bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical mechanical simulation of polymeric DNA melting with MELTSIM.
Authors: Blake R D , Bizzaro J W , Blake J D , Day G R , Delcourt S G , Knowles J , Marx K A , SantaLucia J 
Published: July 2002

Abstract
MOTIVATION: MELTSIM is a windows-based statistical mechanical program for simulating melting curves of DNAs of known sequence and genomic dimensions under different conditions of ionic strength with great accuracy. The program is useful for mapping variations of base compositions of sequences, conducting studies of denaturation, establishing appropriate conditions for hybridization and renaturation, determinations of sequence complexity, and sequence divergence. RESULTS: Good agreement is achieved between experimental and calculated melting curves of plasmid, bacterial, yeast and human DNAs. Denaturation maps that accompany the calculated curves indicate non-coding regions have a significantly lower (G+C) composition than coding regions in all species examined. Curves of partially sequenced human DNA suggest the current database may be heavily biased with coding regions, and excluding large (A+T)-rich elements. AVAILABILITY: MELTSIM 1.0 is available at: //www.uml.edu/Dept/Chem/UMLBIC/Apps/MEL TSIM/MELTSIM-1.0-Win/meltsim. zip. Melting curve plots in this paper were made with GNUPLOT 3.5, available at: http://www.cs.dartmouth.edu/gnuplot_inf o.html Contact : blake@maine.maine.edu;
A historical perspective on gene/protein functional assignment
Authors: Hodgman T. C. 
Published: July 2002

Abstract
Sequence determination and analysis began on proteins in the 1950s, with RNA starting about a decade later and DNA a similar period later still. Hence many of the concepts for function prediction were first developed by looking at amino acid sequences. Over time these methods have become much more sophisticated, allowing better discrimination of only weak similarities. The most recent developments concern an examination of contextual information, such as operon structure, metabolic reconstruction or co-expression profiles.
Contact: ch18380@ggr.co.uk
JenPep: a database of quantitative functional peptide data for
immunology
Authors: Blythe Martin J. , Doytchinova Irini A. , Flower Darren R. 
Published: July 2002

Abstract
Motivation: The compilation of quantitative binding data underlies attempts to derive tools for the accurate prediction of epitopes in cellular immunology and is part of our concerted goal to develop practical computational vaccinology.
Results: JenPep is a family of relational databases supporting the growing community of immunoinformaticians. It contains quantitative data on peptide binding to Major Histocompatibility Complexes (MHCs) and to Transmembrane Peptide Transporter (TAP), as well as an annotated list of T-cell epitopes.
Availability: The database is available via the Internet. An HTML interface allowing searching of the database can be found at the following address: http://www.jenner.ac.uk/JenPep.
Contact: darren.flower@jenner.ac.uk
* To whom correspondence should be addressed.
Dating the common ancestor of SIVcpz and HIV‐1 group M and the origin of HIV‐1 subtypes by using a new method to uncover clock‐like molecular evolution
Authors: Salemi Marco , Strimmer Korbinian , Hall William W. , Duffy Margaret , Delaporte Eric , Mboup Souleymane , Peeters Martine , Vandamme Anne‐Mieke 
Published: July 2002

ABSTRACTAttempts to estimate the time of origin of human immunodeficiency virus (HIV)‐1 by using phylogenetic analysis are seriously flawed because of the unequal evolutionary rates among different viral lineages. Here, we report a new method of molecular clock analysis, called Site Stripping for Clock Detection (SSCD), which allows selection of nucleotide sites evolving at an equal rate in different lineages. The method was validated on a dataset of patients all infected with hepatitis C virus in 1977 by the same donor, and it was able to date exactly the ‘known’ origin of the infection. Using the same method, we calculated that the origin of HIV‐1 group M radiation was in the 1930s. In addition, we show that the coalescence time of the simian ancestor of HIV‐1 group M and its closest related cpz strains occurred around the end of the XVII century, a date that could be considered the upper limit to the time of simian‐to‐human transmission of HIV‐1 group M. The results show also that SSCD is an easy‐to‐use method of general applicability in molecular evolution to calibrate clock‐like phylogenetic trees.
Artificial Intelligence in Breast Cancer Screening
Authors: Potnis Kunal C. , Ross Joseph S. , Aneja Sanjay , Gross Cary P. , Richman Ilana B. 
Published: November 2022

ImportanceContemporary approaches to artificial intelligence (AI) based on deep learning have generated interest in the application of AI to breast cancer screening (BCS). The US Food and Drug Administration (FDA) has approved several next-generation AI products indicated for BCS in recent years; however, questions regarding their accuracy, appropriate use, and clinical utility remain.ObjectivesTo describe the current FDA regulatory process for AI products, summarize the evidence used to support FDA clearance and approval of AI products indicated for BCS, consider the advantages and limitations of current regulatory approaches, and suggest ways to improve the current system.Evidence ReviewPremarket notifications and other publicly available documents used for FDA clearance and approval of AI products indicated for BCS from January 1, 2017, to December 31, 2021.FindingsNine AI products indicated for BCS for identification of suggestive lesions and mammogram triage were included. Most of the products had been cleared through the 510(k) pathway, and all clearances were based on previously collected retrospective data; 6 products used multicenter designs; 7 products used enriched data; and 4 lacked details on whether products were externally validated. Test performance measures, including sensitivity, specificity, and area under the curve, were the main outcomes reported. Most of the devices used tissue biopsy as the criterion standard for BCS accuracy evaluation. Other clinical outcome measures, including cancer stage at diagnosis and interval cancer detection, were not reported for any of the devices.Conclusions and RelevanceThe findings of this review suggest important gaps in reporting of data sources, data set type, validation approach, and clinical utility assessment. As AI-assisted reading becomes more widespread in BCS and other radiologic examinations, strengthened FDA evidentiary regulatory standards, development of postmarketing surveillance, a focus on clinically meaningful outcomes, and stakeholder engagement will be critical for ensuring the safety and efficacy of these products.
Impact of the COVID‐19 Pandemic on Early Career Investigators in Rheumatology: Recommendations to Address Challenges to Early Research Careers
Authors: Kuhn Kristine A. , Stahly Andrew , Konig Maximilian F. , Carandang Kristine , Herndon Connie , Backman Catherine , Callahan Leigh F. , Schulert Grant , Fraenkel Liana , Ogdie Alexis ,   the American College of Rheumatology Committee on Research
Published: November 2022

ObjectiveThe COVID‐19 pandemic has impacted the careers of trainees and early career investigators (ECIs). We sought to assess how the American College of Rheumatology (ACR) and the Rheumatology Research Foundation (RRF) can address the needs of those pursuing research careers.MethodsThe Committee on Research created a survey to assess the impact of COVID‐19 and identify topics for the ACR and the RRF to address. In fall of 2020, we surveyed postdoctoral trainees and ECIs within 9 years of terminal training. Responses were analyzed using descriptive statistics and qualitative content analysis.ResultsTwenty‐one percent of invitees responded to the survey (n = 365); of these, 60% were pursuing careers in academic research. Seventy‐five percent of respondents in academic research career paths placed their primary projects on hold during the pandemic. The number of individuals pursuing a research career from 2020 to 2021 decreased by 5%. Respondents reported funding, caregiving, and lack of preliminary data as significant challenges. Suggested impactful interventions included increased funding, funding process reform, and expanding mentoring and networking resources.ConclusionMajor stressors identified during the pandemic included increased caregiving responsibilities and difficulty obtaining data and funding, for which respondents suggested increases and changes in funding programs as well as more mentoring and networking opportunities. Based on these, the Committee on Research proposes 3 priorities: 1) flexible funding mechanisms for ECIs and additional support for those impacted by caregiving; 2) virtual and in‐person programs for career development and networking; and 3) curated content relevant to building a research career available on demand.
Programmable Wavefront Control in the Visible Spectrum Using Low‐Loss Chalcogenide Phase‐Change Metasurfaces
Authors: Moitra Parikshit , Wang Yunzheng , Liang Xinan , Lu Li , Poh Alyssa , Mass Tobias W.W. , Simpson Robert E. , Kuznetsov Arseniy I. , Paniagua‐Dominguez Ramon 
Published: November 2022

AbstractAll‐dielectric metasurfaces provide unique solutions for advanced wavefront manipulation of light with complete control of amplitude and phase at sub‐wavelength scales. One limitation, however, for most of these devices is the lack of any post‐fabrication tunability of their response. To break this limit, a promising approach is employing phase‐change materials (PCMs), which provide fast, low energy, and non‐volatile means to endow metasurfaces with a switching mechanism. In this regard, great advancements have been done in the mid‐infrared and near‐infrared spectrum using different chalcogenides. In the visible spectral range, however, very few devices have demonstrated full phase manipulation, high efficiencies, and reversible optical modulation. In this work, a programmable all‐dielectric Huygens’ metasurface made of antimony sulfide (Sb2S3) PCM is experimentally demonstrated, a low loss and high‐index material in the visible spectral range with a large contrast (≈0.5) between its amorphous and crystalline states. ≈2π phase modulation is shown with high associated transmittance and it is used to create programmable beam‐steering devices. These novel chalcogenide PCM metasurfaces have the potential to emerge as a platform for next‐generation spatial light modulators and to impact application areas such as programmable and adaptive flat optics, light detection and ranging (LiDAR), and many more.
The Negative‐Charge‐Triggered “Dead Zone” between Electrode and Current Collector Realizes Ultralong Cycle Life of Aluminum‐Ion Batteries
Authors: Guan Wei , Huang Zheng , Wang Wei , Song Wei‐Li , Tu Jiguo , Luo Yiwa , Lei Haiping , Wang Mingyong , Jiao Shuqiang 
Published: November 2022

AbstractTypically, volume expansion of the electrodes after intercalation of active ions is highly undesirable yet inetvitable, and it can significantly reduce the adhesion force between the electrodes and current collectors. Especially in aluminum‐ion batteries (AIBs), the intercalation of large‐sized AlCl4− can greatly weaken this adhesion force and result in the detachment of the electrodes from the current collectors, which seems an inherent and irreconcilable problem. Here, an interesting concept, the “dead zone”, is presented to overcome the above challenge. By incorporating a large number of OH− and COOH− groups onto the surface of MXene film, a rich negative‐charge region is formed on its surface. When used as the current collector for AIBs, it shields a tiny area of the positive electrode (adjacent to the current collector side) from AlCl4− intercalation due to the repulsion force, and a tiny inert layer (dead zone) at the interface of the positive electrode is formed, preventing the electrode from falling off the current collector. This helps to effectively increase the battery's cycle life to as high as 50 000 times. It is believed that the proposed concept can be an important reference for future development of current collectors in rocking chair batteries.
Simultaneous Photoelectrocatalytic Oxidation and Nitrite‐Ammonia Conversion with Artificial Photoelectrochemistry Cells
Authors: Song Yurou , Wu Yunzhen , Cao Shuyan , Zhang Yanxue , Luo Degen , Gao Junfeng , Li Zhuwei , Sun Licheng , Hou Jungang 
Published: November 2022

AbstractArtificial photoelectrochemistry system harvests solar energy for solar fuel conversion by use of semiconductor anode and cathode. However, the low overall performance of this integrated system is limited by the compatibility and durability. Herein, a compact heterostructure photoanode exhibits >98% selective photoelectrocatalytic oxidation conversion and >99% Faradaic efficiency of benzyl alcohol oxidation at 0.67 V versus reversible hydrogen electrode in comparison of single‐phase photoanodes. Density functional theory calculations reveal the heterointerface is responsible for the appreciable electronic interaction and the accelerated charge transport, exploring the radical relay pathway as the selective oxidation mechanism. Especially, the integrated photoelectrochemistry cell is developed by heterostructure photoanode and protective photocathode, simultaneously enabling the efficient photoelectrocatalytic oxidation conversion and nitrite reduction reaction to ammonia synthesis under ambient conditions with a maximum Faradaic efficiency >98%. This work sheds light on rational design and the construction of artificial photoelectrochemistry cells towards solar energy conversion.
Ionic Organic Thermoelectrics with Impressively High Thermopower for Sensitive Heat Harvesting Scenarios
Authors: Pai Ya‐Hsin , Tang Junhui , Zhao Yan , Liang Ziqi 
Published: November 2022

AbstractAs the worldwide energy crisis is worsened, thermoelectric materials that can harvest low‐grade waste heat and directly convert it into electricity provide promising alternative energy sources. Emerging ionic thermoelectrics (iTEs) have recently attracted widespread attention thanks to their impressively high thermopower that can reach hundreds of times more than conventional electronic thermoelectrics (eTEs). Based on the Soret effect, the performances of iTEs depend on the thermo‐diffusion of mobile ions in electrolytes, resulting in electrical characteristics distinct from eTE materials and opening up additional potential applications of thermoelectrics. Among these materials, organics‐based iTEs (i‐OTEs) provide unique advantages such as low‐cost, light‐weight, and eco‐friendliness, thereby offering more promising application scenarios that can utilize dissipated heat, for example, from human bodies or mobile devices. This concise review begins with the comparison of iTE and eTE, and then discusses their different mechanisms and applied devices in detail. Next, the recent advances of i‐OTEs will be in‐depth highlighted, including the merits and weaknesses of representative types of materials, effects of additives, and effective strategies for performance optimization. Finally, the state‐of‐the‐art achievements of i‐OTEs are summarized, and an overview is provided of the existing challenges and an outlook of prospective development and applications in future efforts.
Steel Anti‐Corrosion Strategy Enables Long‐Cycle Zn Anode
Authors: Tian Han , Yang Jin‐Lin , Deng Yirui , Tang Wenhao , Liu Ruiping , Xu Chenyang , Han Peng , Fan Hong Jin 
Published: November 2022

AbstractThe progress of aqueous zinc batteries (AZBs) is limited by the poor cycling life due to Zn anode instability, including dendrite growth, surface corrosion, and passivation. Inspired by the anti‐corrosion strategy of steel industry, a compounding corrosion inhibitor (CCI) is employed as the electrolyte additive for Zn metal anode protection. It is shown that CCI can spontaneously generate a uniform and ≈30 nm thick solid‐electrolyte interphase (SEI) layer on Zn anode with a strong adhesion via ZnO bonding. This SEI layer efficiently prohibits water corrosion and guides homogeneous Zn deposition without obvious dendrite formation. This enables reversible Zn deposition and dissolution for over 1100 h under the condition of 1 mA cm−2 and 1 mAh cm−2 in symmetric cells. The Zn‐MnO2 full cells with CCI‐modified electrolyte deliver an ultralow capacity decay rate (0.013% per cycle) at 0.5 A g−1 over 1000 cycles. Such an innovative strategy paves a low‐cost way to achieve AZBs with long lifespan.
Kontrolle der Selektivität in Shuttle‐Heterodifunktionalisierungen: Elektrochemische Transfer‐Halothiolierung von Alkinen
Authors: Dong Xichang , Klein Martin , Waldvogel Siegfried R. , Morandi Bill 
Published: November 2022

AbstractDie Shuttle‐Heterodifunktionalisierungsreaktion, bei der zwei chemisch unterschiedliche funktionelle Gruppen zwischen zwei Molekülen übertragen werden, war lange Zeit ein unerreichtes Ziel, da die Kontrolle der Chemo‐, Regio‐ und Stereoselektivität eine große Herausforderung darstellt. Wir präsentieren hier eine elektrochemische Shuttle‐Reaktion (e‐Shuttle), um selektiv eine RS‐ und eine X‐Gruppe zwischen β‐Halogensulfiden und ungesättigten Kohlenwasserstoffen über einen konsekutiv gepaarten Elektrolyse‐Mechanismus zu übertragen. Die bevorzugte anodische Oxidation des einen Anions gegenüber dem anderen, welche aus ihren unterschiedlichen Redoxpotentialen resultiert, spielt eine entscheidende Rolle bei der Kontrolle der hohen Chemoselektivität dieses Prozesses. Diese leicht skalierbare Methode ermöglicht die Herstellung einer Vielzahl von unterschiedlich funktionalisierten β‐Halogenalkenylsulfiden in beispielloser Chemo‐, Regio‐ und Stereoselektivität unter Verwendung leicht handhabbarer Surrogate, z. B. 2‐Bromethyl‐sulfiden, wodurch die Handhabung von korrosiven und oxidativ wirkenden RS−Br‐Reagenzien vermieden wird. In einem breiteren Zusammenhang eröffnen diese Ergebnisse neue Strategien für selektive Shuttle‐Difunktionalisierungsreaktionen.
Effect of Proton Transfer on Electrocatalytic Water Oxidation by Manganese Phosphates
Authors: Yang Shujiao , Li Xialiang , Li Yifan , Wang Yabo , Jin Xiaotong , Qin Lingshuang , Zhang Wei , Cao Rui 
Published: November 2022

AbstractThe effect of proton transfer on water oxidation has hardly been measurably established in heterogeneous electrocatalysts. Herein, two isomorphous manganese phosphates (NH4MnPO4 ⋅ H2O and KMnPO4 ⋅ H2O) were designed to form an ideal platform to study the effect of proton transfer on water oxidation. The hydrogen‐bonding network in NH4MnPO4 ⋅ H2O has been proven to be solely responsible for its better activity. The differences of the proton transfer kinetics in the two materials indicate a fast proton hopping transfer process with a low activation energy in NH4MnPO4 ⋅ H2O. In addition, the hydrogen‐bonding network can effectively promote the proton transfer between adjacent Mn sites and further stabilize the MnIII−OH intermediates. The faster proton transfer results in a higher proportion of zeroth‐order in [H+] for OER. Thus, proton transfer‐affected electrocatalytic water oxidation has been measurably observed to bring detailed insights into the mechanism of water oxidation.
Comparative analysis of intracardiac neural structures in the aged rats with essential hypertension
Authors: Pauziene Neringa , Ranceviene Dalia , Rysevaite‐Kyguoliene Kristina , Inokaitis Hermanas , Saburkina Inga , Plekhanova Khrystyna , Sabeckiene Deimante , Sabeckis Ignas , Martinaityte Rugile , Pilnikovaite Ernesta , Pauza Dainius H. 
Published: November 2022

AbstractPersistent arterial hypertension initiates cardiac autonomic imbalance and alters cardiac tissues. Previous studies have shown that neural component contributes to arterial hypertension etiology, maintenance, and progression and leads to brain damage, peripheral neuropathy, and remodeling of intrinsic cardiac neural plexus. Recently, significant structural changes of the intracardiac neural plexus were demonstrated in young prehypertensive and adult hypertensive spontaneously hypertensive rats (SHR), yet structural alterations of intracardiac neural plexus that occur in the aged SHR remain undetermined. Thus, we analyzed the impact of uncontrolled arterial hypertension in old (48–52 weeks) SHR and the age‐matched Wistar‐Kyoto rats (WKY). Intrinsic cardiac neural plexus was examined using a combination of immunofluorescence confocal microscopy and transmission electron microscopy in cardiac sections and whole‐mount preparations. Our findings demonstrate that structural changes of intrinsic cardiac neural plexus caused by arterial hypertension are heterogeneous and may support recent physiological implications about cardiac denervation occurring together with the hyperinnervation of the SHR heart. We conclude that arterial hypertension leads to (i) the decrease of the neuronal body area, the thickness of atrial nerves, the number of myelinated nerve fibers, unmyelinated axon area and cumulative axon area in the nerve, and the density of myocardial nerve fibers, and (ii) the increase in myelinated nerve fiber area and density of neuronal bodies within epicardiac ganglia. Despite neuropathic alterations of myelinated fibers were exposed within intracardiac nerves of both groups, SHR and WKY, we consider that the determined significant changes in structure of intrinsic cardiac neural plexus were predisposed by arterial hypertension.
The pseudo‐complex General Relativity and effects of a minimal length on the structure of black holes
Authors: Maghlaoui Leila , Hess Peter O. 
Published: November 2022

AbstractAfter resuming some main predictions of the pseudo‐complex General Relativity (pcGR), the effects of a minimal length, on the structure near the event horizon of a Schwarzschild and Kerr black hole, are investigated within the pcGR. It is shown that for small mass black holes there are strong effects, for example, avoiding the accumulation of mass, which might be important in the formation of primordial black holes during the Big Bang. The pcGR adds to the metric a contribution characterized by a parameter , which has a critical value at which barely an event horizon exists. For macroscopic black holes, these effects vanished for below and above this critical value, but at the critical value effects still persist up to cm, though quickly disappearing. For very large mass black holes the minimal length can be safely neglected. The limit between a small and a macroscopic black hole, in units of length, is between cm and cm.
On quantum‐induced revisiting Einstein tensor in the relativistic regime
Authors: Tawfik Abdel Nasser 
Published: November 2022

AbstractFor a rigorous approach to reconcile principles of general relativity (GR) and quantum mechanics (QM), we suggest applying the generalized relativistic noncommutative Heisenberg algebra on spacetime coordinates and momenta of a test particle on curved Riemann geometry manifold, which in turn is extended to an eight‐dimensional manifold. The natural generalization of the four‐dimensional Riemann geometry is the Finsler geometry, in which the quadratic restriction on the length measure is relaxed. With the minimum measurable length derived from the relativistic generalized four‐dimensional uncertainty principle, the quantum‐induced corrections to the fundamental tensor could be determined in the relativistic regime. Accordingly, the affine connections could be revisited. With the quantum‐induced revisiting Riemann curvature tensor and its contractions, the Ricci curvature tensor, and then the Ricci scalar, we have been able to construct a quantum‐induced revision of the Einstein tensor, in which besides quantum‐induced corrections, additional geometric structures emerge. On the surface of the 2‐sphere, we compared the quantum‐induced revisiting and non‐revisiting Einstein tensor and concluded that the difference between both versions strongly depends on the minimum measurable length and the local geodesics of the test particle through the additional curvature.