bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Human Immunodeficiency Virus Under Selection and Weak Recombination
Authors: Rouzine I M , Coffin J M 
Published: March 2005

Abstract
To predict emergence of drug resistance in patients undergoing antiretroviral therapy, we study accumulation of preexisting beneficial alleles in a haploid population of N genomes. The factors included in the model are selection with the coefficient s and recombination with the small rate per genome r (r ≪ s$\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\sqrt{\overline{\mathit{k}}}\) \end{document}$, where k̅ is the average number of less-fit loci per genome). Mutation events are neglected. To describe evolution at a large number of linked loci, we generalize the analytic method we developed recently for an asexual population. We show that the distribution of genomes over the deleterious allele number moves in time as a “solitary wave” that is quasi-deterministic in the middle (on the average) but has stochastic edges. We arrive at a single-locus expression for the average accumulation rate, in which the effects of linkage, recombination, and random drift are all accounted for by the effective selection coefficient s ln$\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\left(\mathit{Nr}\right)\) \end{document}$/ln$\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\left(\mathit{Ns}^{2}\overline{\mathit{k}}/\mathit{r}\right)\) \end{document}$. At large N, the effective selection coefficient approaches the single-locus value s. Below the critical size Nc ∼ 1/r, a population eventually becomes a clone, recombination cannot produce new sequences, and virus evolution stops. Taking into account finite mutation rate predicts a small, finite rate of evolution at N &lt; Nc. We verify the accuracy of the results analytically and by Monte Carlo simulation. On the basis of our findings, we predict that partial depletion of the HIV population by combined anti-retroviral therapy can suppress emergence of drug-resistant strains.
Differential Activation of M26-Containing Meiotic Recombination Hot Spots in Schizosaccharomyces pombe
Authors: Pryce David W , Lorenz Alexander , Smirnova Julia B , Loidl Josef , McFarlane Ramsay J 
Published: March 2005

Abstract
Certain genomic loci, termed hot spots, are predisposed to undergo genetic recombination during meiosis at higher levels relative to the rest of the genome. The factors that specify hot-spot potential are not well understood. The M26 hot spot of Schizosaccharomyces pombe is dependent on certain trans activators and a specific nucleotide sequence, which can function as a hot spot in a position- and orientation-independent fashion within ade6. In this report we demonstrate that a linear element (LE) component, Rec10, has a function that is required for activation of some, but not all, M26-containing hot spots and from this we propose that, with respect to hot-spot activity, there are three classes of M26-containing sequences. We demonstrate that the localized sequence context in which the M26 heptamer is embedded is a major factor governing whether or not this Rec10 function is required for full hot-spot activation. Furthermore, we show that the rec10-144 mutant, which is defective in full activation of ade6-M26, but proficient for activation of other M26-containing hot spots, is also defective in the formation of LEs, suggesting an intimate link between higher-order chromatin structure and local influences on hot-spot activation.
Lineage-Specific Loss of Function of Bitter Taste Receptor Genes in Humans and Nonhuman PrimatesSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AB198983, AB199308.
Authors: Go Yasuhiro , Satta Yoko , Takenaka Osamu , Takahata Naoyuki 
Published: March 2005

Abstract
Since the process of becoming dead genes or pseudogenes (pseudogenization) is irreversible and can occur rather rapidly under certain environmental circumstances, it is one plausible determinant for characterizing species specificity. To test this evolutionary hypothesis, we analyzed the tempo and mode of duplication and pseudogenization of bitter taste receptor (T2R) genes in humans as well as in 12 nonhuman primates. The results show that primates have accumulated more pseudogenes than mice after their separation from the common ancestor and that lineage-specific pseudogenization becomes more conspicuous in humans than in nonhuman primates. Although positive selection has operated on some amino acids in extracellular domains, functional constraints against T2R genes are more relaxed in primates than in mice and this trend has culminated in the rapid deterioration of the bitter-tasting capability in humans. Since T2R molecules play an important role in avoiding generally bitter toxic and harmful substances, substantial modification of the T2R gene repertoire is likely to reflect different responses to changes in the environment and to result from species-specific food preference during primate evolution.
Revisiting Purine-Histidine Cross-Pathway Regulation in Saccharomyces cerevisiae
Authors: Rébora Karine , Laloo Benoît , Daignan-Fornier Bertrand 
Published: March 2005

Abstract
Because some metabolic intermediates are involved in more than one pathway, crosstalk between pathways is crucial to maintaining homeostasis. AMP and histidine biosynthesis pathways are coregulated at the transcriptional level in response to adenine availability. 5′-Phosphoribosyl-4-carboxamide-5-aminoimidazole (AICAR), a metabolic intermediate at the crossroads between these two pathways, is shown here to be critical for activation of the transcriptional response in the absence of adenine. In this study, we show that both AMP and histidine pathways significantly contribute to AICAR synthesis. Furthermore, we show that upregulation of the histidine pathway clearly interferes with regulation of the AMP pathway, thus providing an explanation for the regulatory crosstalk between these pathways. Finally, we revisit the histidine auxotrophy of ade3 or ade16 ade17 mutants. Interestingly, overexpression of PMU1, encoding a potential phosphomutase, partially suppresses the histidine requirement of an ade3 ade16 ade17 triple mutant, most probably by reducing the level of AICAR in this mutant. Together our data clearly establish that AICAR is not just a metabolic intermediate but also acts as a true regulatory molecule.
Safety and Efficacy of Midline vs Peripherally Inserted Central Catheters Among Adults Receiving IV Therapy
Authors: Thomsen Simon L. , Boa Rikke , Vinter-Jensen Lars , Rasmussen Bodil S. 
Published: February 2024

ImportanceMidline catheters (MCs) are widely used, but safety and efficacy compared with peripherally inserted central catheters (PICCs) has not been adequately evaluated.ObjectiveTo compare the safety and efficacy of MCs with PICCs among adult patients with an anticipated intravenous therapy lasting from 5 to 28 days.Design, Setting, and ParticipantsThis parallel, 2-group, open-label, randomized clinical trial (RCT) was conducted in Denmark from October 2018 to February 2022 at a single academic tertiary care center. Adult inpatients and outpatients were consecutively randomized.InterventionPatients were randomized in a 1:1 ratio to either the MC group or the PICC control group.Main Outcomes and MeasuresThe primary outcome was catheter-related bloodstream infection (CRBSI), analyzed using the Fisher exact test. Secondary outcomes were symptomatic catheter-related thrombosis and catheter failure, including mechanical cause, phlebitis, infiltration, pain in relation to drug or fluid administration, and leaking from the puncture site. Incidence rate ratios (IRRs) were calculated to assess between-group failure rates over device dwell time using Poisson regression. An intention-to-treat analysis was performed.ResultsA total of 304 patients (mean [SD] age, 64.6 [13.5] years; 130 [42.8%] female) were included in the analysis, and 152 patients were allocated to each catheter group. The incidence of CRBSI was low, with 0 in the MC group and 1 in the PICC control group (P &amp;gt; .99). The MC group had a higher catheter-related complication rate (20 [13.2%] vs 11 [7.2%]), and an IRR of 2.37 (95% CI, 1.12-5.02; P = .02) for complications compared with the PICC control group. In a post hoc analysis stratified by catheter dwell time, no significant difference in complication rate (IRR, 1.16; 95% CI, 0.50-2.68; P = .73) was found between the 2 groups for catheters used less than 16 days.Conclusions and RelevanceIn this RCT with patients who received medium- to long-term intravenous therapy, the incidence of CRBSI was low, with no difference between MCs and PICCs. The use of MCs resulted in a higher incidence of catheter-related complications compared with use of PICCs. This finding should be balanced in the decision of type of catheter used at the individual patient level.Trial RegistrationClinicalTrials.gov Identifier: NCT04140916
Directional, Silanized Plant‐Based Sponge for Oil Collection
Authors: Kim Jongbeom , Deng Jingyu , Cho Nam‐Joon , Han Seung Min 
Published: February 2024

AbstractPorous materials are commonly employed to combat marine pollution by absorbing oil. However, the release of microplastics or nanoparticles from their synthetic components further exacerbates environmental concerns. In this study, a sustainable and reusable pollen sponge derived from eco‐friendly pollen grains and fabricated using a directional freeze‐drying method is introduced for the first time. These grains undergo a defatting process followed by a controlled hydrolysis process, transforming them into a pollen microgel made of sporopollenin, the primary constituent of a pollen grain's outer layer. The directional freeze‐drying technique is used to fabricate porous structures with controlled orientation using the pollen microgel. The application of a chemical vapor deposition with dodecyltrimethoxysilane (DDTS) grants sponge hydrophobic properties, making it ideal for selective oil absorption. This modified pollen sponge boasts superior absorption capacities (15–59 times its weight) compared to most natural sponges. Additionally, its excellent durability and ability to recover up to 65% of deformation even after 60% strain compression are remarkable with the silanization process tripling the recoverability of pollen sponges. Remarkably, the silanized directional pollen sponge (SDPS) retains this resilience after 100 compression cycles. Therefore, the SDPS emerges as an eco‐conscious solution for repeated and selective oil absorption tasks.
Accelerating Discovery of Polyimides with Intrinsic Microporosity for Membrane‐Based Gas Separation: Synergizing Physics‐Informed Performance Metrics and Active Learning
Authors: Wang Mao , Jiang Jianwen 
Published: February 2024

AbstractPolymer membranes are widely used for gas separation, addressing critical environmental and energy issues. Nevertheless, crafting high‐performance polymer membranes remains a challenging task, often relies on labor‐intensive trial‐and‐error experiments. Different from the traditional Edisonian approach, machine learning offers significant potential to expedite the design of new polymer membranes for gas separation, yet it faces a substantial hurdle due to limited data availability. To overcome this challenge, in this study two physics‐informed performance metrics are introduced, namely fractional free volume and average void size, to assess the separation performance of polymer membranes. By employing active learning and multi‐target screening, top‐performing polyimides with intrinsic microporosity are efficiently discovered from a pool of 155 610 candidates, through calculations of only 709 (0.45%) in the entire search space. As validated by molecular simulations, the top‐performing polyimides exhibit exceptional separation performance for CO2/N2, CO2/CH4, and O2/N2 mixtures, superior to existing polymers and surpassing the current upper bound. The utilization of physics‐informed performance metrics provides a novel strategy to advance the design and accelerate the discovery of new polymer membranes for gas separation and many other important applications.
Electrolytes Design for Extending the Temperature Adaptability of Lithium‐Ion Batteries: from Fundamentals to Strategies
Authors: Wan Shuang , Ma Weiting , Wang Yutong , Xiao Ying , Chen Shimou 
Published: February 2024

AbstractWith the continuously growing demand for wide‐range applications, lithium‐ion batteries (LIBs) are increasingly required to work under conditions that deviate from room temperature (RT). However, commercial electrolytes exhibit low thermal stability at high temperatures (HT) and poor dynamic properties at low temperatures (LT), hindering the operation of LIBs under extreme conditions. The bottleneck restricting the practical applications of LIBs has promoted researchers to pay more attention to developing a series of innovative electrolytes. This review primarily covers the design of electrolytes for LIBs from a temperature adaptability perspective. First, the fundamentals of electrolytes concerning temperature, including donor number (DN), dielectric constant, viscosity, conductivity, ionic transport, and theoretical calculations are elaborated. Second, prototypical examples, such as lithium salts, solvent structures, additives, and interfacial layers in both liquid and solid electrolytes, are presented to explain how these factors can affect the electrochemical behavior of LIBs at high or low temperatures. Meanwhile, the principles and limitations of electrolyte design are discussed under the corresponding temperature conditions. Finally, a summary and outlook regarding electrolytes design to extend the temperature adaptability of LIBs are proposed.
Backside Coating for Stable Zn Anode with High Utilization Rate
Authors: Yang Nute , Gao Yong , Bu Fan , Cao Qinghe , Yang Jiayu , Cui Jiaojiao , Wang Yuxuan , Chen Jipeng , Liu Xiangye , Guan Cao 
Published: February 2024

AbstractStable Zn anodes with high utilization rate are urgently required to promote the specific and volumetric energy densities of Zn‐ion batteries for practical applications. Herein, contrary to the widely utilized surface coating on Zn anodes, this work shows that a zinc foil with a backside coated layer delivers much enhanced cycling stability even under high depth of discharge. The backside coating significantly reduces stress concentration, accelerates heat diffusion, and facilitates electron transfer, thus effectively preventing dendrite growth and structural damage at high Zn utilization. As a result, the developed anode can be stably cycled for 334 h at 85.5% Zn utilization, which outperforms bare Zn and previously reported results on surface‐coated Zn foils. An NVO‐based full cell also shows stable performance with high Zn utilization rate (69.4%), low negative‐positive electrodes ratio (1.44), and high specific/volumetric energy densities (155.8 Wh kg−1/178 Wh L−1), which accelerates the progress toward practical zinc‐ion batteries.
Epitaxial Growth of MgGa2O4/CsPbBr3 Heterostructure with Controlled Defect Tolerance for Dynamic Photoluminescence
Authors: Liu Peng , Yi Zishuo , Li Bohan , Xia Zhiguo , Xu Yan 
Published: February 2024

AbstractEpitaxial growth of halide perovskite heterostructures endows unique electronic structures for diversified luminescent properties. Herein, an epitaxial growth strategy is proposed to assemble MgGa2O4/CsPbBr3 heterostructure with dynamic photoluminescence. Interface defect passivation during integration transforms interstitial and antisite interface defects of CsPbBr3 nanocrystals to shallow states, enhancing photoluminescence stability of the heterostructure against irradiation, solvents, and heat as well. Finally, the as‐constructed heterostructure shows a reversible dynamic photoluminescence from green to blue under 254 nm ultraviolet (UV) irradiation, which is attributed to the electron injection from shallow defects to the emission centers in MgGa2O4 and CsPbBr3 with different radiative recombination rates. Encryption applying binary encoding method based on MgGa2O4/CsPbBr3 and dynamic anti‐counterfeiting feature of its polymer hybrid film are further investigated.
Position and Number Do Matter: Tuning Room Temperature Phosphorescence in Bromo‐1,8‐Naphthalimides through H‐Aggregation and Halogen Bonding
Authors: Chatterjee Oendrila , Biswas Suprakash , Pramanik Anup , Silswal Akshay , Paliwal Bharti , Koner Apurba Lal 
Published: February 2024

AbstractDevelopment of purely organic room temperature phosphors can often be obtained via introduction of heavy atoms into the organic scaffold. However, the task of controlling emission properties in room temperature phosphorescent (RTP) crystals via heavy atom substitution has met limited success. Herein, two classes of molecules (NIpBr1‐2 and NImBr1‐2) are designed by varying position (para and meta) as well as number of bromo substituents in 1,8‐naphthalimide to modulate intermolecular interactions and their phosphorescence properties. NIpBr2 features only halogen bonding. NIpBr, NImBr, and NImBr2 feature H‐aggregation in their crystalline packing wherein the efficiency of H‐aggregation increases as NIpBr < NImBr < NImBr2. NImBr2 also features halogen bonding in addition to H‐aggregation. Relative phosphorescence intensity, phosphorescence lifetime and quantum yield increase in the order NIpBr2 < NIpBr < NImBr < NImBr2, endorsing cruciality of bromine atom positioning and numbering in tuning the RTP performance. Amplification of phosphorescence in meta derivatives over the para congeners leads to tunable emission color of the crystals from blue to orange. These results outline a predictive structure‐property relationship wherein judicious choice of both position and number of bromine substitution can help in regulating emission behavior, providing a major step forward in expanding the fundamentals of organic RTP.
Household resilience and coping strategies to food insecurity: An empirical analysis from Tajikistan
Authors: Egamberdiev Bekhzod , Bobojonov Ihtiyor , Kuhn Lena , Glauben Thomas , Akramov Kamiljon 
Published: February 2024

AbstractBy applying Resilience Index Measurement Analysis to data from Tajikistan, this paper measures food insecurity resilience capacity. Another objective of this paper is to construct and integrate coping strategies into resilience discussions. The final objective is to analyze the role of resilience capacity and coping strategy in food security with an Instrumental Variable approach. Our results generally confirm that resilience and coping strategies increase food security, determined by food expenditure, household adequacy of fruit and vegetable consumption, and household food expenditure share. Moreover, resilience capacity has a moderating role in mitigating negative impacts of shocks on food security.
Real‐world experience of pegcetacoplan in paroxysmal nocturnal hemoglobinuria
Authors: Griffin Morag , Kelly Richard , Brindel Isabelle , Maafa Lynda , Trikha Roochi , Muus Petra , Munir Talha , Varghese Abraham Mullasseril , Mitchell Lindsay , Nagumantry Sateesh , Gandhi Shreyans , Pike Alex , Kulasekararaj Austin G. , Peffault de Latour Regis 
Published: February 2024

AbstractPegcetacoplan significantly improves outcomes for patients with paroxysmal nocturnal hemoglobinuria (PNH) experiencing extravascular hemolysis (EVH) on eculizumab, leading to approval in 2021/2022 (USA/Europe). We report the first collaborative real‐world evidence on pegcetacoplan use in UK and France. A total of 48 patients were either currently receiving or previously received pegcetacoplan (2019–2023). A total of 12 patients had participated in the PEGASUS clinical trial, continuing treatment after trial completion. Five patients were on combination treatment of C5 inhibition and pegcetacoplan. Mean pegcetacoplan duration was 20.2 months. Indication for pegcetacoplan was EVH on C5 inhibitors (Eculizumab, n = 29, Ravulizumab n = 16, others n = 3) with 35/48 patients requiring blood transfusion within the previous 12 months. Mean hemoglobin and reticulocyte count at pegcetacoplan commencement and after 3 months: 91 g/L and 205 × 109/L and 115.8 g/L and 107 × 109/L, respectively, resulting in mean Hb change of 22.3 g/L. Mean LDH pre‐ and post‐pegcetacoplan was unchanged. Six patients have stopped pegcetacoplan. A total of 32 breakthrough hemolysis (BTH) events occurred in 13/48 patients. A total of 14 events were within clinical trials (reported separately). Six patients experienced 18 acute BTH events outside clinical trials, 7/18 associated with complement activating conditions. Successful clinical management included daily pegcetacoplan subcutaneously for 3 days or single eculizumab doses; these events are manageable with prompt intervention. Pegcetacoplan is effective for patients with PNH experiencing EVH. In this large patient cohort, treatment was well tolerated with improved hemoglobin and reticulocytes and maintained LDH control. Although BTH occurs, this is manageable by acute dose modification, with the majority of patients being maintained on pegcetacoplan.
EFEMP1 haploinsufficiency causes a Marfan‐like hereditary connective tissue disorder
Authors: Forghani Irman , Lang Steven H. , Rodier Matthew J. , Bivona Stephanie A. ,   Undiagnosed Diseases Network, Morales Alejo A. , Zuchner Stephan , Bademci Guney , Tekin Mustafa 
Published: February 2024

AbstractPhenotypic features of a hereditary connective tissue disorder, including craniofacial characteristics, hyperextensible skin, joint laxity, kyphoscoliosis, arachnodactyly, inguinal hernia, and diverticulosis associated with biallelic pathogenic variants in EFEMP1 have been previously described in four patients. Genome sequencing on a proband and her mother with comparable phenotypic features revealed that both patients were heterozygous for a stop‐gain variant c.1084C>T (p.Arg362*). Complementary RNA‐seq on fibroblasts revealed significantly reduced levels of mutant EFEMP1 transcript. Considering the absence of other molecular explanations, we extrapolated that EFEMP1 could be the cause of the patient's phenotypes. Furthermore, nonsense‐mediated decay was demonstrated for the mutant allele as the principal mechanism for decreased levels of EFEMP1 mRNA. We provide strong clinical and genetic evidence for the haploinsufficiency of EFEMP1 due to nonsense‐medicated decay to cause severe kyphoscoliosis, generalized hypermobility of joints, high and narrow arched palate, and potentially severe diverticulosis. To the best of our knowledge, this is the first report of an autosomal dominant EFEMP1‐associated hereditary connective tissue disorder and therefore expands the phenotypic spectrum of EFEMP1 related disorders.