bluuebunny/crossref_metadata_2025_split huggingface dataset:
The health effects of ecstasy: a literature review
Authors: GOWING LINDA R. , HENRY‐EDWARDS SUSAN M. , IRVINE RODNEY J. , ALI ROBERT L. 
Published: July 2002

AbstractEcstasy (3,4‐methylenedioxymethamphetamine, MDMA) is the third most used illicit drug, after cannabis and amphetamines. There has been considerable interest in the adverse effects of use, with particular attention given to a small number of deaths related to ecstasy use, and the neurotoxic effects of MDMA. This paper reviews case reports of adverse effects attributed to ecstasy use, and the findings of animal and human studies, so as to identify the health effects of ecstasy use, and factors contributing to their occurrence. The incidence of serious acute adverse events related to ecstasy is low. It is the unpredictability of those adverse events and the risk of mortality and substantial morbidity that makes the health consequences of ecstasy significant. Hyperthermia and hyponatraemia are the most significant acute adverse effects, and can occur even when MDMA is the only drug used. Ecstasy users should be aware of the importance of controlling body temperature and fluid intake, early signs of adverse effects, and the need to seek medical assistance promptly. Neurotoxicity is potentially the most significant long‐term effect of ecstasy. The clinical implications of neurotoxicity are uncertain at this time, but short‐term memory impairment may be significant.
Microtubule Targeting of Substrate Contacts Promotes Their Relaxation and Dissociation
Authors: Kaverina Irina , Krylyshkina Olga , Small J. Victor 
Published: July 2002

We recently showed that substrate contact sites in living fibroblasts are specifically targeted by microtubules (Kaverina, I., K. Rottner, and J.V. Small. 1998. J. Cell Biol. 142:181–190). Evidence is now provided that microtubule contact targeting plays a role in the modulation of substrate contact dynamics. The results are derived from spreading and polarized goldfish fibroblasts in which microtubules and contact sites were simultaneously visualized using proteins conjugated with Cy-3, rhodamine, or green fluorescent protein.
For cells allowed to spread in the presence of nocodazole the turnover of contacts was retarded, as compared with controls and adhesions that were retained under the cell body were dissociated after microtubule reassembly. In polarized cells, small focal complexes were found at the protruding cell front and larger adhesions, corresponding to focal adhesions, at the retracting flanks and rear. At retracting edges, multiple microtubule contact targeting preceded contact release and cell edge retraction. The same effect could be observed in spread cells, in which microtubules were allowed to reassemble after local disassembly by the application of nocodazole to one cell edge. At the protruding front of polarized cells, focal complexes were also targeted and as a result remained either unchanged in size or, more rarely, were disassembled. Conversely, when contact targeting at the cell front was prevented by freezing microtubule growth with 20 nM taxol and protrusion stimulated by the injection of constitutively active Rac, peripheral focal complexes became abnormally enlarged. We further found that the local application of inhibitors of myosin contractility to cell edges bearing focal adhesions induced the same contact dissociation and edge retraction as observed after microtubule targeting.
Our data are consistent with a mechanism whereby microtubules deliver localized doses of relaxing signals to contact sites to retard or reverse their development. We propose that it is via this route that microtubules exert their well-established control on cell polarity.
Interferon γ Gene Expression in Sensory Neurons: Evidence for Autocrine Gene Regulation
Authors: Neumann Harald , Schmidt Hannes , Wilharm Elke , Behrens Lüder , Wekerle Hartmut 
Published: July 2002

We explored expression and possible function of interferon-γ (IFN-γ) in cultured fetal (E15) rat dorsal root ganglion neurons combining whole cell patch-clamp electrophysiology with single cell reverse transcriptase polymerase chain reaction and confocal laser immunocytochemistry. Morphologically, we located IFN-γ protein in the cytoplasm of the neurons in culture as well as in situ during peri- and postnatal development. Transcripts for classic IFN-γ and for its receptor were determined in probes of cytoplasm sampled from individual cultured neurons, which had been identified by patch clamp electrophysiology. In addition, the cultured neurons expressed both chains of the IFN-γ receptor.
Locally produced IFN-γ acts back on its cellular source. Phosphorylation and nuclear translocation of the IFN-inducible transcriptional factor STAT1 as well as IFN-γ–dependent expression of major histocompatibility complex class I molecules on the neuronal membrane were noted in untreated cultures. However, both processes were substantially blocked in the presence of antibodies neutralizing IFN-γ. Our findings indicate a role of IFN-γ in autocrine regulation of sensory neurons.
The Costs and Benefits of Consuming
Authors: Csikszentmihalyi Mihaly 
Published: July 2002

Abstract
Consuming is defined as behavior whereby entropy is increased in exchange for existential or experiential rewards. Existential rewards are well known—for example, the satisfaction of Maslowian needs. But experiential rewards are perhaps just as important: these refer to the temporary improvement in positive mood people experience when they are acting in goal-directed, purposeful ways. Consuming is one way for obtaining such experiences. It is suggested that in order to evaluate the impact of consuming it is necessary to measure the entropy costs of the behavior balanced against the psychic benefits it provides.
Combining evidence using p-values: application to sequence homology searches.
Authors: Bailey T L , Gribskov M 
Published: July 2002

Abstract
MOTIVATION: To illustrate an intuitive and statistically valid method for combining independent sources of evidence that yields a p-value for the complete evidence, and to apply it to the problem of detecting simultaneous matches to multiple patterns in sequence homology searches. RESULTS: In sequence analysis, two or more (approximately) independent measures of the membership of a sequence (or sequence region) in some class are often available. We would like to estimate the likelihood of the sequence being a member of the class in view of all the available evidence. An example is estimating the significance of the observed match of a macromolecular sequence (DNA or protein) to a set of patterns (motifs) that characterize a biological sequence family. An intuitive way to do this is to express each piece of evidence as a p-value, and then use the product of these p-values as the measure of membership in the family. We derive a formula and algorithm (QFAST) for calculating the statistical distribution of the product of n independent p-values. We demonstrate that sorting sequences by this p-value effectively combines the information present in multiple motifs, leading to highly accurate and sensitive sequence homology searches.
Structural basis for triplet repeat disorders: a computational
analysis
Authors: Baldi Pierre , Brunak Søren , Chauvin Yves , Gorm Pedersen Anders 
Published: July 2002

Abstract
Motivation: Over a dozen major degenerative disorders, including myotonic distrophy, Huntington’s disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases?
Results: Using several different computational models of DNA structure, we show that the triplets involved in the pathological repeats generally fall into extreme classes. Thus, CAG/CTG repeats are particularly flexible, whereas GCC, CGG and GAA repeats appear to display both flexible and rigid (but curved) characteristics depending on the method of analysis. The fact that (1) trinucleotide repeats often become increasingly unstable when they exceed a length of approximately 50 repeats, and (2) repeated 12-mers display a similar increase in instability above 13 repeats, together suggest that approximately 150 bp is a general threshold length for repeat instability. Since this is about the length of DNA wrapped up in a single nucleosome core particle, we speculate that chromatin structure may play an important role in the expansion mechanism. We furthermore suggest that expansion of a dodecamer repeat, which we predict to have very high flexibility, may play a role in the pathogenesis of the neurodegenerative disorder multiple system atrophy (MSA).
Contact: pfbaldi@ics.uci.edu, yves@netid.com, brunak@cbs.dtu.dk, gorm@cbs.dtu.dk
A comparison of sequence and structure protein domain families as a basis for structural genomics.
Authors: Elofsson A , Sonnhammer E L 
Published: July 2002

Abstract
MOTIVATION: Protein families can be defined based on structure or sequence similarity. We wanted to compare two protein family databases, one based on structural and one on sequence similarity, to investigate to what extent they overlap, the similarity in definition of corresponding families, and to create a list of large protein families with unknown structure as a resource for structural genomics. We also wanted to increase the sensitivity of fold assignment by exploiting protein family HMMs. RESULTS: We compared Pfam, a protein family database based on sequence similarity, to Scop, which is based on structural similarity. We found that 70% of the Scop families exist in Pfam while 57% of the Pfam families exist in Scop. Most families that occur in both databases correspond well to each other, but in some cases they are different. Such cases highlight situations in which structure and sequence approaches differ significantly. The comparison enabled us to compile a list of the largest families that do not occur in Scop; these are suitable targets for structure prediction and determination, and may be useful to guide projects in structural genomics. It can be noted that 13 out of the 20 largest protein families without a known structure are likely transmembrane proteins. We also exploited Pfam to increase the sensitivity of detecting homologs of proteins with known structure, by comparing query sequences to Pfam HMMs that correspond to Scop families. For SWISSPROT+TREMBL, this yielded an increase in fold assignment from 31% to 42% compared to using FASTA only. This method assigned a structure to 22% of the proteins in Saccharomyces cerevisiae, 24% in Escherichia coli, and 16% in Methanococcus jannaschii.
Assessing the accuracy of prediction algorithms for
classification: an overview
Authors: Baldi Pierre , Brunak Søren , Chauvin Yves , Andersen Claus A. F. , Nielsen Henrik 
Published: July 2002

Abstract
4 Also at the Department of Biological Sciences, University of California, Irvine, USA, to whom all correspondence should be addressed.
We provide a unified overview of methods that currently are widely used to assess the accuracy of prediction algorithms, from raw percentages, quadratic error measures and other distances, and correlation coefficients, and to information theoretic measures such as relative entropy and mutual information. We briefly discuss the advantages and disadvantages of each approach. For classification tasks, we derive new learning algorithms for the design of prediction systems by directly optimising the correlation coefficient. We observe and prove several results relating sensitivity and specificity of optimal systems. While the principles are general, we illustrate the applicability on specific problems such as protein secondary structure and signal peptide prediction.
Contact: pfbaldi@ics.uci.edu
Tolerating some redundancy significantly speeds up clustering
of large protein databases
Authors: Li Weizhong , Jaroszewski Lukasz , Godzik Adam 
Published: July 2002

Abstract
Motivation: Sequence clustering replaces groups of similar sequences in a database with single representatives. Clustering large protein databases like the NCBI Non-Redundant database (NR) using even the best currently available clustering algorithms is very time-consuming and only practical at relatively high sequence identity thresholds. Our previous program, CD-HI, clustered NR at 90% identity in ∼1 h and at 75% identity in ∼1 day on a 1 GHz Linux PC (Li et al. , Bioinformatics, 17, 282, 2001); however even faster clustering speed is needed because the size of protein databases are rapidly growing and many applications desire a lower attainable thresholds.
Results: For our previous algorithm (CD-HI), we have employed short-word filters to speed up the clustering. In this paper, we show that tolerating some redundancy makes for more efficient use of these short-word filters and increases the program’s speed 100 times. Our new program implements this technique and clusters NR at 70% identity within 2 h, and at 50% identity in ∼5 days. Although some redundancy is present after clustering, our new program’s results only differ from our previous program’s by less than 0.4%.
Availability: The program and its previous version are available at http://bioinformatics.burnham-inst.org/cd-hi
Contact: liwz@burnham-inst.org; adam@burnham-inst.org
* To whom correspondence should be addressed.
Resistance exercise decreases skeletal muscle tumor necrosis factor α in frail elderly humans
Authors: GREIWE JEFFREY S. , CHENG BO , RUBIN DEBORAH C. , YARASHESKI KEVIN E. , SEMENKOVICH CLAY F. 
Published: July 2002

ABSTRACTSkeletal muscle protein and function decline with advancing age but the underlying pathophysiology is poorly understood. To test the hypothesis that the catabolic cytokine tumor necrosis factor alpha (TNF‐α) contributes to this process, we studied the effects of aging and resistance exercise on TNF‐α expression in human muscle. Using in situ hybridization, TNF‐α message was localized to myocytes in sections of skeletal muscle from elderly humans. Both TNF‐α mRNA and protein levels were elevated in skeletal muscle from frail elderly (81±1 year) as compared to healthy young (23±1 year) men and women. To determine whether resistance exercise affects TNF‐α expression, frail elderly men and women were randomly assigned to a training group or to a nonexercising control group. Muscle biopsies were performed before and after 3 months. Muscle TNF‐α mRNA and protein levels decreased in the exercise group but did not change in the control group. Muscle protein synthesis rate in the exercise group was inversely related to levels of TNF‐α protein. These data suggest that TNF‐α contributes to age‐associated muscle wasting and that resistance exercise may attenuate this process by suppressing skeletal muscle TNF‐α expression.—Greiwe, J. S., Cheng, B., Rubin, D. C., Yarasheski, K. E., Semenkovich, C. F. Resistance exercise decreases skeletal muscle tumor necrosis factor α in frail elderly humans. FASEB J. 15, 475‐482 (2001)
Crystal structure of oxidized flavodoxin, an essential protein in Helicobacter pylori
Authors: Freigang Jörg , Diederichs Kay , Schäfer Klaus P. , Welte Wolfram , Paul Ralf 
Published: July 2002

AbstractThe redox protein flavodoxin has been shown earlier to be reduced by the pyruvate‐oxidoreductase (POR) enzyme complex of Helicobacter pylori, and also was proposed to be involved in the pathogenesis of gastric mucosa‐associated lymphoid‐tissue lymphoma (MALToma). Here, we report its X‐ray structure, which is similar to flavodoxins of other bacteria and cyanobacteria. However, H. pylori flavodoxin has an alanine residue near the isoalloxazine ring of its cofactor flavin mononucleotide (FMN), while the other previously crystallized flavodoxins have a larger hydrophobic residue at this position. This creates a solute filled hole near the FMN cofactor of H. pylori flavodoxin. We also show that flavodoxin is essential for the survival of H. pylori, and conclude that its structure can be used as a starting point for the modeling of an inhibitor for the interaction between the POR‐enzyme complex and flavodoxin.
Thermal Camouflaging MXene Robotic Skin with Bio‐Inspired Stimulus Sensation and Wireless Communication
Authors: Li Kerui , Li Zhipeng , Xiong Ze , Wang Yingxi , Yang Haitao , Xu Wenxin , Jing Lin , Ding Meng , Zhu Jian , Ho John S. , Chen Po‐Yen 
Published: March 2022

AbstractCephalopod skin, which is capable of dynamic optical camouflage, environmental perceptions, and herd communication, has long been a source of bio‐inspiration for developing soft robots with incredible optoelectronic functions. Yet, challenges still exist in designing a stretchable and compliant robotic skin with high‐level functional integration for soft robots with infinite degrees of freedom. Herein, an emerging 2D material, Ti3C2Tx MXene, and an interfacial engineering strategy are adopted to fabricate the soft robotic skin with cephalopod skin‐inspired multifunctionality. By harnessing interfacial instability, the MXene robotic skin with reconfigurable microtextures demonstrates tunable infrared emission (0.30–0.80), enabling dynamic thermal camouflage for soft robots. Benefiting from the intrinsic Seebeck effect, crack propagation behaviors as well as high electrical conductivity, the MXene robotic skins are tightly integrated with thermal/strain sensation capabilities and can serve as a deformable antenna for wireless communication. Without additional electronics installed, the soft robots wearing the conformal MXene skins perform adaptive thermal camouflage based on the thermoelectric feedback in response to environmental temperature changes. With built‐in strain sensing and wireless communication capabilities, the soft robot can record its locomotion routes and wirelessly transmit the key information to the following soft robot to keep both in disguise under thermographic cameras.
Anti‐Fatigue and Highly Conductive Thermocells for Continuous Electricity Generation
Authors: Lei Zhouyue , Gao Wei , Zhu Weiyan , Wu Peiyi 
Published: March 2022

AbstractThe integration of wearable technologies with the human body requires power supplies that are mechanically compatible and able to continuously generate electricity like biological systems. Distinct from existing batteries relying on periodic recharging, thermocells added with thermogalvanic ions are a promising candidate because they enable continuous electricity generation through redox reactions driven by ubiquitous waste heat. However, challenges remain in mechanical adaptability, fatigue resistance, and ion conduction, severely limiting thermocells’ sustainability and lifespan in practical applications. Herein, bionic mechanical training is applied to develop anti‐fatigue and highly conductive thermocells with hierarchical fibrils and aligned nanochannels. It achieves simultaneous enhancements in mechanical performance and output power density. Compared with existing quasi‐solid thermocells with disordered nano‐networks, there are ≈1790‐fold and 5‐fold increases in the mechanical toughness and ionic conductivity, respectively. The stretchability can accommodate the human body's deformation, and the power density is comparable to that of state‐of‐the‐art quasi‐solid thermocells. Moreover, this is the first demonstration of an anti‐fatigue thermocell with a threshold of 2500 J m−2, which is comparable to that of natural muscles and enables it to take full advantage of the continuous energy conversion mode.
Structural Modularization of Cu2Te Leading to High Thermoelectric Performance near the Mott–Ioffe–Regel Limit
Authors: Zhao Kunpeng , Zhu Chenxi , Zhu Min , Chen Hongyi , Lei Jingdan , Ren Qingyong , Wei Tian‐Ran , Qiu Pengfei , Xu Fangfang , Chen Lidong , He Jian , Shi Xun 
Published: March 2022

AbstractTo date, thermoelectric materials research stays focused on optimizing the material's band edge details and disfavors low mobility. Here, the paradigm is shifted from the band edge to the mobility edge, exploring high thermoelectricity near the border of band conduction and hopping. Through coalloying iodine and sulfur, the plain crystal structure is modularized of liquid‐like thermoelectric material Cu2Te with mosaic nanograins and the highly size mismatched S/Te sublattice that chemically quenches the Cu sublattice and drives the electronic states from itinerant to localized. A state‐of‐the‐art figure of merit of 1.4 is obtained at 850 K for Cu2(S0.4I0.1Te0.5); and remarkably, it is achieved near the Mott–Ioffe–Regel limit unlike mainstream thermoelectric materials that are band conductors. Broadly, pairing structural modularization with the high performance near the Mott–Ioffe–Regel limit paves an important new path towards the rational design of high‐performance thermoelectric materials.
Combining Perovskites and Quantum Dots: Synthesis, Characterization, and Applications in Solar Cells, LEDs, and Photodetectors
Authors: Rakshit Soumyadipta , Piatkowski Piotr , Mora‐Seró Iván , Douhal Abderrazzak 
Published: March 2022

AbstractMetal halide perovskites having high defect tolerance, high absorption characteristics, and high carrier mobility demonstrate great promise as potential light harvesters in photovoltaics and optoelectronics and have experienced an unprecedented development since their occurrence in 2009. Semiconductor quantum dots (QDs), on the other hand, have also been proved to be very flexible toward shape, dimension, bandgap, and optical properties for constructing optoelectronic devices. Of late, a strategic combination of both materials has demonstrated extraordinary promise in photovoltaic applications and optoelectronic devices. Combining QDs and perovskites has proved to be quite an effective strategy toward the formation of pinhole‐free and more stable perovskite crystals along with tunability of other properties. To boost this exciting research field, it is imperative to summarize the work done so far in recent years to provide an intriguing insight. This review is a critical account of the advanced strategy toward combining these two fascinating materials, including their different synthetic approaches regarding heteroepitaxial growth of perovskite crystals on QDs, carrier dynamics at the interface and potential application in the field of solar cells, light emitting diodes, and photodetectors.
MolNet‐3D: Deep Learning of Molecular Representations and Properties from 3D Topography
Authors: Liu Yuanbin , Hong Weixiang , Cao Bingyang 
Published: March 2022

AbstractA new paradigm combining quantum‐mechanical calculations with machine learning (ML) to rationally design compounds with specific properties from extremely large chemical space is emerging and developing at a rapid pace. In this context, appropriately describing molecules and efficiently extracting patterns from electronic‐structure calculations are the core challenges for the success of the quantum‐mechanics‐based ML approaches. Here, MolNet‐3D is introduced, a strong deep learning architecture capable of mapping from a flexible and universal 3D topography descriptor to quantum‐mechanical observables of molecules of arbitrary shape. The model can learn an invariant representation without the need for the transformation of atom coordinates into interatomic distances, thus preserving the intrinsic 3D topography information of molecules. The capabilities of MolNet‐3D are shown by accurately predicting the various density functional theory calculated properties for molecules, including energetic, electronic, and thermodynamic properties. Compared with the previously proposed ML methods in the MoleculeNet benchmarks, our model generally offers the best performance in those quantum‐mechanical tasks, elucidating the importance of intrinsic topography information in molecular representation learning. This work may provide new insight into the construction of molecular ML models from 3D topography recognition perspectives.