bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjustments and measures of differential expression for
microarray data
Authors: Tsodikov A. , Szabo A. , Jones D. 
Published: July 2002

Abstract
Motivation: Existing analyses of microarray data often incorporate an obscure data normalization procedure applied prior to data analysis. For example, ratios of microarray channels intensities are normalized to have common mean over the set of genes. We made an attempt to understand the meaning of such procedures from the modeling point of view, and to formulate the model assumptions that underlie them. Given a considerable diversity of data adjustment procedures, the question of their performance, comparison and ranking for various microarray experiments was of interest.
Results: A two-step statistical procedure is proposed: data transformation (adjustment for slide-specific effect) followed by a statistical test applied to transformed data. Various methods of analysis for differential expression are compared using simulations and real data on colon cancer cell lines. We found that robust categorical adjustments outperform the ones based on a precisely defined stochastic model, including some commonly used procedures.
Availability: A program implementing the proposed adjustment and test procedures is available at http://www.hci.utah.edu/groups/biostat/szabo.html.
Contact: alexander.tsodikov@hci.utah.edu
* To whom correspondence should be addressed.
Transcriptional regulation of human insulin receptor gene by the high‐mobility group protein HMGI(Y)
Authors: BRUNETTI ANTONIO , MANFIOLETTI GUIDALBERTO , CHIEFARI EUSEBIO , GOLDFINE IRA D. , FOTI DANIELA 
Published: July 2002

ABSTRACTWe have previously identified two closely related nuclear binding proteins that specifically interact with two unique functional AT‐rich sequences of the 5′ regulatory region of the human insulin receptor gene. Expression of these nuclear binding proteins increases during myocyte and adipocyte differentiation, and in other tissues appears to correlate with insulin receptor content. We have hypothesized, therefore, that insulin receptor expression in the insulin target tissues is regulated at least in part by these nuclear proteins. Here we show data on purification and biochemical characterization of these DNA binding proteins. Using a conventional chromatographic purification procedure combined with electrophoresis mobility shift assay and immunoblot analyses, a unique ~15 kDa protein, either identical to or highly related to the architectural transcription factor HMGI(Y), has now been identified, suggesting an essential role for HMGI(Y) in regulating insulin receptor gene transcription. Direct evidence of HMGI(Y) insulin receptor promoter interactions is provided by functional analysis with the CAT reporter gene and by hormone binding studies in cells expressing HMGI(Y) antisense RNA. In these experiments, antisense HMGI(Y) specifically inhibits insulin receptor promoter function and insulin receptor protein expression, indicating that HMGI(Y) is required for proper transcription of insulin receptor gene. Moreover, our data consistently support the hypothesis that a putative defect in this nuclear binding protein may cause insulin receptor dysfunction with subsequent impairment of insulin signaling and action.—Brunetti, A., Manfioletti, G., Chiefari, E., Goldfine, I. D., Foti, D. Transcriptional regulation of human insulin receptor gene by the high‐mobility group protein HMGI(Y). FASEB J. 15, 492‐500 (2001)
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Authors: Galagan James E. , Nusbaum Chad , Roy Alice , Endrizzi Matthew G. , Macdonald Pendexter , FitzHugh Will , Calvo Sarah , Engels Reinhard , Smirnov Serge , Atnoor Deven , Brown Adam , Allen Nicole , Naylor Jerome , Stange-Thomann Nicole , DeArellano Kurt , Johnson Robin , Linton Lauren , McEwan Paul , McKernan Kevin , Talamas Jessica , Tirrell Andrea , Ye Wenjuan , Zimmer Andrew , Barber Robert D. , Cann Isaac , Graham David E. , Grahame David A. , Guss Adam M. , Hedderich Reiner , Ingram-Smith Cheryl , Kuettner H. Craig , Krzycki Joseph A. , Leigh John A. , Li Weixi , Liu Jinfeng , Mukhopadhyay Biswarup , Reeve John N. , Smith Kerry , Springer Timothy A. , Umayam Lowell A. , White Owen , White Robert H. , de Macario Everly Conway , Ferry James G. , Jarrell Ken F. , Jing Hua , Macario Alberto J.L. , Paulsen Ian , Pritchett Matthew , Sowers Kevin R. , Swanson Ronald V. , Zinder Steven H. , Lander Eric , Metcalf William W. , Birren Bruce 
Published: July 2002

Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome ofM. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of metabolic and cellular capabilities. The presence of novel methyltransferases indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene cluster and two complete chemotaxis gene clusters were identified. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology.[Sequence, data, annotations, and analyses are available athttp://www-genome.wi.mit.edu/. The sequence data described in this paper have been submitted to the GenBank data library under accession no. AE010299.]
A structural basis for processivity
Authors: Breyer Wendy A. , Matthews Brian W. 
Published: July 2002

AbstractThe structures of a number of processive enzymes have been determined recently. These proteins remain attached to their polymeric substrates and may perform thousands of rounds of catalysis before dissociating. Based on the degree of enclosure of the substrate, the structures fall into two broad categories. In one group, the substrate is partially enclosed, while in the other class, enclosure is complete. In the latter case, enclosure is achieved by way of an asymmetric structure for some enzymes while others use a symmetrical toroid. In those cases where the protein completely encloses its polymeric substrate, the two are topologically linked and an immediate explanation for processivity is provided. In cases where there is only partial enclosure, the structural basis for processivity is less obvious. There are, for example, pairs of proteins that have quite similar structures but differ substantially in their processivity. It does appear, however, that the enzymes that are processive tend to be those that more completely enclose their substrates. In general terms, proteins that do not use topological restraint appear to achieve processivity by using a large interaction surface. This allows the enzyme to bind with moderate affinity at a multitude of adjacent sites distributed along its polymeric substrate. At the same time, the use of a large interaction surface minimizes the possibility that the enzyme might bind at a small number of sites with much higher affinity, which would interfere with sliding. Proteins that can both slide along a polymeric substrate, and, as well, recognize highly specific sites (e.g., some site‐specific DNA‐binding proteins) appear to undergo a conformational change between the cognate and noncognate‐binding modes.
Breaking the singleton of germination protease
Authors: Pei Jimin , Grishin Nick V. 
Published: July 2002

AbstractGermination protease (GPR) plays an important role in the germination of spores of Bacillus and Clostridium species. A few very similar GPRs form a singleton group without significant sequence similarities to any other proteins. Their active site locations and catalytic mechanisms are unclear, despite the recent 3‐D structure determination of Bacillus megaterium GPR. Using structural comparison and sequence analysis, we show that GPR is homologous to bacterial hydrogenase maturation protease (HybD). HybD's activity relies on the recognition and binding of metal ions in Ni–Fe hydrogenase, its substrate. Two highly conserved motifs are shared among GPRs, hydrogenase maturation proteases, and another group of hypothetical proteins. Conservation of two acidic residues in all these homologs indicates that metal binding is important for their function. Our analysis helps localize the active site of GPRs and provides insight into the catalytic mechanisms of a superfamily of putative metal‐regulated proteases.
Financial Disclosures Reported by Industry Among Authors of the American Academy of Ophthalmology Clinical Practice Guidelines
Authors: Nguyen Anne Xuan-Lan , Joly-Chevrier Maxine , Nguyen David-Dan , Wu Albert Y. 
Published: March 2023

ImportanceRecommendations of clinical guidelines affect physicians’ care delivery. Potential bias and undeclared conflicts of interests (COIs) among guideline authors can impact clinical practice decisions.ObjectiveTo assess financial disclosures reported by physician authors of the American Academy of Ophthalmology (AAO) Practice Pattern Guidelines compared with those reported by industry to evaluate the disclosures’ accuracy.Design, Setting, and ParticipantsIn this cross-sectional study, all clinical guidelines in the AAO Preferred Practice Patterns (PPP) since 2013 (first year with publicly available industry payment reports) were reviewed on May 1, 2022. Guideline physician authors’ name and their reported COI disclosure were extracted from the guideline publication. Payments to physician authors reported by industry were retrieved from the US Centers for Medicare &amp;amp; Medicaid Open Payments database. Physician authors serving on the AAO guideline committee were included.Main Outcomes and MeasuresThe primary outcome measure was the accuracy of authors’ COIs disclosure. Secondary outcome measures were payments to physician authors reported by industry, the types of payments, and authors’ gender.ResultsA total of 24 AAO guidelines released between 2016 and 2020 were included. Per guideline, there was a mean (SD) of 7.83 (2.24) physician authors. After removing 14 nonphysician authors, 188 physician author names remained, including 83 names assigned as women (44.1%) and 105 names assigned as men (55.9%). Authors could be counted multiple times in these 188 names. According to the Open Payments database, industry reported that 112 of 188 physician authors (59.6%) had at least received 1 payment while serving on the guideline committee, with a payment mean (SD) of $29 849.35 ($54 131.56). According to AAO guidelines, 149 authors (79.3%) had no financial disclosures while serving on the guideline committee. Among these 149 authors, most authors (81 [54.4%]) had payments reported by industry on the Open Payments database not disclosed within the guideline reports. Women physicians were paid significantly more than men for total payments (median [IQR] payments, $15 265 [$598.47-$41 104.67] vs $301.48 [$218.85-$14 615.09]; difference, $14 963.52; P = .003).Conclusions and RelevanceIndustry reported physician guideline authors to have received significant industry payments, some of which were not disclosed within information of the guidelines. To strengthen author transparency regarding these reported disclosures, the authors may want to review and resolve such potential discrepancies during the review and subsequent publication of guidelines.
Injectable, Self‐Contained, Subaqueously Cross‐Linking Laminous Adhesives for Biophysical‐Chemical Modulation of Osteochondral Microenvironment
Authors: Xu Tianpeng , Yang Yuhe , Yeung Elton Hau‐Lam , Chen Qunchao , Bei Ho‐Pan , Yang Qiang , Yang Mo , Hao Yuefeng , Li Bin , Zhao Xin 
Published: March 2023

AbstractCurrent osteochondral (OC) defect repair approaches using premade scaffolds face clinical limitations due to invasiveness, weak integrity, and/or insufficient interfacial bonding. An injectable hydrophobic laminous adhesive is developed that rapidly photocross‐link subaqueously and forms robust bi‐layered structure that orchestrates biophysical‐chemical cues for stimulating OC repair. Liquid hydrophobic photo‐cross‐linkable poly (lactide‐co‐propylene glycol‐co‐lactide) dimethacrylates (PmLnDMA) are adopted as cartilage phase and PmLnDMA encapsulating methacrylated hydroxyapatite nanoparticles (PmLnDMA/MH) as the mineralized subchondral bone phase. Both phases exhibit strong interfacial bonding due to the presence of “CC”. Mechanotransduction and growth factor‐mediated signaling pathways are enchanced by matching the mechanical properties of two phases to native cartilage and bone via systematical modulation of the adhesives’ composition and encapsulated growth factors’ release profile. This enhances mesenchymal stem cells’ commitment to corresponding chondrocytes and osteoblasts to augment OC repair in vitro and in vivo, and ultimately benefits patients suffering from OC fracture, osteoarthritis, and osteoporosis.
Multifunctional Coatings on Sulfide‐Based Solid Electrolyte Powders with Enhanced Processability, Stability, and Performance for Solid‐State Batteries
Authors: Hood Zachary D. , Mane Anil U. , Sundar Aditya , Tepavcevic Sanja , Zapol Peter , Eze Udochukwu D. , Adhikari Shiba P. , Lee Eungje , Sterbinsky George E. , Elam Jeffrey W. , Connell Justin G. 
Published: March 2023

AbstractSulfide‐based solid‐state electrolytes (SSEs) exhibit many tantalizing properties including high ionic conductivity and favorable mechanical properties for next‐generation solid‐state batteries. Widespread adoption of these materials is hindered by their intrinsic instability under ambient conditions, which makes them difficult to process at scale, and instability at the Li||SSE and cathode||SSE interfaces, which limits cell performance and lifetime. Atomic layer deposition is leveraged to grow thin Al2O3 coatings on Li6PS5Cl powders to address both issues simultaneously. These coatings can be directly grown onto Li6PS5Cl particles with negligible chemical modification of the underlying material and enable exposure of powders to pure and H2O‐saturated oxygen environments for ≥4 h with minimal reactivity, compared with significant degradation of the uncoated powder. Pellets fabricated from coated powders exhibit ionic conductivities up to 2× higher than those made from uncoated material, with a simultaneous decrease in electronic conductivity and significant suppression of chemical reactivity at the Li‐SSE interface. These benefits result in significantly improved room temperature cycle life at high capacity and current density. It is hypothesized that this enhanced performance derives from improved intergranular properties and improved Li metal adhesion. This work points to a completely new framework for designing active, stable, and scalable materials for next‐generation solid‐state batteries.
Asymmetric Coordination Induces Electron Localization at Ca Sites for Robust CO2 Electroreduction to CO
Authors: Wang Qiyou , Dai Minyang , Li Hongmei , Lu Ying‐Rui , Chan Ting‐Shan , Ma Chao , Liu Kang , Fu Junwei , Liao Wanru , Chen Shanyong , Pensa Evangelina , Wang Ye , Zhang Shiguo , Sun Yifei , Cortés Emiliano , Liu Min 
Published: March 2023

AbstractMain group single atom catalysts (SACs) are promising for CO2 electroreduction to CO by virtue of their ability in preventing the hydrogen evolution reaction and CO poisoning. Unfortunately, their delocalized orbitals reduce the CO2 activation to *COOH. Herein, an O doping strategy to localize electrons on p‐orbitals through asymmetric coordination of Ca SAC sites (Ca‐N3O) is developed, thus enhancing the CO2 activation. Theoretical calculations indicate that asymmetric coordination of Ca‐N3O improves electron‐localization around Ca sites and thus promotes *COOH formation. X‐ray absorption fine spectroscopy shows the obtained Ca‐N3O features: one O and three N coordinated atoms with one Ca as a reactive site. In situ attenuated total reflection infrared spectroscopy proves that Ca‐N3O promotes *COOH formation. As a result, the Ca‐N3O catalyst exhibits a state‐of‐the‐art turnover frequency of ≈15 000 per hour in an H‐cell and a large current density of −400 mA cm−2 with a CO Faradaic efficiency (FE) ≥ 90% in a flow cell. Moreover, Ca‐N3O sites retain a FE above 90% even with a 30% diluted CO2 concentration.
Biomimetic Construction of Ferrite Quantum Dot/Graphene Heterostructure for Enhancing Ion/Charge Transfer in Supercapacitors
Authors: Fu Min , Chen Wei , Lei Yu , Yu Hao , Lin Yuxiao , Terrones Mauricio 
Published: March 2023

AbstractSpinel ferrites are regarded as promising electrode materials for supercapacitors (SCs) in virtue of their low cost and high theoretical specific capacitances. However, bulk ferrites suffer from limited electrical conductivity, sluggish ion transport, and inadequate active sites. Therefore, rational structural design and composition regulation of the ferrites are approaches to overcome these limitations. Herein, a general biomimetic mineralization synthetic strategy is proposed to synthesize ferrite (XFe2O4, X = Ni, Co, Mn) quantum dot/graphene (QD/G) heterostructures. Anchoring ferrite QD on the graphene sheets not only strengthens the structural stability, but also forms the electrical conductivity network needed to boost the ion diffusion and charge transfer. The optimized NiFe2O4 QD/G heterostructure exhibits specific capacitances of 697.5 F g−1 at 1 A g−1, and exceptional cycling performance. Furthermore, the fabricated symmetrical SCs deliver energy densities of 24.4 and 17.4 Wh kg−1 at power densities of 499.3 and 4304.2 W kg−1, respectively. Density functional theory calculations indicate the combination of NiFe2O4 QD and graphene facilitates the adsorption of potassium atoms, ensuring rapid ion/charge transfer. This work enriches the application of the biomimetic mineralization synthesis and provides effective strategies for boosting ion/charge transfer, which may offer a new way to develop advanced electrodes for SCs.
Module‐Assembled Elastomer Showing Large Strain Stiffening Capability and High Stretchability
Authors: Nakagawa Shintaro , Aoki Daisuke , Asano Yuki , Yoshie Naoko 
Published: March 2023

AbstractElastomers are indispensable materials due to their flexible, stretchable, and elastic nature. However, the polymer network structure constituting an elastomer is generally inhomogeneous, limiting the performance of the material. Here, a highly stretchable elastomer with unprecedented strain‐stiffening capability is developed based on a highly homogeneous network structure enabled by a module assembly strategy. The elastomer is synthesized by efficient end‐linking of a star‐shaped aliphatic polyester precursor with a narrow molecular‐weight distribution. The resulting product shows high strength (≈26 MPa) and remarkable stretchability (stretch ratio at break ≈1900%), as well as good fatigue resistance and notch insensitivity. Moreover, it shows extraordinary strain‐stiffening capability (>2000‐fold increase in the apparent stiffness) that exceeds the performance of any existing soft material. These unique properties are due to strain‐induced ordering of the polymer chains in a uniformly stretched network, as revealed by in situ X‐ray scattering analyses. The utility of this great strain‐stiffening capability is demonstrated by realizing a simple variable stiffness actuator for soft robotics.
Competition between Carrier Injection and Structural Distortions in Electron‐Doped Perovskite Nickelate Thin Films
Authors: Hadjimichael Marios , Mundet Bernat , Domínguez Claribel , Waelchli Adrien , De Luca Gabriele , Spring Jonathan , Jöhr Simon , McKeown Walker Siobhan , Piamonteze Cinthia , Alexander Duncan T. L. , Triscone Jean‐Marc , Gibert Marta 
Published: March 2023

AbstractThe discovery of superconductivity in doped infinite‐layer nickelate thin films has brought increased attention to the behavior of the doped perovskite phase. Despite this interest, the majority of existing studies pertain to hole‐doped perovskite rare‐earth nickelate thin films, while most electron‐doping studies have been performed on bulk materials so far. To tackle this imbalance, a detailed study that addresses doping of NdNiO3 thin films using A‐site substitution is presented, using Pb as a dopant and taking advantage of its valence‐skipping nature. Through a combination of complementary techniques including X‐ray diffraction, transport measurements, X‐ray absorption spectroscopy, electron energy‐loss spectroscopy and scanning transmission electron microscopy, the valence of Pb in the Nd1−xPbxNiO3 structure is confirmed to be 4+, and the behavior of the doped thin films is found to be controlled by a competition between carrier injection and structural distortions, which respectively reduce and increase the metal‐to‐insulator transition temperature. This work provides a systematic study of electron doping in NdNiO3, demonstrating that A‐site substitution with Pb is an appropriate method for such doping in perovskite rare‐earth nickelate systems.
Practical considerations for adaptive strategies by US grazing land managers with a changing climate
Authors: Derner Justin D. , Wilmer Hailey , Stackhouse‐Lawson Kim , Place Sara , Boggess Mark 
Published: March 2023

AbstractWe outline practical considerations for grazing land adaptations with a changing climate, with an emphasis on the ranch operation scale and specific attention to directional climate changes and increased climate variability. These adaptive strategies fall into two themes: flexibility and learning under uncertainty. Ranches and livestock operations with greater land, social, or other capital resources may have more flexibility. Risk can be reduced for managers (ranchers, farmers, operators, and livestock managers) through participation in conservation or farm policy programs and/or market‐based approaches. Bolstering adaptive capacity across landscapes and time can originate from social capital of operators and strategic collaborations among managers and scientists. As climate diverges from historical baselines and the realm of managers’ experiential knowledge, new conceptual frameworks are needed to structure conversations, influence research relevancy and impact, and drive imaginative solutions among researchers, managers, and local communities for socio‐ecological systems. We provide simplified frameworks to help guide conversation, future research, and new imaginative solutions for systems‐scale knowledge needs and adaptation to address increasingly uncertain and complex change at multiple scales. Practical considerations for adaptive strategies by grazing land managers with a changing climate will be accelerated through (1) collaborative efforts among managers and explicitly with science–management partnerships becoming more mainstream, (2) co‐produced research with managers and researchers at ranch scales, (3) development of communities of practice and associated learning opportunities, and (4) continued co‐development and advancement of technologies and tools that result in high uptake adoption by ranch managers.