bluuebunny/crossref_metadata_2025_split huggingface dataset:
Models@Home: distributed computing in bioinformatics using a
screensaver based approach
Authors: Krieger Elmar , Vriend Gert 
Published: July 2002

Abstract
Motivation: Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world’s largest distributed computing project.
Results: We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster. We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.
Availability: Models@Home is freely available including source code and detailed instructions from http://www.cmbi.nl/models.
Contact: elmar.krieger@cmbi.kun.nl
* To whom correspondence should be addressed.
Adaptive quality-based clustering of gene expression profiles
Authors: De Smet Frank , Mathys Janick , Marchal Kathleen , Thijs Gert , De Moor Bart , Moreau Yves 
Published: July 2002

Abstract
Motivation: Microarray experiments generate a considerable amount of data, which analyzed properly help us gain a huge amount of biologically relevant information about the global cellular behaviour. Clustering (grouping genes with similar expression profiles) is one of the first steps in data analysis of high-throughput expression measurements. A number of clustering algorithms have proved useful to make sense of such data. These classical algorithms, though useful, suffer from several drawbacks (e.g. they require the predefinition of arbitrary parameters like the number of clusters; they force every gene into a cluster despite a low correlation with other cluster members). In the following we describe a novel adaptive quality-based clustering algorithm that tackles some of these drawbacks.
Results: We propose a heuristic iterative two-step algorithm: First, we find in the high-dimensional representation of the data a sphere where the ‘density’ of expression profiles is locally maximal (based on a preliminary estimate of the radius of the cluster—quality-based approach). In a second step, we derive an optimal radius of the cluster (adaptive approach) so that only the significantly coexpressed genes are included in the cluster. This estimation is achieved by fitting a model to the data using an EM-algorithm. By inferring the radius from the data itself, the biologist is freed from finding an optimal value for this radius by trial-and-error. The computational complexity of this method is approximately linear in the number of gene expression profiles in the data set. Finally, our method is successfully validated using existing data sets.
Availability: http://www.esat.kuleuven.ac.be/~thijs/Work/Clustering.html
Contact: frank.desmet@esat.kuleuven.ac.be
* To whom correspondence should be addressed.
Trees tell of past climates: but are they speaking less clearly today?
Authors: Briffa K. R. , Schweingruber F. H , Jones P. D. , Osborn T. J. , Harris I. C. , Shiyatov S. G. , Vaganov E. A. , Grudd H. 
Published: July 2002

The annual growth of trees, as represented by a variety of ring–width, densitometric, or chemical parameters, represents a combined record of different environmental forcings, one of which is climate. Along with climate, relatively large–scale positive growth influences such as hypothesized ‘fertilizationrsquo; due to increased levels of atmospheric carbon dioxide or various nitrogenous compounds, or possibly deleterious effects of ‘acid rain’ or increased ultra–violet radiation, might all be expected to exert some influence on recent tree growth rates. Inferring the details of past climate variability from tree–ring data remains a largely empirical exercise, but one that goes hand–in–hand with the development of techniques that seek to identify and isolate the confounding influence of local and larger–scale non–climatic factors.By judicious sampling, and the use of rigorous statistical procedures, dendroclimatology has provided unique insight into the nature of past climate variability, but most significantly at interannual, decadal, and centennial timescales. Here, examples are shown that illustrate the reconstruction of annually resolved patterns of past summer temperature around the Northern Hemisphere, as well as some more localized reconstructions, but ones which span 1000 years or more. These data provide the means of exploring the possible role of different climate forcings; for example, they provide evidence of the large–scale effects of explosive volcanic eruptions on regional and hemispheric temperatures during the last 400 years.However, a dramatic change in the sensitivity of hemispheric tree–growth to temperature forcing has become apparent during recent decades, and there is additional evidence of major tree–growth (and hence, probably, ecosystem biomass) increases in the northern boreal forests, most clearly over the last century. These possibly anthropogenically related changes in the ecology of tree growth have important implications for modelling future atmospheric CO2concentrations. Also, where dendroclimatology is concerned to reconstruct longer (increasingly above centennial) temperature histories, such alterations of ‘normal’ (pre–industrial) tree–growth rates and climate–growth relationships must be accounted for in our attempts to translate the evidence of past tree growth changes.
Association of Inherited Genetic Factors With Drug-Induced Hepatic Damage Among Children With Acute Lymphoblastic Leukemia
Authors: Yang Wenjian , Karol Seth E. , Hoshitsuki Keito , Lee Shawn , Larsen Eric C. , Winick Naomi , Carroll William L. , Loh Mignon L. , Raetz Elizabeth A. , Hunger Stephen P. , Winter Stuart S. , Dunsmore Kimberly P. , Devidas Meenakshi , Relling Mary V. , Yang Jun J. 
Published: December 2022

ImportanceAcute lymphoblastic leukemia (ALL) is the most common childhood cancer. Hepatotoxic effects, including hyperbilirubinemia and elevated alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, are common during all phases of therapy and are linked to several chemotherapeutic agents, including asparaginase, mercaptopurine, and methotrexate.ObjectiveTo determine which genetic variants were associated with hyperbilirubinemia and elevated ALT and AST levels in children, adolescents, and young adults treated for ALL.Design, Setting, and ParticipantsThis retrospective analysis of a multiethnic genome-wide association study was conducted between January 1, 2019, and April 15, 2022, including patients treated as part of Children’s Oncology Group (COG) trials with centers in the United States, Canada, and Australia, which accrued data from December 29, 2003, to January 21, 2011 (AALL0232), and from January 22, 2007, to July 24, 2014 (AALL0434). Germline genotypes were interrogated using genome-wide arrays and imputed using a National Institutes of Health TOPMed Imputation server. Mixed-effects logistic regressions were used to account for multiple episodes for an individual patient. Genotype × treatment phase interaction was tested to uncover phase-specific genetic risk factors.ExposuresTotal duration of multiagent protocol chemotherapy ranging from 2.5 to 3.5 years.Main Outcomes and MeasuresThe primary outcomes were National Cancer Institute Common Terminology Criteria for Adverse Events (version 4) hyperbilirubinemia of grade 3 or higher and elevated liver ALT and AST levels.ResultsA total of 3557 participants were included in the analysis (2179 [61.3%] male; median age, 11.1 [range, 1-30] years). Among 576 known variants associated with these liver function test results in the general population, UGT1A1 variant rs887829 and PNPLA3 variant rs738409 were associated with increased risk of hyperbilirubinemia (odds ratio [OR], 2.18 [95% CI, 1.89-2.53]; P = 6.7 × 10−27) and ALT and AST levels (OR, 1.27 [95% CI, 1.15-1.40]; P = 3.7 × 10−7), respectively, during treatment for ALL. Corresponding polygenic risk scores were associated with hepatotoxic effects across all therapy phases and were largely driven by UGT1A1 and PNPLA3 variants. Genome-wide association analysis revealed an age-specific variant near the CPT1A gene that was only associated with elevated ALT and AST levels among patients younger than 10 years (OR, 1.28 [95% CI, 1.18-1.39]; P = 8.7 × 10−10).Conclusions and RelevanceThese results suggest a strong genetic basis for interpatient variability in hyperbilirubinemia and aminotransferase level elevations during leukemia chemotherapy.
Gardeners' farmland in Komagome as seen in the “Ansei period Komagome Fuji shrine area map and illustration”
Authors: Watanabe Miki 
Published: December 2022

AbstractIn this study, we focused on contents described in the ‘Ansei period Komagome Fuji Shrine area map and illustration’. We verified the contents of the ‘Ansei period map’ and considered the aspects of gardeners' farmland in this area. Consequently, the following findings were obtained.(1) Most of the farmers in this area also work as gardeners.(2) A large number of farmers surnamed “Takagi,” “Utsumi,” and “Shimizu” already owned the lands in several distant places.(3) From the address on the 1912 cadastral map, many locations matched the houses on the Ansei period map.
Compute in‐Memory with Non‐Volatile Elements for Neural Networks: A Review from a Co‐Design Perspective
Authors: Haensch Wilfried , Raghunathan Anand , Roy Kaushik , Chakrabarti Bhaswar , Phatak Charudatta M. , Wang Cheng , Guha Supratik 
Published: December 2022

AbstractDeep learning has become ubiquitous, touching daily lives across the globe. Today, traditional computer architectures are stressed to their limits in efficiently executing the growing complexity of data and models. Compute‐in‐memory (CIM) can potentially play an important role in developing efficient hardware solutions that reduce data movement from compute‐unit to memory, known as the von Neumann bottleneck. At its heart is a cross‐bar architecture with nodal non‐volatile‐memory elements that performs an analog multiply‐and‐accumulate operation, enabling the matrix‐vector‐multiplications repeatedly used in all neural network workloads. The memory materials can significantly influence final system‐level characteristics and chip performance, including speed, power, and classification accuracy. With an over‐arching co‐design viewpoint, this review assesses the use of cross‐bar based CIM for neural networks, connecting the material properties and the associated design constraints and demands to application, architecture, and performance. Both digital and analog memory are considered, assessing the status for training and inference, and providing metrics for the collective set of properties non‐volatile memory materials will need to demonstrate for a successful CIM technology.
In‐Silico Device Performance Prediction of Cosensitizer Dye Pairs for Dye‐Sensitized Solar Cells
Authors: Devereux Leon R. , Vázquez‐Mayagoitia Álvaro , Sternberg Michael G. , Cole Jacqueline M. 
Published: December 2022

AbstractEndeavors in the field of dye‐sensitized solar cells (DSCs) have shown great promise when adopting a data‐driven approach to materials discovery, such as successful molecular‐scale predictions of light‐harvesting chromophores. However, predictions of DSC dyes would become much more sophisticated if a molecular‐to‐macroscopic DSC device prediction methodology existed. Thereby, a fully computational pipeline is presented that predicts device‐performance parameters of DSCs which contain varying dye combinations. Optimal pairing of complementary dyes is identified via a data‐driven workflow that affords cosensitized DSCs with maximum power‐conversion efficiencies. Six high‐performing DSC dyes are paired with partner dyes that are screened from a database of 8488 compounds using sequential heuristic filters. Existing models that predict short‐circuit‐current density (JSC) and open‐circuit voltage (VOC) parameters are adapted to predict singly sensitized and cosensitized DSC performance. The predictions for Jsc values of singly sensitized devices match experimental literature values with comparable accuracy to more computationally costly methods. Five out of six dye pairings are predicted to have greater JSC values when cosensitized compared to their corresponding singly sensitized devices, including two pairs that show strong Jsc boosts of +13% and +12% when cosensitized. Thus, the prospect of an entirely in‐silico prediction pipeline for DSC performance that can be used to realize the fully automated design of optimized cosensitized DSCs is demonstrated.
Trends in obesity and severe obesity prevalence in the United States from 1999 to 2018
Authors: Fan Kexin , Lv Feifei , Li Huawei , Meng Fei , Wang Tao , Zhou Yunping 
Published: December 2022

AbstractBackgroundThe national obesity epidemic and trend of obesity prevalence have been characterized by a series of cross‐sectional surveys in the United States, however, less is known about obesity prevalence trajectory by birth cohort. This study aimed to investigate whether trends in obesity and severe obesity prevalence varied by birth cohorts among 1940s–1990s in the United States.MethodsUsing data from the National Health and Nutrition Examination Survey 1999–2018. The trends of obesity and severe obesity prevalence were conducted with synthetic birth cohort.ResultsThere were 60 981 participants (weighted mean age, 38.1 years; female, 50.1%) assigned in 6 birth cohorts (1990s, 1980s, 1970s, 1960s, 1950s, and 1940s) over 1999–2018. The prevalence of obesity and severe obesity increased significantly with age during all birth cohorts except for the 1940s (Ptrend <0.001). For obesity, a significant positive quadratic trend was observed among 1990s birth cohort (Pnon‐linearity = 0.037), while a significant positive linear trend (Plinearity <0.001) among 1980s, 1970s, 1960s, and 1950s birth cohorts. Corresponding to same weighted mean age, the prevalence of both obesity and severe obesity in younger birth cohorts were much higher than the older birth generations.ConclusionsThe continued upward trend in obesity and severe obesity prevalence by birth cohort highlighted the need for continuing focus on surveillance of body mass index and identification, implementation, and evaluation of evidence‐based interventions to address this major health problem in the United States.
Regional variation in growth status: A cross‐sectional survey among Tibetan adolescents living at three different high altitudes in Tibet, China
Authors: Bi Cunjian , Lin Hongniu , Zhang Jie , Gui Xiaoying , Shi Zhen 
Published: December 2022

AbstractObjectiveTo explore the regional and age variation in growth status and age‐by‐site interaction effect on the growth status among Chinese Tibetan adolescents at different altitudes in Tibet, China.MethodsThe research was conducted in three regions of Tibet, China: Nyingchi (average altitude 3100 m), Lhasa (average altitude 3650 m), and Nagqu (average altitude 4500 m). A total of 3817 Chinese Tibetan adolescents aged 12–18 years were tested for height, weight, chest circumference, and waist circumference. One‐way ANOVA was used to compare the growth status of Chinese Tibetan adolescents. Two‐way ANOVA was used to explore the age‐by‐site interaction effect on the growth status of Chinese Tibetan adolescents.ResultsThe height, weight, and chest circumference of Chinese Tibetan adolescents in Nagqu are the lowest among the three cities. Age and site have an interaction effect influence on the growth status of Chinese Tibetan adolescents (p < .01).ConclusionsThe growth indicators (height, weight, chest circumference, WC) of Chinese Tibetan adolescents differed with altitudes. Policies to improve the growth status of Chinese Tibetan adolescents in Nagqu are urgently needed.
A Triply Negatively Charged Nanographene Bilayer with Spin Frustration
Authors: Wang Wenqing , Ma Xiao‐Hui , Liu Min , Tang Shuxuan , Ding Xuguang , Zhao Yue , Tan Yuan‐Zhi , Kertesz Miklos , Wang Xinping 
Published: December 2022

AbstractWe report on the largest open‐shell graphenic bilayer and also the first example of triply negatively charged radical π‐dimer. Upon three‐electron reduction, bilayer nanographene fragment molecule (C96H24Ar6)2(Ar=2,6‐dimethylphenyl) (12) was transformed to a triply negatively charged species123.−, which has been characterized by single‐crystal X‐ray diffraction, electron paramagnetic resonance (EPR) spectroscopy and magnetic properties on a superconducting quantum interference device (SQUID).123.−features a 96‐center‐3‐electron (96c/3e) pancake bond with a doublet ground state, which can be thermally excited to a quartet state. It consists of 34 π‐fused rings with 96 conjugatedsp2carbon atoms. Spin frustration is observed with the frustration parameterf>31.8 at low temperatures in123.−, which indicates graphene upon reduction doping may behave as a quantum spin liquid.
Centro‐symmetric copper complex as a novel antitumor drug for therapeutic applications: Fabrication, structure, theoretical calculations, cytotoxicity, DNA binding/cleavage, and molecular docking
Authors: Zekrallah Marwa , Mashaly Mahmoud M. , Saif Mona , Fouad Rania 
Published: December 2022

This study presents the fabrication and structural analysis of the newly synthesized Cu(AHC)2 complex to explore its biological functionalities such as cytotoxicity, DNA binding, and DNA cleavage. For the Cu(AHC)2 complex synthesis, the bioactive 3‐acetyl‐4‐hydroxy coumarin (AHC) has been used as a ligand. The complex has been investigated using analytical and spectroscopic techniques. The resultant data have demonstrated that the AHC is coordinated to the metal ion in a monoanionic form with bidentate through O, O donor atoms forming a square planner coordinated compound. X‐ray diffraction and transmittance electron microscope analysis have shown that Cu(AHC)2 complex has hybrid morphology of irregular nano‐sphere (5 nm) and irregular sheets arranged in the format of a cluster with crystallinity form. The Cu(AHC)2 complex has been screened for in vitro cytotoxicity against HepG‐2 cell line. If it compared with different standard drugs, copper complex, it can be said, has excellent cytotoxicity (IC50 = 6.8 μg ml−1). Furthermore, the binding properties of Cu(AHC)2 complex with herring sperm DNA has been detected via UV–Vis spectroscopy and viscosity measurements. The electronic absorption spectroscopic data have revealed that the prepared Cu(AHC)2 complex strongly binds to herring sperm DNA through intercalative mode with Kb of 0.19 × 106 M−1. Confirming previously obtained spectroscopy data, the interaction of Cu(AHC)2 complex with DNA has also been explored via molecular docking analysis. DNA cleavage study has been, moreover, carried out by agarose gel electrophoresis. The data have shown that the complex has a good ability to destroy DNA. In supporting experimental data, theoretical calculations and optimized Cu(AHC)2 complex structure have been obtained from density functional theory calculations. The calculated results are consistent with the experimental findings. In conclusion, the data discussed above may offer helpful information that helps in the design of a novel copper complex that can function as a potent pharmaceutical agent.
The Use of Redox Mediators in Electrocatalysis and Electrosynthesis
Authors: Shao Weide , Lu Biao , Cao Jinpeng , Zhang Jianing , Cao Hairu , Zhang Feifei , Zhang Chunling 
Published: December 2022

AbstractElectrocatalysis and electrosynthesis, which convert the electrical energy and store them in the chemical forms, have been considered as promising technologies to utilize green renewable energy sources. Most of the studies focused on developing novel active molecules or advanced electrodes to improve the performance. However, the direct acquisition and electron transferring will be limited by the intrinsic characters of the electrodes. The introduce of redox mediators, which are served as the intermediate electron carriers or reservoirs without changing the final products, provide a unique approach to accelerate the electrochemical performance of these energy conversions. This review provides an overview of the recent development of electrocatalysis and electrosynthesis by using redox mediators, and provides a comprehensive discussion toward focusing on the principles and construction of these systems.
1D Chiral Lead Bromide Perovskite with Superior Second‐Order Optical Nonlinearity, Photoluminescence, and High‐Temperature Reversible Phase Transition
Authors: Peng Xin‐Lin , Han Rui‐Rui , Tang Yun‐Zhi , Tan Yu‐Hui , Fan Xiao‐Wei , Wang Fang‐Xin , Zhang Hao 
Published: December 2022

AbstractMultifunctional materials are an attractive research area. Organic‐inorganic hybrid perovskites are widely used in the design of these materials due to their rich properties and flexible composition. It is easy to obtain more photoelectric properties by introducing chiral groups as ligands. In this work, we synthesized chiral one‐dimensional organic‐inorganic hybrid perovskites, namely (R/S‐3‐HP)PbBr3 (1R/1S) (3‐HP=3‐hydroxy‐piperidine). The enantiomer compounds undergo reversible phase transition at 349/336 K. Under the excitation light of 339 nm, 1R and 1S have a wide emission peak at 635 nm, showing orange light. In addition, the indirect bandgap is 3.29 eV and the SHG intensity is comparable to that of KDP. This work provides a way to design multifunctional chiral perovskite materials.
Production cell analysis and compound‐based boosting of small extracellular vesicle secretion using a generic and scalable production platform
Authors: Keysberg Christoph , Schneider Helga , Otte Kerstin 
Published: December 2022

AbstractExtracellular vesicles (EVs) are a novel format of advanced therapeutical medicinal products (ATMPs). They can act regenerative or immune‐modulatory as cell therapy substitutes or as a platform for designer exosomes. The biotechnological production of therapeutic EVs is still very much uncharted territory so standardized host cells, production setups, and isolation methods are not yet implemented. In this work, we present a tangential flow filtration (TFF) and fast‐performance liquid chromatography (FPLC)‐based size exclusion chromatography (SEC) purification setup that is compatible for industry applications. Moreover, we evaluated a series of potential host cell lines regarding their EV productivity, characteristics, and biological functionality. It was found that telomerase‐immortalized Wharton's jelly mesenchymal stromal cells (WJ‐MSC/TERT273) secrete high amounts of EVs per cell with regenerative capabilities. On the other hand, Cevec's amniocyte producer cells® (CAP®) and human embryonic kidney (HEK293) suspension cells are suitable platforms for designer EVs with high yields. Finally, we aimed to boost the EV secretion of HEK293 cells via chemical adjuvants and verified four compounds that heighten cellular EV secretion in a presumably cAMP‐dependent manner. A combination of fenoterol, iodoacetamide, and dinitrophenol increased the EV yield in HEK293 cells threefold and cellular secretion rate fivefold.