bluuebunny/crossref_metadata_2025 huggingface dataset:
The melon Fom‐1–Prv resistance gene pair: Correlated spatial expression and interaction with a viral protein
Authors: Normantovich Michael , Amitzur Arie , Offri Sharon , Pashkovsky Ekaterina , Shnaider Yula , Nizan Shahar , Yogev Ohad , Jacob Avi , Taylor Christopher G. , Desbiez Cécile , Whitham Steven A. , Bar‐Ziv Amalia , Perl‐Treves Rafael
Published: February 2024

The head‐to‐head oriented pair of melon resistance genes, Fom‐1 and Prv, control resistance to Fusarium oxysporum races 0 and 2 and papaya ringspot virus (PRSV), respectively. They encode, via several RNA splice variants, TIR‐NBS‐LRR proteins, and Prv has a C‐terminal extra domain with a second NBS homologous sequence. In other systems, paired R‐proteins were shown to operate by “labor division,” with one protein having an extra integrated domain that directly binds the pathogen's Avr factor, and the second protein executing the defense response. We report that the expression of the two genes in two pairs of near‐isogenic lines was higher in the resistant isoline and inducible by F. oxysporum race 2 but not by PRSV. The intergenic DNA region separating the coding sequences of the two genes acted as a bi‐directional promoter and drove GUS expression in transgenic melon roots and transgenic tobacco plants. Expression of both genes was strong in melon root tips, around the root vascular cylinder, and the phloem and xylem parenchyma of tobacco stems and petioles. The pattern of GUS expression suggests coordinated expression of the two genes. In agreement with the above model, Prv's extra domain was shown to interact with the cylindrical inclusion protein of PRSV both in yeast cells and in planta.
The effects of biological crowders on fibrillization, structure, diffusion, and conformational dynamics of α‐synuclein
Authors: Heravi Sina , Power Jude Vincent Dobbin , Yethiraj Anand , Booth Valerie
Published: February 2024

α‐synuclein is an intrinsically disordered protein (IDP) whose aggregation in presynaptic neuronal cells is a pathological hallmark of Lewy body formation and Parkinson's disease. This aggregation process is likely affected by the crowded macromolecular cellular environment. In this study, α‐synuclein was studied in the presence of both a synthetic crowder, Ficoll70, and a biological crowder composed of lysed cells that better mimics the biocomplexity of the cellular environment. 15N‐1H HSQC NMR results show similar α‐synuclein chemical shifts in non‐crowded and all crowded conditions implying that it remains similarly unstructured in all conditions. Nevertheless, both HSQC NMR and fluorescence measurements indicate that, only in the cell lysate, α‐synuclein forms aggregates over a timescale of 48 h. 15N‐edited diffusion measurements indicate that all crowders slow down the α‐synuclein's diffusivity. Interestingly, at high concentrations, α‐synuclein diffuses faster in cell lysate than in Ficoll70, possibly due to additional soft (e.g., electrostatic or hydrophobic) interactions. 15N‐edited relaxation measurements show that some residues are more mobile in cell lysate than in Ficoll70; the rates that are most different are predominantly in hydrophobic residues. We thus examined cell lysates with reduced hydrophobicity and found slower dynamics (higher relaxation rates) in several α‐synuclein residues. Taken together, these experiments suggest that while cell lysate does not substantially affect α‐synuclein structure (HSQC spectra), it does affect chain dynamics and translational diffusion, and strongly affects aggregation over a timescale of days, in a manner that is different from either no crowder or an artificial crowder: soft hydrophobic interactions are implicated.
Toward physics‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants
Authors: Meller Artur , Kelly Devin , Smith Louis G. , Bowman Gregory R.
Published: February 2024

The goal of precision medicine is to utilize our knowledge of the molecular causes of disease to better diagnose and treat patients. However, there is a substantial mismatch between the small number of food and drug administration (FDA)‐approved drugs and annotated coding variants compared to the needs of precision medicine. This review introduces the concept of physics‐based precision medicine, a scalable framework that promises to improve our understanding of sequence–function relationships and accelerate drug discovery. We show that accounting for the ensemble of structures a protein adopts in solution with computer simulations overcomes many of the limitations imposed by assuming a single protein structure. We highlight studies of protein dynamics and recent methods for the analysis of structural ensembles. These studies demonstrate that differences in conformational distributions predict functional differences within protein families and between variants. Thanks to new computational tools that are providing unprecedented access to protein structural ensembles, this insight may enable accurate predictions of variant pathogenicity for entire libraries of variants. We further show that explicitly accounting for protein ensembles, with methods like alchemical free energy calculations or docking to Markov state models, can uncover novel lead compounds. To conclude, we demonstrate that cryptic pockets, or cavities absent in experimental structures, provide an avenue to target proteins that are currently considered undruggable. Taken together, our review provides a roadmap for the field of protein science to accelerate precision medicine.
Design, synthesis, antibacterial evaluation of isopropylamine linked with different substituted phenol and piperazine novel derivatives
Authors: Wang Wen‐Hang , Li Zhu‐Rui , Zhu Dan‐Xue , Chen Jia‐Yi , Zhou Yue , Li Cheng‐Peng , Shao Li‐Hui , Qiu Xue‐Mei , Zhu Mei , Long Hai‐Tao , Chen Dan‐Ping , Ouyang Gui‐Ping , Rong Zi‐Qiang , Wang Zhen‐Chao
Published: February 2024

BACKGROUND

Xanthomonas oryzae pv. oryzae (Xoo) is often considered one of the most destructive bacterial pathogens causing bacterial leaf blight (BLB), resulting in significant yield and cost losses in rice. In this study, a series of novel derivatives containing the isopropanolamine moiety linked to various substituted phenols and piperazines were designed, synthesized and screened.

RESULTS

Antibacterial activity results showed that most compounds had good inhibitory effects on Xoo, among which compound W2 (EC50 = 2.74 μg mL−1) exhibited the most excellent inhibitory activity, and W2 also had a certain curative effect (35.89%) on rice compared to thiodiazole copper (TC) (21.57%). Scanning electron microscopy (SEM) results indicated that compound W2 could cause rupture of the Xoo cell membrane. Subsequently, proteomics and quantitative real‐time polymerase chain reaction revealed that compound W2 affected the physiological processes of Xoo and may exert antibacterial activity by targeting the two‐component system pathway. Interestingly, W2 upregulated Xoo's methyltransferase to impact on its pathogenicity.

CONCLUSION

The present study offers a promising phenolic‐piperazine‐sopropanolamine compound as an innovative antibacterial strategy by specifically targeting the two‐component system pathway and inducing upregulation of methyltransferase to effectively impact Xoo's pathogenicity. © 2024 Society of Chemical Industry.
Design, synthesis and bioactivity of a new class of antifungal amino acid‐directed phthalide compounds
Authors: Wang Meizi , Li Guangyao , Zhou Lin , Hao Youwu , Wang Longfei , Mao Xuewei , Zhang Guoyan , Zhao Chenxiang
Published: February 2024

BACKGROUND

Peanut southern blight disease, caused by Sclerotium rolfsii, is a destructive soil‐borne fungal disease. The current control measures, which mainly employ succinate dehydrogenase inhibitors, are prone to resistance and toxicity to non‐target organisms. As a result, it is necessary to explore the potential of eco‐friendly fungicides for this disease.

RESULTS

Fourteen novel phthalide compounds incorporating amino acid moieties were designed and synthesized. The in vitro activity of analog A1 [half maximal effective concentration (EC50) = 332.21 mg L−1] was slightly lower than that of polyoxin (EC50 = 284.32 mg L−1). It was observed that on the seventh day, the curative activity of A1 at a concentration of 600.00 mg L−1 was 57.75%, while the curative activity of polyoxin at a concentration of 300.00 mg L−1 was 42.55%. These results suggested that our compound exhibited in vivo activity. Peanut plants treated with A1 showed significant agronomic improvements compared to the untreated control. Several compounds in this series exhibited superior root absorption and conduction in comparison to the endothermic fungicide thifluzamide. The growth promotion and absorption‐conduction experiments demonstrated the reason for the superior in vivo activity of the target compound. Cytotoxic assays have demonstrated that this series of targeted compounds exhibit low toxicity levels toward human lo2 liver cells.

CONCLUSION

Our results provide a new strategy for the design and synthesis of novel green compounds. Furthermore, the target compound A1 can serve as a lead for further development of green fungicides. © 2024 Society of Chemical Industry.
Gyroscopic precession control for maneuvering two‐wheeled robot recoil stabilization
Authors: Çetin Gökhan , Ünker Faruk
Published: February 2024

A two‐wheeled robot has high maneuverability and can spin around with a high velocity but is prone to roll over under a recoil force. Because the wheels are only used to control the maneuver speed of the robot. However, a two‐wheeled robot using a gyroscope does not need the control of the wheels and can maintain the stability of the robot under a recoil force during maneuvers even if the gimbal of the gyroscope is not controlled by a torque. In this study, the equations of motion of the gyroscopic robot are derived via Lagrangian equations, and the balancing performance of the uncontrolled gyroscope is simulated via Matlab to determine a desired configuration for mechatronics system design. Then, a linear‐quadratic regulator (LQR) is implemented to the chosen control moment gyroscope (CMG) configuration and compared in simulations of RecurDyn. LQR controller was used to prevent oscillating motions of double CMGs under the recoil force of a weapon. The simulation results showed that the gyroscopic two‐wheeled robot is improved using an LQR controller and powerfully balanced in static with excellent performance.
Production of hydrogen via water oxidation using mesoporous‐assembled SiO2@TiN nanocomposite electrocatalyst
Authors: Alothman Asma A. , Shah Syed Imran Abbas , Abid Abdul Ghafoor , Nisa Mehar Un , Bibi Nasreen , Jabbour Karam , Anwar Muhammad Imran , Ehsan Muhammad Fahad , Manzoor Sumaira
Published: February 2024

Electrochemical water splitting is one of the promising approaches for the production of molecular hydrogen as well as to meet the clean and sustainable energy demand of the modern world. However, the key task for the research communities is to design a cost‐effective and efficient electrocatalyst to contribute positively to recent world crises. This study presents a novel SiO2@TiN nanocomposite and utilize it for oxygen evolution reaction (OER) as an electrocatalysts. The different techniques use for the characterization of SiO2@TiN nanocomposite. The electrochemical investigations encompass linear sweep voltammetry (LSV), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) which collectively yield critical parameters for assessing electrocatalytic performance. At a current density of 10 mAcm−2 the SiO2@TiN nanocomposite has a substantially lower overpotential of 256 mV compared to pure SiO2 and TiN. The composite also shows smaller tafel slope of 40 mV dec−1 as well as lower overpotential. The SiO2@TiN nanocomposite also demonstrates the enhanced redox activity as a result of its synergistic effect. Consequently, the increased electrical conductivity of TiN facilitates the attachment of metal oxides and more active sites are exposed to improve the OER activity of the fabricated materials.
Instability Mechanism in Thermoelectric Mg2(Si,Sn) and the Role of Mg Diffusion at Room Temperature
Authors: Duparchy Amandine , Deshpande Radhika , Sankhla Aryan , Ghosh Sanyukta , Camut Julia , Park Sungjin , Park SuDong , Ryu Byungki , Mueller Eckhard , de Boor Johannes
Published: February 2024

Mg2(Si,Sn) shows great promise as thermoelectric material as it is made from non‐toxic, abundant, and cost‐effective elements offering high performance. This has been emphasized by several thermoelectric generator prototypes, demonstrating technological maturity. However, material stability is paramount for large‐scale applications whereas we reveal here that the thermal stability of n‐type Mg2(Si,Sn) may be limited even at room temperature (RT). Integral thermoelectric properties measurements, locally resolved Seebeck coefficient analysis, scanning electron microscopy/energy‐dispersive X‐ray spectroscopy, and atomic force microscopy are employed to assess changes of n‐type samples stored in ambient atmosphere for years, revealing the evolution of the carrier concentration and transport properties in the material as well as surface degradation. This is caused by the diffusion of loosely bound Mg from the bulk towards the surface and subsequent oxidation, leading to a change of Mg‐based intrinsic defect concentrations, thereby degrading the thermoelectric performance. This microscopic mechanism is backed up by first‐principles calculations, revealing that Mg diffusivity in Mg2(Si,Sn) is high at RT and that diffusion occurs mainly via Mg vacancies. The observed much faster degradation of Sn‐rich Mg2(Si,Sn) can be correlated with the higher density of Mg vacancies in Mg2Sn compared to Mg2Si, as predicted from defect formation energies.
Subclinical thiamine deficiency results in failed reproduction in Arctic foxes
Authors: Jackson Craig , Furnes Marianne , Rød‐Eriksen Lars , Yap Kang Nian , Davey Marie , Fossøy Frode , Flagstad Øystein , Eide Nina E. , Mjøen Toralf , Ulvund Kristine
Published: February 2024

Thiamine deficiency can result in life‐threatening physiological and neurological complications. While a thiamine‐deficient diet may result in the onset of such symptoms, the presence of thiaminase – an enzyme that breaks down thiamine – is very often the cause. In such instances, thiaminase counteracts the bioavailability and uptake of thiamine, even when food‐thiamine levels are adequate. Here, we report on a case of failed reproduction in seven Arctic fox (Vulpes lagopus) breeding pairs kept at a captive breeding facility, including the presentation of severe thiamine deficiency symptoms in two male foxes. Symptoms included ataxia, obtundation, truncal sway, star‐gazing and visual impairment. Blood tests were inconclusive, yet symptoms resolved following treatment with a series of thiamine hydrochloride injections, thereby verifying the diagnosis. A fish‐dominated feed, which for the first time had been frozen for a prolonged period, was identified as the likely source of thiaminase and subsequent deterioration in the animals’ health. Symptoms in the two males arose during the annual mating period. All seven breeding pairs at the captive breeding station failed to reproduce – a phenomenon never recorded during the captive breeding facility's preceding 17‐year operation. Relating our findings to peer‐reviewed literature, the second part of this case report assesses how thiamine deficiency (due to thiaminase activity) likely resulted in subclinical effects that impaired the production of reproduction hormones, and thereby led to a complete breeding failure. While previous work has highlighted the potentially lethal effects of thiamine deficiency in farmed foxes, this is, to our knowledge the first study showing how subclinical effects in both males and females may inhibit reproduction in foxes in general, but specifically Arctic foxes. The findings from our case report are not only relevant for captive breeding facilities, but for the welfare and management of captive carnivorous animals in general.
Reactions of Dichloroacetyl Fluoride in Superacidic Media
Authors: Steiner Sebastian , Nitzer Alexander , Jessen Christoph , Kornath Andreas J.
Published: February 2024

Dichloroacetyl fluoride was investigated in the superacids HF/MF5 and DF/MF5 (M=As, Sb). The O‐hemiprotonated species of dichloroacetyl fluoride is formed in the binary superacidic systems HF/MF5 and DF/MF5 (M=As, Sb) as hexafluoridoarsenates and hexafluoridoantimonates. With an excess of the strong Lewis acid SbF5 dichloroacetyl fluoride reacts under the formation of the oxonium salt [CCl2HCF2OX2][SbF6] in the superacidic system XF/SbF5 (X=H, D) after HF‐ or DF‐addition, respectively. The colorless salts were characterized by low‐temperature vibrational spectroscopy, NMR spectroscopy, and single‐crystal X‐ray diffraction. [CCl2HC(OH)F][(CCl2HCOF)2H][SbF6][Sb2F11] and [CCl2HCF2OH2][SbF6] crystallize in the monoclinic space groups P21/c and P21/m, respectively, with two formula units per unit cell each. The crystal structure of the oxonium salt shows strong O(−H)⋅⋅⋅F hydrogen bonds and strong F⋅⋅⋅F interactions. The experimental data are discussed together with quantum chemical calculations at the ωB97XD/aug‐cc‐pVTZ‐level of theory.
Global anomalies & bordism of non-supersymmetric strings
Authors: Basile Ivano , Debray Arun , Delgado Matilda , Montero Miguel
Published: February 2024

Abstract

The three tachyon-free non-supersymmetric string theories in ten dimensions provide a handle on quantum gravity away from the supersymmetric lamppost. However, they have not been shown to be fully consistent; although local anomalies cancel due to versions of the Green-Schwarz mechanism, there could be global anomalies, not cancelled by the Green-Schwarz mechanism, that could become fatal pathologies. We compute the twisted string bordism groups that control these anomalies via the Adams spectral sequence, showing that they vanish completely in two out of three cases (Sugimoto and SO(16)2) and showing a partial vanishing also in the third (Sagnotti 0’B model). We also compute lower-dimensional bordism groups of the non-supersymmetric string theories, which are of interest to the classification of branes in these theories via the Cobordism Conjecture. We propose a worldvolume content based on anomaly inflow for the SO(16)2 NS5-brane, and discuss subtleties related to the torsion part of the Bianchi identity. As a byproduct of our techniques and analysis, we also reprove that the outer ℤ2 automorphism swapping the two E8 factors in the supersymmetric heterotic string is also non-anomalous.
Towards a complete classification of 6D supergravities
Authors: Hamada Yuta , Loges Gregory J.
Published: February 2024

Abstract

The constraints arising from anomaly cancellation are particular strong for chiral theories in six dimensions. We make progress towards a complete classification of 6D supergravities with minimal supersymmetry and non-abelian gauge group. First, we generalize a previously known infinite class of anomaly-free theories which has 𝑇 ≫ 9 to essentially any semi-simple gauge group and infinitely many choices for hypermultiplets. The construction relies on having many decoupled sectors all selected from a list of four simple theories which we identify. Second, we use ideas from graph theory to rephrase the task of finding anomaly-free theories as constructing cliques in a certain multigraph. A branch-and-bound type algorithm is described which can be used to explicitly construct, in a 𝑇-independent way, anomaly-free theories with an arbitrary number of simple factors in the gauge group. We implement these ideas to generate an ensemble of $$ \mathcal{O} $$
O
(107) irreducible cliques from which anomaly-free theories may be easily built, and as a special case obtain a complete list of 19,847 consistent theories for 𝑇 = 0, for which the maximal gauge group rank is 24. Modulo U(1), SU(2) and SU(3) simple factors and the new infinite families, we give a complete characterization of anomaly-free theories and show that the bound 𝑇 ≤ 273 is sharp.
Retrospective assessment of neoadjuvant camrelizumab combined with induction chemotherapy: efficacy in laryngeal preservation for advanced hypopharyngeal and laryngeal squamous cell carcinoma
Authors: Peng Jin , Luo Guangfeng , Yu Yongchao , Ning Kang , Liu Xuekui
Published: February 2024

Background

Hypopharyngeal and laryngeal squamous cell carcinoma (SCC) account for 25–30% of head and neck SCC. Total laryngectomy, while effective, compromises the quality of life. Immune checkpoint inhibitors such as Camrelizumab offer potential in laryngeal preservation. The study investigated Camrelizumab combined with TP regimen as a neoadjuvant therapy for laryngeal preservation in advanced hypopharyngeal and laryngeal SCC.

Methods

A retrospective study was conducted at Sun Yat-sen University Cancer Center on patients diagnosed with locally advanced SCC of the hypopharynx and larynx from October 1, 2019, to October 25, 2022. The efficacy of a first-line treatment combining Camrelizumab (200 mg) and TP regimen (Albumin-bound paclitaxel at 260 mg/m2 and Cisplatin at 60 mg/m2) was evaluated using RECIST 1.1 criteria. Outcomes included overall survival (OS), progression-free survival (PFS), laryngectomy-free survival (LFS), and response rates.

Results

Of the 71 included patients, the median age was 60.7 years. Post the first-line treatment, 90.1% demonstrated an overall response. The one-year and two-year OS rates were 91.5% and 84.3%, respectively. One-year and two-year PFS rates were 92.9% and 83.9%, respectively, with LFS at 85.6% and 73.2%. The initial T4 stage as significantly associated with reduced OS and LFS. Skin reaction was the predominant adverse event.

Conclusion

The Camrelizumab-TP regimen demonstrated promising results for advanced hypopharyngeal/laryngeal SCC patients, exhibiting high response rates, OS, and LFS, positioning it as a potential primary option for laryngeal preservation. Further comprehensive, randomized controlled studies are imperative to validate these initial observations and elucidate the regimen's full clinical efficacy in optimizing laryngeal outcomes.
Synthesis of a novel green biopolymer-based composites beads for removal of methylene blue from aquatic medium: isotherm, thermodynamic and kinetic investigation
Authors: Parlayici Şerife , Aras Aslı
Published: February 2024

The increase in the world population and the decrease in clean water resources increase people's interest in water purification technologies. Many industries, such as the textile industry, leather industry, cosmetics and food industry, color their products with substances such as dyes and pigments. In this study, a cheap, useful, innovative, environmentally friendly, and sustainable adsorbent was developed for the removal of Methylene Blue (MB), one of the dyes that is harmful to the environment. In fruit tree cultivation, in addition to the product, very high amounts of by-products/waste (branches, bark, leaves, fruit seeds, fruit shells, etc.) are produced. In this direction, walnut tree and olive tree wastes were immobilized with chitosan, made magnetic (m-WCH and m-OCH), and the adsorption of MB on the developed adsorbents was examined in a batch system. Characterization of the synthesized biocomposite adsorbents was performed by FT-IR, SEM, EDX and XRD analyzes. It has been thoroughly described how the pH solution of the MB dye compares to the pHPZC of the adsorbent surface. The pHPZC values for m-WCH and m-OCH were 5.2 and 5.5 respectively. MB adsorption of biocomposites depends on the pH of the environment (3–8), amount of adsorbent (2–10 gL−1), contact time (5–360 min), temperature (25–55 °C) and initial dye concentration (10–250 ppm) was examined as a function. The obtained data were evaluated with kinetic and isotherm models. Using adsorption equilibrium data obtained from MB adsorption studies using m-WCH and m-OCH biocomposite adsorbents, their suitability to Langmuir, Freundlich, Stachard, Dubinin–Radushkevich and Temkin models was examined. The empirical data of MB adsorption by m-WCH and m-OCH showed agreement with the Langmuir isotherm model. The maximum adsorption capacity for MB by m-WCH and m-OCH was estimated to be 85.47 mg g−1 and 53.48 mg g−1, respectively. The result showed that a higher adsorption selectivity on m-WCH compares to m-OCH. Among the kinetic models applied, the pseudo-second-order kinetic model was identified with the highest regression coefficients. In the light of these results, it was determined that there are new promising adsorbents of natural origin, with higher adsorption capacity, lower cost, and alternatives to commercially used adsorbents in the removal of MB from aqueous media.

Graphical abstract
The 2023 Türkiye-Syria earthquakes: analysis of pediatric victims with crush syndrome and acute kidney Injury
Authors: Döven Serra Sürmeli , Tezol Özlem , Yeşil Edanur , Durak Fatma , Mısırlıoğlu Merve , Alakaya Mehmet , Karahan Feryal , Kıllı İsa , Akça Mehtap , Erdoğan Semra , Can Mevlüt , Delibaş Ali
Published: February 2024

Background

On February 6th, 2023, two consecutive earthquakes struck southeastern Türkiye with magnitudes of 7.7 and 7.6, respectively. This study aimed to analyze the clinical and laboratory findings, as well as management of pediatric victims with Crush Syndrome (CS) and Acute Kidney Injury (AKI).

Methods

The study included pediatric earthquake victims who were presented to Mersin University Hospital. Clinical and laboratory characteristics of the patients were collected retrospectively.

Results

Among 649 patients, Crush injury (CI), CS and AKI was observed in 157, 59, and 17 patients, respectively. White blood cell count (12,870 [IQR: 9910–18700] vs. 10,545 [IQR: 8355–14057] /µL, P < 0.001), C-reactive protein (51.27 [IQR: 14.80–88.78] vs. 4.59 [1.04–18.25] mg/L, P < 0.001) and myoglobin levels (443.00 [IQR: 198.5–1759.35] vs. 17 [11.8–30.43] ng/ml) were higher in patients with CS, while their sodium (IQR: 134 [131–137] vs. 136 [134–138] mEq/L, P < 0.001) levels were lower compared to non-CS patients. An increase in myoglobin levels was identified as an independent risk factor for developing CS (OR = 1.017 [1.006–1.027]). Intravenous fluid replacement was administered to the patients with CS at a dose of 4000 cc/m2/day. Hypokalemia was observed in 51.9% of the CS patients on the third day. All patients with AKI showed improvement and no deaths were reported.

Conclusions

Hyponatremia and increase in inflammation markers associated with CS may be observed. An increase in myoglobin levels was identified as a risk factor for CS. Hypokalemia may be seen as a complication of vigorous fluid therapy during hospitalization.

Graphical abstract
Hybrid 2D/3D-quantitative structure–activity relationship studies on the bioactivities and molecular mechanism of antibacterial peptides
Authors: Yan Qingguo , Wang Fangfang , Zhou Bo , Lin Xiangna
Published: February 2024

Antimicrobial peptide (AMP) is the polypeptide, which protects the organism avoiding attack from pathogenic bacteria. Studies have shown that there were some antimicrobial peptides with molecular action mechanism involved in crossing the cell membrane without inducing severe membrane collapse, then interacting with cytoplasmic target-nucleic acid, and exerting antibacterial activity by interfacing the transmission of genetic information of pathogenic microorganisms. However, the relationship between the antibacterial activities and peptide structures was still unclear. Therefore, in the present work, a series of AMPs with a sequence of 20 amino acids was extracted from DBAASP database, then, quantitative structure–activity relationship (QSAR) methods were conducted on these peptides. In addition, novel antimicrobial peptides with  stronger antimicrobial activities were designed according to the information originated from the constructed models. Hence, the outcome of this study would lay a solid foundation for the in-silico design and exploration of novel antibacterial peptides with improved activity activities.
Sustainable farm work in agroecology: how do systemic factors matter?
Authors: Volken Sandra , Bottazzi Patrick
Published: February 2024

Agroecological farming is widely considered to reconcile improved working and living conditions of farmers while promoting social, economic, and ecological sustainability. However, most existing research primarily focuses on relatively narrow trade-offs between workload, economic and ecological outcomes at farm level and overlooks the critical role of contextual factors. This article conducts a critical literature review on the complex nature of agroecological farm work and proposes the holistic concept of sustainable farm work (SFW) in agroecology together with a heuristic evaluation framework. The latter was applied to ten case studies to test its relevance, affirming positive outcomes of agroecology on SFW, such as improved food sovereignty, biodiversity conservation, and social inclusiveness, but also showing trade-offs, including increased workload and potential yield reductions. Further, results show that contextual factors, such as policy support, market regulation, and access to resources, heavily influence the impact of agroecological practices on SFW. This article strongly argues for the importance of a holistic understanding of SFW and its contextualization within multiple socio-ecological system levels. The proposed framework establishes clear relationships between agroecology and SFW. An explicit recognition of these multidimensional relationships is essential for maximizing positive outcomes of agroecology in different contexts and fostering SFW. On a theoretical level, this research concludes that, from a holistic perspective, work is an entry point to studying the potential of agroecology to drive a sustainable agroecological transition in economic, social, and ecological terms.
Sequential composition of propositional logic programs
Authors: Antić Christian
Published: February 2024

This paper introduces and studies the sequential composition and decomposition of propositional logic programs. We show that acyclic programs can be decomposed into single-rule programs and provide a general decomposition result for arbitrary programs. We show that the immediate consequence operator of a program can be represented via composition which allows us to compute its least model without any explicit reference to operators. This bridges the conceptual gap between the syntax and semantics of a propositional logic program in a mathematically satisfactory way.
Mixed-Method, Multilevel Clustered-Randomized Control Trial for Menstrual Health Disparities
Authors: Houghton Lauren C. , Adkins-Jackson Paris B.
Published: February 2024

Menstrual cycle characteristics are largely considered unmodifiable reproductive factors, a framing that prevents exploration of the ways structural factors interfere with menstrual health. Given the role of structural factors like healthy food and healthcare access on reproductive health and the grave need for structural interventions to known reproductive health disparities that disproportionately target cisgender women racialized as Black, it is imperative that science begin to examine how structural factors influence menstrual health. To explore such research, we employ critical race theory and intersectionality to illustrate what a structural intervention to improve menstrual cycle health could look like. Centering those with the greatest need, persons racialized as Black and/or LatinX living in food and healthcare deserts in Northern Manhattan, our illustrative sample includes four groups of persons who menstruate (e.g., cisgender girls and women) that are pre-menarche, pre-parous, postpartum, or perimenopausal. We describe a hypothetical, multilevel clustered-randomized control trial (cRCT) that provides psychoeducation on racism-related trauma and free delivered groceries to both treatment and control groups, while randomizing 30 clusters of housing associations to receive either sexual health clinics at their housing association or free vouchers for healthcare. We embed mixed methods (diaries, interviews, surveys, mobile apps, observation) into the design to evaluate the effectiveness of the 1-year intervention, in addition to determining the impact on participants through their perspectives. Through this illustration, we provide a novel example of how structural interventions can apply mixed methods to evaluate effectiveness while delivering services to populations impacted by multiple structural factors. We demonstrate how qualitative and quantitative approaches can be paired in clustered RCTs and how a living logic model can empirically incorporate the population perspective into more effective interventions. Lastly, we reveal how sensitive menstrual health is to structural factors and how upstream improvements will trickle down to potentially reduce health disparities in reproductive health.
A Discussion of Implausible Total Solar-Irradiance Variations Since 1700
Authors: Chatzistergos Theodosios
Published: February 2024

The Sun plays a role in influencing Earth’s climate, making it important to have accurate information about variations in the Sun’s radiative output. Models are used to recover total solar-irradiance (TSI) variations in the past when direct space-based measurements are not available. One of the most cryptic such TSI reconstructions is the one by Hoyt and Schatten (J. Geophys. Res. 98, 18, 1993, HS93). The rather vague description of the model methodology, the arbitrary selection of solar indices it employs, and the short overlap between the HS93 series and directly measured TSI values has hindered any evaluation of the performance of this model to this day. Here, we aim at rectifying this by updating the HS93 model with new input data. In this way we are also contributing in the discussion on the possible long-term changes in solar irradiance.

We find that the analysis by HS93 included a number of erroneous processing steps that led to an artificial increasing trend towards the end of the reconstructed TSI series as well as shifting the peak of the TSI in the mid-twentieth century back in time by about 11 years. Furthermore, by using direct measurements of the TSI we determined that the free parameter of the model, the magnitude of variations (here defined as percentage variations of the difference between the maximum to minimum values), is optimal when it is minimised (being ≤0.05%). This is in stark contrast to the high magnitude of variations, of 0.25%, that was imposed by HS93. However, our result is consistent with more recent estimates, such as those from the Spectral And Total Irradiance REconstruction (SATIRE) model and Naval Research Laboratory TSI (NRLTSI), which were used by the Intergovernmental Panel on Climate Change (IPCC). Overall, we find that the previously reported agreement of the HS93 TSI series to temperature on Earth was purely due to improper analysis and artefacts of the processing.
An accuracy characterisation of approximate coherence
Authors: Molinari Giacomo
Published: February 2024

Accuracy-first epistemologists argue that rational agents have probabilistically coherent credences. But why should we care, given that we can’t help being incoherent? A common answer: probabilistic coherence is an ideal to be approximated as best one can. De Bona (in: Philos Sci 84(2), 189–213, 2017) and Staffel (in: Unsettled thoughts: a theory of degrees of rationality, Oxford University Press, 2019) show how accuracy-firsters can spell out this answer by adopting an appropriate notion of approximate coherence. In this essay, I argue that De Bona and Staffel’s proposal is not entirely satisfactory, because it does not show whether, or why, it’s generally better to be more rather than less approximately coherent from an accuracy-first perspective. To address this point, I give a characterisation of their notion of approximate coherence in terms of accuracy. This shows that accuracy-firsters should maintain that more approximately coherent credences are better than less approximately coherent ones if and only if they accept that it’s better to miss out on less rather than more guaranteed accuracy.
The Effect of Discounting on the Formulation of an Aquifer Management Policy Based on Groundwater Trading
Authors: Tsiarapas Athanasios , Mallios Zisis
Published: February 2024

Optimal groundwater management is a necessary condition for achieving the objective of sustainable development, which is directly linked to issues of intergenerational equity. Thus, groundwater management policy shaping has to consider such issues, in particular through the implementation of appropriate discounting methods. The existing literature in the field of groundwater management focuses on a single discount function (DF), the exponential one, without considering the impact of different DFs on the results obtained. At the same time, tradable water rights (TWR) systems have been suggested as policy instruments for more efficient and sustainable water use. This paper focuses on the impact that different DFs have on the formulation of groundwater management policies based on TWR. To this end, a dynamic model is formulated, which concerns groundwater pumping from an aquifer by two groups of users participating in a TWR system and four different DFs are considered to calculate the present value of social welfare: no discounting, exponential, hyperbolic and Gamma discounting. The results of simulations based on data for an aquifer in Northern Greece show that there is a high sensitivity of the results to the DF, which has a direct effect on social welfare from groundwater consumption, aquifer’s hydrological behavior and TWR system intertemporal economic efficiency.
Development of a “Rapid-Crypto Colorimetric LAMP Test” to Detect Cryptosporidiosis in Feces of Newborns Calves
Authors: Karakavuk Muhammet , Can Hüseyin , Can Şengül , Karakavuk Tuğba , Döşkaya Mert , Değirmenci Döşkaya Aysu
Published: February 2024

Background

Cryptosporidiosis is a disease that causes major intestinal damage in humans and animals. The causative agents of the disease are Cryptosporidium species. In newborn calves, diarrhea can lead to death, resulting in significant economic losses for the farms. Therefore, accurate, rapid, and cost-effective diagnosis of the disease is very important.

Material and methods

In this study, a novel colorimetric loop-mediated isothermal amplification (LAMP) test named “Rapid-Crypto Colorimetric LAMP test” targeting Cryptosporidium spp. 18S rRNA gene was developed to detect cryptosporidiosis in the feces of newborn calves. The analytical sensitivity of the test was determined by plasmid controls. Clinical sensitivity was determined using the feces of 127 calves collected from farms in İzmir and Manisa provinces. All of the samples were also investigated with Real-Time PCR targeting the Cryptosporidium spp. COWP gene. Cross-reactivity was tested using the DNA of other parasites and bacteria.

Results

According to the results, the analytical sensitivity of the “Rapid-Crypto Colorimetric LAMP test” was found as 1 copy plasmid/reaction. When the results were compared with the Real-Time PCR test, the sensitivity of the “Rapid-Crypto Colorimetric LAMP test” was 100% and the specificity was 97.4%. The test did not cross-react with other parasites and bacteria.  

Conclusion

The “Rapid-Crypto Colorimetric LAMP test” developed in this study provides an advantage in the diagnosis of Cryptosporidium spp. in calf stool samples since it can be applied in basic laboratories or in the field, does not require experienced personnel, and has high sensitivity. Moreover, diagnosis can be made with the naked eye without using any device.
Home-based exercise interventions’ impact on breast cancer survivors’ functional performance: a systematic review
Authors: Ramos Pedro G.F. , Júdice Pedro B. , Nobre Inês , Carraça Eliana V.
Published: February 2024

Introduction

Home-based exercise (HBE) programs can be a feasible strategy to enhance functional performance and promote physical activity (PA) in breast cancer survivors. A deeper analysis of the effects of HBE interventions, structured by HBE program type and treatment phase, is needed. This systematic review aimed to synthesize the evidence on HBE interventions’ impact on breast cancer survivors’ functional performance, PA levels, and program adherence rates, according to HBE intervention type and treatment phase.

Methods

A comprehensive search of peer-reviewed articles reporting HBE interventions’ effects on the outcomes of interest was performed in Pubmed, Google Scholar, EBSCO, Web of Science, Science Direct, and B-ON until January 15th, 2024. Data were synthesized according to Denton’s domains to classify HBE interventions (prescription: structured vs. unstructured; Delivery method: supervised vs. facilitated vs. unsupervised) and treatment phase. Methodological quality appraisal was performed using the Effective Public Health Practice Project tool.

Results

Twenty-six studies were included. Most studies conducted structured/facilitated interventions and reported positive effects on functional performance (particularly aerobic capacity), increases in PA levels, and high adherence rates (> 70%) during and post-treatment.

Conclusion

HBE interventions may be feasible to improve functional performance and promote physical activity among breast cancer survivors. Further studies are needed to confirm which HBE intervention type is more appropriate for each treatment phase. More evidence applying HBE interventions with different designs is required to allow the drawing of more solid conclusions. Studies exploring the effects of HBE interventions on the pre-treatment phase are needed.
Self-care advice for patients after surgery for oesophageal cancer — a mixed-methods systematic review
Authors: Schandl Anna , Färnqvist Kenneth , Mälberg Kalle , Nielsen Sandra , Lagergren Pernilla
Published: February 2024

Purpose

The aim of the literature review was to identify and synthesise research on self-care advice for oesophageal cancer survivors.

Methods

A mixed-methods systematic review and synthesis of existing literature on the topic. Five databases were searched for studies providing information on self-care advice for survivorship after oesophageal cancer surgery, in English, with no time filter. The Critical Appraisal Skills Program was used to assess the risk of bias. Data were presented by textual descriptions and grouping of data.

Results

Among the 13 studies included in the review, five pieces of self-care advice were identified; reconstructing eating habits, bed-head elevation, health-promoting advice, monitoring symptoms and body functions, and involving family and friends. The self-care advice was experienced to be hard work, but worth the effort. They also provided reassurance and an increased understanding of bodily changes and social consequences of the disease and treatment.

Conclusions

There are is little evidence-based self-care advice for oesophageal cancer survivors. However, the existing self-care advice was appreciated and contributed to an increased understanding of the situation. Comprehensible and easy-to-follow recommendations should be provided to all oesophageal cancer survivors.

Implications for Cancer Survivors

Evidence-based self-care advice helpful for the individual oesophageal cancer survivor may be imperative to cope with the consequences of oesophagectomy after hospital discharge.
Die zirkadiane Uhr und das Verhalten
Authors: Ripperger Jürgen A. , Albrecht Urs
Published: February 2024

Most organisms have evolved an internal clock to predict daily recurring events. This clock with a period of about 24 hours, termed circadian clock, allows organisms to organize biochemical and physiological processes over one day. Changes in lighting conditions as they occur naturally over seasons or man-made by jet lag or shift work, change sleep phase in order to synchronize an organism’s physiology to the environment. A misalignment results in sleep disturbance and mood disorders. Here we discuss how we study various body clocks in mice to understand their synchronization avoiding development of disease.
Strukturbiologie der systemischen Amyloidosen
Authors: Haupt Christian , Schmidt Matthias , Fändrich Marcus
Published: February 2024

Systemic amyloidosis refers to a group of diseases that are caused by the misfolding of proteins and their deposition as amyloid fibrils in various organs. Here we present an overview of the progress made in the understanding of the biochemical and structural characteristics of the pathogenic agents of these diseases, obtained by using cryo-electron microscopy. The observed structures provided insights in the molecular etiology of the diseases and helped to shed light on the mechanism of misfolding in the affected patients.
Genetic Engineering von Mikroalgen für eine nachhaltige Zukunft
Authors: Hallmann Armin
Published: February 2024

The significance of microalgae biotechnology is rising in many fields, including the food, pharmaceutical, nutraceutical, cosmetic, feed, and energy industries. Microalgae can also be genetically modified to give them additional traits and produce substances that are not typically seen in algae. Rapid advances in “omics” technologies and the availability of a variety of molecular tools have been the driving forces behind advancements in genetic engineering of microalgae for a sustainable future.
Virusähnliche Partikel – Impfstoffe, die den Eindringling imitieren
Authors: Klausberger Miriam , Satzer Peter , Aguilar Patricia Pereira
Published: February 2024

Virus-like particle vaccines have emerged as a promising and innovative approach to combat infectious diseases. Despite their immense potential as platform technology, challenges related to their production process need to be addressed to harness their full capabilities and make them widely assessible for human application.
Algorithms Don’t Have A Future: On the Relation of Judgement and Calculation
Authors: Stader Daniel
Published: February 2024

This paper is about the opposite of judgement and calculation. This opposition has been a traditional anchor of critiques concerned with the rise of AI decision making over human judgement. Contrary to these approaches, it is argued that human judgement is not and cannot be replaced by calculation, but that it is human judgement that contextualises computational structures and gives them meaning and purpose. The article focuses on the epistemic structure of algorithms and artificial neural networks to find that they always depend on human judgement to be related to real life objects or purposes. By introducing the philosophical concept of judgement, it becomes clear that the property of judgement to provide meaning and purposiveness is based on the temporality of human life and the ambiguity of language, which quantitative processes lack. A juxtaposition shows that calculations and clustering can be used and referred to in more or less prejudiced and reflecting as well as opaque and transparent ways, but thereby always depend on human judgement. The paper clearly asserts that the transparency of AI is necessary for their autonomous use. This transparency requires the explicitness of the judgements that constitute these computational structures, thereby creating an awareness of the conditionality of such epistemic entities.