H2S gas. The resistive response of the IDE loaded with TOM‐Cu3(HITP)2 film to the 80 ppm H2S gas reaches 78.5 at room temperature, which is 6.7× more than that of the Cu3(HITP)2 film without TOM structure. The method of obvious universality allows the authors to perform in situ synthesis directly on the desired substrate without transfer process.
Polymer‐Assisted Phase Stable γ‐CsPbI3 Perovskite Film for Self‐Powered and Ultrafast Photodiodes
Authors: Zhao Cong , Liu Ping , Cai Wanqing , Xu Wenzhan , Ali Muhammad Umair , Xu Zhuhua , Fu H. Y. , Meng Hong , Li Jingzhou , Wei Guodan 
Published: February 2022

AbstractLead‐halide perovskite materials have emerged as promising alternatives for optoelectronic applications due to their low‐cost, easily tunable bandgaps, and facile solution‐processability. Despite all their exciting merits, perovskite materials are currently suffering the stability issues, such as moisture and oxygen‐induced rapid degradation and phase transition. In this work, γ phase CsPbI3 perovskite thin films with compact grain boundaries and improved ambient stability are successfully developed via introducing poly‐2‐ethyl‐2‐oxazoline (PEOXA) polymer through an effective bonding between CO double bond in PEOXA with perovskite. The optimized photodetectors with the γ‐CsPbI3:5%PEOXA active thickness as thin as 30 nm have a totally excellent performance with a responsivity of 0.16 A W−1, high detectivity of 2.73 × 1012 Jones, linear dynamic range of over 125 dB, and ultrafast rise/decay time of 13.9/12.7 µs. Moreover, the as‐constructed photodetectors have shown a high stability when maintained under ambient conditions. This work provides new insights for the development of highly stable and efficient perovskite‐based optoelectronics.
Structure‐Based Varieties of Polymeric Nanocarriers and Influences of Their Physicochemical Properties on Drug Delivery Profiles
Authors: De Ranjit , Mahata Manoj Kumar , Kim Kyong‐Tai 
Published: February 2022

AbstractCarriers are equally important as drugs. They can substantially improve bioavailability of cargos and safeguard healthy cells from toxic effects of certain therapeutics. Recently, polymeric nanocarriers (PNCs) have achieved significant success in delivering drugs not only to cells but also to subcellular organelles. Variety of natural sources, availability of different synthetic routes, versatile molecular architectures, exploitable physicochemical properties, biocompatibility, and biodegradability have presented polymers as one of the most desired materials for nanocarrier design. Recent innovative concepts and advances in PNC‐associated nanotechnology are providing unprecedented opportunities to engineer nanocarriers and their functions. The efficiency of therapeutic loading has got considerably increased. Structural design‐based varieties of PNCs are widely employed for the delivery of small therapeutic molecules to genes, and proteins. PNCs have gained ever‐increasing attention and certainly paves the way to develop advanced nanomedicines. This article presents a comprehensive investigation of structural design‐based varieties of PNCs and the influences of their physicochemical properties on drug delivery profiles with perspectives highlighting the inevitability of incorporating both the multi‐stimuli‐responsive and multi‐drug delivery properties in a single carrier to design intelligent PNCs as new and emerging research directions in this rapidly developing area.
Soil organic carbon stock is improved by cover crops in a tropical sandy soil
Authors: Cordeiro Carlos Felipe dos Santos , Rodrigues Daniel Rodela , Silva Gustavo Ferreira da , Echer Fábio Rafael , Calonego Juliano Carlos 
Published: February 2022

AbstractSoil organic matter plays an important role in soil quality. In sandy soils of tropical regions, high biological activity in the soil accelerates mineralization and limits increases in organic matter content. The objective of this study was to evaluate the total organic C stock and the chemical and physical fractions of organic C in a sandy soil in Presidente Bernardes, São Paulo, Brazil, as a function of cover cropping with different combinations of grasses and legumes between 2015 and 2020. The treatments comprised fallow (control), cultivation of a single grass or intercropping of two grasses, one grass and one legume, or a mixture of two grasses and one legume during the offseason (April–September). Intercropping two grasses increased total dry matter production (shoot and root) by 138% and decreased the C/N ratio by 19% compared with the fallow and legume systems. The organic C stock in the soil was 46% higher in the mixed cover crop system (36.5 Mg ha−1) than in the fallow system (25 Mg ha−1). Humic acid (0.78–0.82 g kg−1) and humin (1.68–1.99 g kg−1) were lower in the systems with low dry matter production (fallow and grass + legume). Mineral‐associated C content was 114% higher in the mixed cover crop system than in the fallow system. These results show that cover crops can increase C content in all fractions of organic matter in tropical sandy soil, even in a short period of time (5 yr), and that a mix of cover crops is the best option.
Exceptional evolutionary lability of flower‐like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae
Authors: Baczyński Jakub , Sauquet Hervé , Spalik Krzysztof 
Published: February 2022

AbstractPremisePseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower‐like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display.MethodsThe framework for our analyses consisted of a time‐calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net diversification rates and the occurrence of pseudocorollas was analyzed with trait‐independent and trait‐dependent approaches.ResultsPseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in diversification rates identified in this subfamily.ConclusionsOur results suggest that pseudocorollas evolve as an answer to the trade‐off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.