bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aligning gene expression time series with time warping

algorithms
Authors: Aach John , Church George M. 
Published: July 2002

Abstract
Motivation: Increasingly, biological processes are being studied through time series of RNA expression data collected for large numbers of genes. Because common processes may unfold at varying rates in different experiments or individuals, methods are needed that will allow corresponding expression states in different time series to be mapped to one another.
Results: We present implementations of time warping algorithms applicable to RNA and protein expression data and demonstrate their application to published yeast RNA expression time series. Programs executing two warping algorithms are described, a simple warping algorithm and an interpolative algorithm, along with programs that generate graphics that visually present alignment information. We show time warping to be superior to simple clustering at mapping corresponding time states. We document the impact of statistical measurement noise and sample size on the quality of time alignments, and present issues related to statistical assessment of alignment quality through alignment scores. We also discuss directions for algorithm improvement including development of multiple time series alignments and possible applications to causality searches and non-temporal processes (‘concentration warping’).
Availability: Academic implementations of alignment programs genewarp and genewarpi and the graphics generation programs grphwarp and grphwarpi are available as Win32 system DOS box executables on our web site along with documentation on their use. The publicly available data on which they were demonstrated may be found at http://genome-www.stanford.edu/cellcycle/. Postscript files generated by grphwarp and grphwarpi may be directly printed or viewed using GhostView software available at http://www.cs.wisc.edu/~ghost/.
Contact: church@arep.med.harvard.edu
Supplementary information: http://arep.med.harvard.edu/timewarp/supplement.htm.
* To whom correspondence should be addressed.
PROMO: detection of known transcription regulatory elements
using species-tailored searches
Authors: Messeguer Xavier , Escudero Ruth , Farré Domènec , Núñez Oscar , Martı́nez Javier , Albà M.Mar 
Published: July 2002

Abstract
Summary: We have developed a set of tools to construct positional weight matrices from known transcription factor binding sites in a species or taxon-specific manner, and to search for matches in DNA sequences.
Availability: PROMO can be accessed online at http://www.lsi.upc.es/~alggen under the research link.
Supplementary information: An example of the graphic interface (Figure 1) can be visualized at http://www.lsi.upc.es/~alggen/recerca/promo/figuraBioinformatics.html.
Contact: peypoch@lsi.upc.es; m.alba@ucl.ac.uk
* To whom correspondence should be addressed.
Randomized, placebo-controlled studies of inhaled zanamivir in the treatment of influenza
A and B: pooled efficacy analysis
Authors: Monto A. S. , Webster A. , Keene O. 
Published: July 2002

Abstract
Zanamivir, a potent, highly selective inhibitor of influenza virus A and B neuraminidase, has been evaluated in seven, similarly designed, placebo-controlled studies of the treatment of influenza. Patients with typical influenza symptoms were recruited when influenza was known to be circulating in the community. Six of these studies included a zanamivir 10 mg inhaled bd (for 5 days) treatment arm, the dose regimen submitted to regulatory agencies. Pooled analyses were conducted to evaluate efficacy more precisely in terms of the alleviation of symptoms in population subgroups and for secondary endpoints. Median time to alleviation of symptoms, the primary endpoint, was reduced from 6.0 days in the placebo group (n = 1102) to 5.0 days in the zanamivir group (n = 1133), P &lt; 0.001. In febrile, laboratory-confirmed, influenza-positive (IP) patients, time to alleviation was reduced from 6.5 days to 5.0 days, a treatment benefit of 1.5 days (P &lt; 0.001). A larger treatment benefit (3 days) was seen in IP patients who had severe symptoms at entry (n = 474, P &lt; 0.001), compared with 1 day in patients whose symptoms were not severe (n = 1098, P &lt; 0.001). Similarly, a 3 day treatment benefit (P = 0.003) was observed in IP patients aged &lt;50 years (n = 263), compared with 1 day (P &lt; 0.001) in patients aged &lt;50 years. In‘ high-risk’ IP patients (recruited into all treatment studies), there was a treatment benefit of 2.5 days (n = 305, P = 0.006). Pooled analyses of secondary endpoints showed statistically significant reductions in antibiotic use, time to return to normal activities and use of relief medication. In addition, reductions in symptom scores were apparent shortly after commencing zanamivir treatment. By the evening of the second day of treatment, the median total symptom score had fallen by 44% in zanamivir recipients compared with 33% in placebo recipients (P &lt; 0.001). These results highlight the groups likely to show greatest benefit from zanamivir treatment, and confirm the clinical relevance of the treatment benefit.
Formation of Diatexite Migmatite and Granite Magma during Anatexis of Semi-pelitic Metasedimentary Rocks: an Example from St. Malo, France
Authors: MILORD I. , SAWYER E. W. , BROWN M. 
Published: July 2002

Abstract
Petrological and geochemical variations are used to investigate the formation of granite magma from diatexite migmatites derived from metasedimentary rocks of pelitic to greywacke composition at St. Malo, France. Anatexis occurred at relatively low temperatures and pressures (&lt;800°C, 4–7 kbar), principally through muscovite dehydration melting. Biotite remained stable and serves as a tracer for the solid fraction during melt segregation. The degree of partial melting, calculated from modal mineralogy and reaction stoichiometry, was &lt;40 vol. %. There is a continuous variation in texture, mineralogy and chemical composition in the diatexite migmatites. Mesocratic diatexite formed when metasedimentary rocks melted sufficiently to undergo bulk flow or magma flow, but did not experience significant melt–residuum separation. Mesocratic diatexite that underwent melt segregation during flow generated (1) melanocratic diatexites at the places where the melt fraction was removed, leaving behind a biotite and plagioclase residuum (enriched in TiO2, FeOT, MgO, CaO, Sc, Ni, Cr, V, Zr, Hf, Th, U and REE), and (2) a complementary leucocratic diatexite (enriched in SiO2, K2O and Rb) where the melt fraction accumulated. Leucocratic diatexite still contained 5–15 vol. % residual biotite (mg-number 40–44) and 10–20 vol. % residual plagioclase (An22). Anatectic granite magma developed from the leucodiatexite, first by further melt–residuum separation, then through fractional crystallization. Most biotite in the anatectic granite is magmatic (mg-number 18–22).
Natively unfolded proteins: A point where biology waits for physics
Authors: Uversky Vladimir N. 
Published: July 2002

AbstractThe experimental material accumulated in the literature on the conformational behavior of intrinsically unstructured (natively unfolded) proteins was analyzed. Results of this analysis showed that these proteins do not possess uniform structural properties, as expected for members of a single thermodynamic entity. Rather, these proteins may be divided into two structurally different groups: intrinsic coils, and premolten globules. Proteins from the first group have hydrodynamic dimensions typical of random coils in poor solvent and do not possess any (or almost any) ordered secondary structure. Proteins from the second group are essentially more compact, exhibiting some amount of residual secondary structure, although they are still less dense than native or molten globule proteins. An important feature of the intrinsically unstructured proteins is that they undergo disorder–order transition during or prior to their biological function. In this respect, the Protein Quartet model, with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed.
Metal–Organic Frameworks Nanoarchitectures Boost Catalytic Activity for the Construction of Sensitive Immunosensor
Authors: Su Dandan , Wang Tuhui , Li Aixin , Ma Yuan , Liu Xiaomin , Wang Chenguang , Jia Xiaoteng , Sun Peng , Liu Fangmeng , Yan Xu , Lu Geyu 
Published: July 2022

AbstractBenefiting from the distinct structural features, metal‐organic frameworks (MOFs) open new significant opportunities for biomacromolecule encapsulation to design biofunctional composites, whereas their biological activity and utilization efficiency remain challenging for the construction of advanced immunosensor. Herein, biomacromolecules are spatially encapsulated integration on the cavity of peptide‐mediated MOFs with controllable nanoarchitectures, which amplifies the immunosensor signals via boosting bioactivity and utilization efficiency. Notably, the morphological evolution of MOFs composite including dodecahedrons, nanostars and flower‐shaped nanostructures is achieved by introducing peptide surface modifier to trigger the coordination defects procedure. Nanostars are evidenced with the enhanced catalytic activity of biomacromolecules, which amplifies the recognition signal via regulating the pore channel and particle size of biomacromolecules@MOFs composite, shortening the diffusion path of substrate molecules and promoting the interfacial contact. As proof‐of‐principle, imidacloprid is chosen as a model target to demonstrate the superiority of biomacromolecules@MOFs‐based immunosensor. Combining the enhanced activity of biomacromolecules with size tunability of biomacromolecules@MOFs composite, 160‐fold improvement in the sensitivity is obtained in comparison with the conventional enzyme‐based immunoassay, paving the way for the employment of controllable nanostructures for high‐sensitive biosensors.
Neuron Inspired All‐Around Universal Telechelic Polyurea with High Stiffness, Excellent Crack Tolerance, Record‐High Adhesion, Outstanding Triboelectricity, and AIE Fluorescence
Authors: Chen Haiming , Sun Zaizheng , Lin Haohao , He Chaobin , Mao Dongsheng 
Published: July 2022

AbstractDeveloping high‐performance polymeric elastomer with exceptional mechanical and physical properties such as mechanical toughness, stiffness and rapid healable properties is crucial for wide application, but it remains challenging. Herein, a series of telechelic elastomers inspired by the neurons are developed. The hierarchical hydrogen‐bonds (H‐bonds) networks constructed by 2‐ureido‐4 pyrimidinone and urea groups, as well as their reversible dynamics, contribute to enormous energy dissipation, exceptional mechanical robustness, rapid self‐healing ability (92%, 0.5 h). The excellent crack tolerance of 187 kJ m−2 of the elastomer is comparable to that of the metals and alloys. The stiffness of 97.9 MPa has far exceeded that of the usual high‐performance thermoplastic elastomers. The adhesion strength bonded with iron plates of 20.7 MPa, to the best knowledge, will be the record‐high value for hot‐melt adhesives. Intriguingly, the telechelic elastomer can be positively charged after friction with copper, exhibiting a much higher open circuit voltage than that of the most commonly used positively charged polyamide. More interestingly, the intrinsic blue fluorescence is also observed, which is ascribed to the aggregation induced emission of a tertiary amine. Thus a thermoplastic elastomer is represented in this work with remarkable mechanical properties, rapid self‐healing ability and tailorable important functions.
Optofluidic Platform for the Manipulation of Water Droplets on Engineered LiNbO3 Surfaces
Authors: Zaltron Annamaria , Ferraro Davide , Meggiolaro Alessio , Cremaschini Sebastian , Carneri Mattia , Chiarello Enrico , Sartori Paolo , Pierno Matteo , Sada Cinzia , Mistura Giampaolo 
Published: July 2022

AbstractThe actuation and control of liquid droplets on a surface have important implications in many industrial applications and microfluidics. In recent years, various strategies have been used. Here, an optofluidic platform that performs the basic droplet handling operations required in a common microfluidic device is presented. It is based on z‐cut, iron‐doped lithium niobate crystals that, when illuminated, generate surface charges of opposite sign at the two crystal faces because of the photovoltaic effect. The face of the crystal in contact with the droplets is coated with a lubricant‐infused layer, which guarantees hydrophobicity and, more importantly, a very slippery and robust surface for prolonged use. In this way, sessile water droplets having volumes of microliters, corresponding to millimeters in size, can be easily actuated, guided, merged, and split by projection on the crystal of suitable static or dynamic light patterns. The actuated droplets can cover distances of centimeters on a timescale of a few seconds. The resulting platform is highly flexible and reconfigurable and does not require moving parts.
Logic Circuits Based on Chemical Volume Phase Transition Transistors for Planar Microfluidics and Lab‐on‐a‐Chip Automation
Authors: Beck Anthony , Mehner Philipp Jan , Voigt Andreas , Obst Franziska , Marschner Uwe , Richter Andreas 
Published: July 2022

AbstractDespite great progress of lab‐on‐a‐chip (LoC) technology platforms in the last 30 years, there is a lack of standardized microfluidic components, real on‐chip automation and progressive functional scalability of the fluidic circuits. Hydrogel‐based microfluidic circuits have a high scaling potential and provide on‐chip automation, but are complex in system design. An advanced circuit concept for planar microfluidic chip architectures, originating from the early era of the semiconductor‐based resistor‐transistor‐logic (RTL) is presented and the hydrogel‐based chemical volume phase transition transistor (CVPT) for logic gate operations is implemented. The circuit concept (CVPT‐RTL) is robust and simple in design, feasible with common materials and manufacturing techniques of the LoC technology. Thereby, three major challenges are solved: contamination issues, maintaining the signal compliance for cascadability, and chemical signal inversion. As a central element, a CVPT cascode is introduced. The functionality of the concept is verified by a 24 h test of the NAND gate operation and a self‐automated chemofluidic analog‐to‐digital converter, utilized as interface between bioreactors and extended microfluidic logic circuits. Moreover, the CVPT‐RTL cascode demonstrates the expected self‐stabilizing performance of the NAND gate. Accompanying simulations of the component behavior based on a network description implemented in Matlab Simscape match with the experimental results.
Delivery of Dissociated Islets Cells within Microporous Annealed Particle Scaffold to Treat Type 1 Diabetes
Authors: Roosa Colleen A. , Ma Mingyang , Chhabra Preeti , Brayman Kenneth , Griffin Donald 
Published: July 2022

AbstractType 1 diabetes (T1D) is caused by the autoimmune loss of insulin‐producing beta cells in the pancreas. The only clinical approach to patient management of blood glucose that doesn't require exogenous insulin is pancreas or islet transplantation. Unfortunately, donor islets are scarce and there is substantial islet loss immediately after transplantation due, in part, to the local inflammatory response. The delivery of stem cell‐derived beta cells (e.g., from induced pluripotent stem cells) and dissociated islet cells hold promise as a treatment for T1D; however, these cells typically require re‐aggregation in vitro prior to implantation. Microporous scaffolds have shown high potential to serve as a vehicle for organization, survival, and function of insulin‐producing cells. In this study, the use of microporous annealed particle (MAP) scaffold for delivery of enzymatically dissociated islet cells, a model beta cell source, within the scaffold's interconnected pores is investigated. It is found that MAP‐based cell delivery enables survival and function of dissociated islets cells both in vitro and in an in vivo mouse model of T1D.
Computational Pourbaix Diagrams for MXenes: A Key Ingredient toward Proper Theoretical Electrocatalytic Studies
Authors: López Martí , Exner Kai S. , Viñes Francesc , Illas Francesc 
Published: July 2022

AbstractMXenes, a rather new family of 2D carbides and nitrides, have shown to be promising materials in many technological applications, particularly in electrocatalysis. The as‐synthesized MXenes exhibit a variety of surface terminations involving mixtures of O, OH, H, or F surface groups. These terminations play a crucial role in the electrocatalytic performance of these materials as these may change depending on the reaction conditions. The Pourbaix diagrams have long being used to provide the thermodynamically stable surface under certain conditions of pH and potential, U. However, experimental determination of Pourbaix diagrams may be quite challenging while first‐principles studies, considering the most likely terminations, allow deriving reliable insights. Here, Pourbaix diagrams for a series of representative MXenes are provided; the Ti2C, Ti3C2, V2C, and Mo2C MXenes, with the novelty of considering single and several double mixed terminations. The possible implications of the obtained results are discussed, especially for a proper choice of models in theoretical electrocatalysis studies, including the water splitting related hydrogen evolution reaction (HER), or the oxygen reduction reaction (ORR), but also serving as a guide to any further computational studies and also to electrocatalytic experiments.
Laser‐assisted preparation of monolithic acidic catalysts for biomass conversion
Authors: Cao Jinzhe , Zhang Jiangwei , Tao Shengyang 
Published: July 2022

Abstract5‐(Hydroxymethyl)furfural (5‐HMF) is a vital platform molecule from which a variety of high‐value‐added fine chemicals and polymerizable monomers can be prepared. The use of solid acids to catalyze the conversion of biomass into 5‐HMF is environmentally friendly and economical. However, exploiting the high yield of 5‐HMF in a highly concentrated reactant system is challenging. Herein, we present a laser‐assisted method for preparing highly acidic monolithic acidic catalysts. A monolithic acidic catalyst based on metal Zr sheets was synthesized and used to catalytically convert 30 wt% fructose into 5‐HMF (conversion rate: 96%; yield: 95%). The catalyst was immediately separated from the reaction solution by direct removal at the end of the reaction. Catalytic efficiency was largely unaffected after 10 cycles of use, and the same catalytic efficiency was observed after laser‐regeneration, highlighting the potential industrial applicability of the developed catalyst.
Body height, weight, and Body Mass Index – magnitude and pace of secular changes in children and adolescents from Kraków (Poland) between 1983 and 2020
Authors: Kryst Łukasz , Żegleń Magdalena , Woronkowicz Agnieszka , Kowal Małgorzata 
Published: July 2022

AbstractObjectiveThe aim of this study was to analyze the occurrence and pace of secular trends regarding body height, weight, and Body Mass Index (BMI) among children and adolescents from Kraków (Poland) examined in 1983, 2000, 2010, and 2020.MethodsThe study group consisted of 17 407 individuals (8650 girls and 8757 boys) aged 3–18 included in four cross‐sectional studies conducted in 1983, 2000, 2010, and 2020.Analyzed anthropometric characteristics included body height (measured according to Martin's technique, with an anthropometer) and body weight. BMI was calculated as follows: body weight (kg)/body height2 (m).ResultsResults of the current study suggest that there was a cessation of previously observed secular increase of the body height in the examined population in the recent decade. Additionally, secular changes regarding body height, body mass, and BMI occurred noticeably slower in the recent decade compared to the previous years.ConclusionsIn conclusion, the rapid increase of body height in the years 1983–2000 and later secular increase of the body mass and BMI in 2000–2010 were probably associated mainly with significant socio‐economic progress of the country. On the other hand, deceleration of those trends in 2010–2020, especially in regards to body height, may be associated with reaching the maximum genetically attainable body height in the examined population.
The actions and interactions of family genetic risk scores for alcohol use disorder and major depression on the risk for these two disorders
Authors: Kendler Kenneth S. , Lönn Sara L. , Sundquist Jan , Sundquist Kristina 
Published: July 2022

AbstractWe know little about how genetic risk factors for two disorders jointly act and interact in predisposing to illness. Therefore, in the Swedish population, born 1970–1990 (n = 2,116,082) and followed through 2015, we examine, using additive Cox models, the impact of the family genetic risk scores (FGRS) for alcohol use disorder (AUD) and major depression (MD), their interaction with each other and with the relevant comorbid disorder on risk for AUD and MD. FGRS scores are constructed using rates of illness in first‐fourth degree relatives. FGRS for AUD and MD interacted in predicting of both disorders and one FRGS (e.g., for AUD) interacted with the phenotype of MD to predict that disorder (e.g., AUD). These FGRS interactions were not substantially attenuated by adding interactions with the disorders. These results replicated across sexes. In predicting risk for a given disorder, we rarely consider genetic liabilities for other disorders. But such effects were here significant and interactive. Furthermore, the primary disorder genetic risk interacts with comorbid disorders. The pathways to risk for disorders from their and other disorders' genetic liability may be more complex than commonly considered.
Medical genetics in the 19th century as background to the development of psychiatric genetics
Authors: Kendler Kenneth S. 
Published: July 2022

AbstractThis article examines the relationship between the early efforts of alienists to understand the role of heredity in the etiology of insanity in the 19th century and the parallel efforts of the nascent discipline of medical genetics. I review three monographs on general medical genetics: Adams in 1814, Steinau in 1843, and Lithgow in 1889. Numerous parallels were seen between their writings and those of their contemporary alienists working on mental disorders including (i) an emphasis on the transmission of the liability to illness rather than the illness itself, (ii) discussions of the homogeneous versus heterogeneous nature of familial transmission of disease, (iii) the relative value of direct versus indirect hereditary effects, (iv) the role of mothers versus fathers in transmitting liability, (v) possible environmental sources of familial clustering, and (vi) the transmission of age at onset of illness. All three medical genetic authors noted that insanity was among the more heritable of human disorders. Furthermore, Lithgow noted the importance of heritable influences on the non‐psychotic forms of psychiatric illness rarely seen in asylums. This survey demonstrates substantial consilience in the topics of interest and conclusions of the nascent general medical and psychiatric genetics' communities in the 19th century.