bluuebunny/crossref_metadata_2025 huggingface dataset:
The maximal and current accuracy of rigorous protein-ligand binding free energy calculations
Authors: Ross Gregory A. , Lu Chao , Scarabelli Guido , Albanese Steven K. , Houang Evelyne , Abel Robert , Harder Edward D. , Wang Lingle
Published: October 2023

Computational techniques can speed up the identification of hits and accelerate the development of candidate molecules for drug discovery. Among techniques for predicting relative binding affinities, the most consistently accurate is free energy perturbation (FEP), a class of rigorous physics-based methods. However, uncertainty remains about how accurate FEP is and can ever be. Here, we present what we believe to be the largest publicly available dataset of proteins and congeneric series of small molecules, and assess the accuracy of the leading FEP workflow. To ascertain the limit of achievable accuracy, we also survey the reproducibility of experimental relative affinity measurements. We find a wide variability in experimental accuracy and a correspondence between binding and functional assays. When careful preparation of protein and ligand structures is undertaken, FEP can achieve accuracy comparable to experimental reproducibility. Throughout, we highlight reliable protocols that can help maximize the accuracy of FEP in prospective studies.
Ab-initio simulations of coherent phonon-induced pumping of carriers in zirconium pentatelluride
Authors: Jiang Tao , Orth Peter P. , Luo Liang , Wang Lin-Lin , Zhang Feng , Wang Cai-Zhuang , Zhao Jin , Ho Kai-Ming , Wang Jigang , Yao Yong-Xin
Published: October 2023

Laser-driven coherent phonons can act as modulated strain fields and modify the adiabatic ground state topology of quantum materials. Here we use time-dependent first-principles and effective model calculations to simulate the effect of the coherent phonon induced by strong terahertz electric field on electronic carriers in the topological insulator ZrTe5. We show that a coherentA1gRaman mode modulation can effectively pump carriers across the band gap, even though the phonon energy is about an order of magnitude smaller than the equilibrium band gap. We reveal the microscopic mechanism of this effect which occurs via Landau–Zener-Stückelberg tunneling of Bloch electrons in a narrow region in the Brillouin zone center where the transient energy gap closes when the system switches from strong to weak topological insulator. The quantum dynamics simulation results are in excellent agreement with recent pump-probe experiments in ZrTe5at low temperature.
The autoregressive neural network architecture of the Boltzmann distribution of pairwise interacting spins systems
Authors: Biazzo Indaco
Published: October 2023

Autoregressive Neural Networks (ARNNs) have shown exceptional results in generation tasks across image, language, and scientific domains. Despite their success, ARNN architectures often operate as black boxes without a clear connection to underlying physics or statistical models. This research derives an exact mapping of the Boltzmann distribution of binary pairwise interacting systems in autoregressive form. The parameters of the ARNN are directly related to the Hamiltonian’s couplings and external fields, and commonly used structures like residual connections and recurrent architecture emerge from the derivation. This explicit formulation leverages statistical physics techniques to derive ARNNs for specific systems. Using the Curie–Weiss and Sherrington–Kirkpatrick models as examples, the proposed architectures show superior performance in replicating the associated Boltzmann distributions compared to commonly used designs. The findings foster a deeper connection between physical systems and neural network design, paving the way for tailored architectures and providing a physical lens to interpret existing ones.
Establishment of a transparent soil system to study Bacillus subtilis chemical ecology
Authors: Lozano-Andrade Carlos N , Nogueira Carla G , Henriksen Nathalie N S E , Wibowo Mario , Jarmusch Scott A , Kovács Ákos T
Published: October 2023

Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS, and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.
Motion of nanovehicles on pristine and vacancy-defected silicene: implications for controlled surface motion
Authors: Youzi Mehrdad , Kianezhad Mohammad , Vaezi Mehran , Nejat Pishkenari Hossein
Published: October 2023

Understanding the motion of surface-rolling nanomachines has attracted lots of attention in recent studies, due to their ability in carrying molecular payloads and nanomaterials on the surface.
Bandgap lowering in mixed alloys of Cs3Bi2−xSbxBr9 perovskite powders
Authors: Dai Siqi , Gan Xiaoyan , Li Kegui , Huang Qiang , Guo Liling , Liu Hanxing
Published: October 2023

Sb–Br perovskite alloys of Cs3Bi2−xSbxBr9 were synthesized and their crystal structures and optical bandgaps characterized by X-ray diffraction and UV-Vis spectroscopy. Electronic structures were calculated using DFT to gain a deeper understanding of the reasons for the variations in the bandgaps.
Interfacial chemistry and ion-transfer mechanism for a tailored poly(thioether)-enabled hybrid solid polymer electrolyte with electrochemical properties in all-solid-state lithium–sulfur batteries
Authors: Li Yuhan , Xi Kai , Ma Mingbo , Lu Shiyao , Wu Hu , Cao Xiaohan , Zhang Xinghong , Ding Shujiang
Published: October 2023

The solid polymer electrolyte we are introducing benefited from the synergy between polyethylene oxide and oligomer poly(thioether) plasticizer, which exhibits enhanced electrochemical, mechanical tensile and good thermochemical properties.
Node authentication and encrypted data transmission in mobile ad hoc network using the swarm intelligence‐based secure ad‐hoc on‐demand distance vector algorithm
Authors: Patil Anita R. , Borkar Gautam M.
Published: October 2023

In a mobile ad hoc network (MANET), all nodes are communicated with one another across wireless networks to create a temporary network without the support of centralised management. Due to dynamic topology in MANET, secure routing is a crucial issue. The existing secure routing protocol and their security concerns are analysed in this work. The suggested Swarm Intelligence‐based Secure Ad‐hoc On‐demand Distance Vector (SIS‐AODV) algorithm offers security by applying a secret key and hash mechanism to prevent the involvement of malicious nodes in routing operations. A secure routing system of MANET guards against internal and external network attacks. The proposed SIS‐AODV algorithm consists of two sections: the secret key value generated by applying Elliptical Curve Cryptography (ECC)‐based algorithm and the PRESENT algorithm to encrypt the data packets. Besides, authentication and non‐repudiation are applied using the H‐PRESENT 128 algorithm. The PRESENT algorithm and H‐PRESENT 128 hash function require less computational power. Centralised management is optional in this scheme, so overhead decreases. The second section of SIS‐AODV consists of Ant Colony Grey Wolf Optimization over the AODV algorithm to improve network performance while implementing a security algorithm over MANET. Analysis results show maximum performance with a packet delivery ratio of 98% and throughput of 85%. In addition, end‐to‐end delay is reduced by up to 25%, and routing overhead decreases by up to 20%. Keywords: AODV, Elliptical Curve, PRESENT, H‐PRESENT, Euclidean Algorithm, ACO, GWO, Blackhole attack.
Examination of the metallization behaviour of an ABS surface
Authors: Ünlü Büsra , Öz Yahya , Erdoğan Metehan , Karakaya İshak
Published: October 2023

The main scope of this work is the metallization of high density Acryonitrile Butadiene Styrene (ABS) surfaces for aerospace applications. Originality and main focused area of the study is to grasp the mechanism of physical properties of the surface and the effect of wet chemical processes on the surface of the ABS substrate. After surface sensitization and metallization with nano-sized ions, the polyurethane surface is metallized and nickel (Ni) coated with electroless and elecrolytic Ni plating processes. The ultimate goal of these advances is the production of composite lay-up tools for the production of primary and secondary composite aircraft parts from nanoscale to macro level. Composite lay-up tool requirements of the aerospace industry include a minimum thickness of 5 mm, acceptability of airtightness testing and reduced surface roughness. Results show that increasing current density adversely affects the surface morphology and metallization processes enhance the surface conductivity of the foam.
Performance of electrochemically deposited hydroxyapatite on textured 316L SS for applications in biomedicine
Authors: Health Royal Hermonson R. , Thanigaivelan R. , Kavya Vinod , Rathinasamy K. , Jagadeesha T.
Published: October 2023

This study investigates the biocompatibility of laser-textured 316L stainless steel (SS) coated with hydroxyapatite (HA) for orthopaedic implants. Powdered HA was electrochemically deposited on the laser-textured surface of 316L SS, and various tests were conducted on its surface to assess its biocompatibility. A particle size analyser was used to determine the average HA particle size, and a 3D optical profilometer was employed to characterise the surface roughness of the laser-textured samples. Contact angle measurement results provide insights into the wettability of the substrate. Microscopy tests revealed that, compared to those without HA coating, HA coatings on spherical dimpled textures exhibited better cell adherence. Among the tested samples, a sample with 98% laser energy input, 40.45° contact angle, and 75.976 µm HA coating thickness was found to be the most suitable for bone implantation.
Characterization of diterpene synthase genes in Brachypodium distachyon, a monocotyledonous model plant, provides evolutionary insight into their multiple homologs in cereals
Authors: Shimada Takeru , Minato Shiho , Hasegawa Yuto , Miyamoto Koji , Minato Yasumasa , Shenton Matthew R , Okada Kazunori , Kawaide Hiroshi , Toyomasu Tomonobu
Published: October 2023

Gibberellins are diterpenoid phytohormones that regulate plant growth, and are biosynthesized from a diterpene intermediate, ent-kaurene, which is produced from geranylgeranyl diphosphate via ent-copalyl diphosphate (ent-CDP). The successive 2 cyclization reactions are catalyzed by 2 distinct diterpene synthases, ent-CDP synthase (ent-CPS) and ent-kaurene synthase (KS). Various diterpene synthase genes involved in specialized metabolism were likely created through duplication and neofunctionalization of gibberellin-biosynthetic ent-CPS and KS genes in crops. Brachypodium distachyon is a monocotyledonous species that is a model plant in grasses. We herein found 1 ent-CPS gene homolog BdCPS and 4 tandemly arrayed KS-like genes BdKS1, KSL2, KSL3, and KSL4 in the B. distachyon genome, a simpler collection of paralogs than in crops. Phylogenetic and biochemical analyses showed that BdCPS and BdKS1 are responsible for gibberellin biosynthesis. BdKSL2 and BdKSL3 are suggested to be involved in specialized diterpenoid metabolism. Moreover, we restored KS activity of BdKSL2 through amino acid substitution.
PreHom-PCLM: protein remote homology detection by combing motifs and protein cubic language model
Authors: Shao Jiangyi , Zhang Qi , Yan Ke , Liu Bin
Published: October 2023

Protein remote homology detection is essential for structure prediction, function prediction, disease mechanism understanding, etc. The remote homology relationship depends on multiple protein properties, such as structural information and local sequence patterns. Previous studies have shown the challenges for predicting remote homology relationship by protein features at sequence level (e.g. position-specific score matrix). Protein motifs have been used in structure and function analysis due to their unique sequence patterns and implied structural information. Therefore, designing a usable architecture to fuse multiple protein properties based on motifs is urgently needed to improve protein remote homology detection performance. To make full use of the characteristics of motifs, we employed the language model called the protein cubic language model (PCLM). It combines multiple properties by constructing a motif-based neural network. Based on the PCLM, we proposed a predictor called PreHom-PCLM by extracting and fusing multiple motif features for protein remote homology detection. PreHom-PCLM outperforms the other state-of-the-art methods on the test set and independent test set. Experimental results further prove the effectiveness of multiple features fused by PreHom-PCLM for remote homology detection. Furthermore, the protein features derived from the PreHom-PCLM show strong discriminative power for proteins from different structural classes in the high-dimensional space. Availability and Implementation: http://bliulab.net/PreHom-PCLM.
JCcirc: circRNA full-length sequence assembly through integrated junction contigs
Authors: Zhang Jingjing , Zhang Huiling , Ju Zhen , Peng Yin , Pan Yi , Xi Wenhui , Wei Yanjie
Published: October 2023

Recent studies have shed light on the potential of circular RNA (circRNA) as a biomarker for disease diagnosis and as a nucleic acid vaccine. The exploration of these functionalities requires correct circRNA full-length sequences; however, existing assembly tools can only correctly assemble some circRNAs, and their performance can be further improved. Here, we introduce a novel feature known as the junction contig (JC), which is an extension of the back-splice junction (BSJ). Leveraging the strengths of both BSJ and JC, we present a novel method called JCcirc (https://github.com/cbbzhang/JCcirc). It enables efficient reconstruction of all types of circRNA full-length sequences and their alternative isoforms using splice graphs and fragment coverage. Our findings demonstrate the superiority of JCcirc over existing methods on human simulation datasets, and its average F1 score surpasses CircAST by 0.40 and outperforms both CIRI-full and circRNAfull by 0.13. For circRNAs below 400 bp, 400–800 bp, 800 bp–1200 bp and above 1200 bp, the correct assembly rates are 0.13, 0.09, 0.04 and 0.03 higher, respectively, than those achieved by existing methods. Moreover, JCcirc also outperforms existing assembly tools on other five model species datasets and real sequencing datasets. These results show that JCcirc is a robust tool for accurately assembling circRNA full-length sequences, laying the foundation for the functional analysis of circRNAs.
One-year outcomes following operative or non-operative management of adhesional small bowel obstruction
Authors: Mortensen Marie R , Alouda Mohammad , Bond Zara , Burcharth Jakob , Finne Katrine F , Jensen Thomas K , Lolle Ida , Malik Talha , Ngo-Stuyt Loan , Nielsen Liv B J , Olausson Maria , Skovsen Anders P , Tolver Mette A , Smith Henry G
Published: October 2023

Background

A trial of initial non-operative management is recommended in stable patients with adhesional small bowel obstruction. However, recent retrospective studies have suggested that early operative management may be of benefit in reducing subsequent recurrences. This study aimed to compare recurrence rates and survival in patients with adhesional small bowel obstruction treated operatively or non-operatively.

Methods

This was a prospective cohort study conducted at six acute hospitals in Denmark, including consecutive patients admitted with adhesional small bowel obstruction over a 4-month interval. Patients were stratified into two groups according to their treatment (operative versus non-operative) and followed up for 1 year after their index admission. Primary outcomes were recurrence of small bowel obstruction and overall survival within 1 year of index admission.

Results

A total of 201 patients were included, 118 (58.7 per cent) of whom were treated operatively during their index admission. Patients undergoing operative treatment had significantly better 1-year recurrence-free survival compared with patients managed non-operatively (operative 92.5 per cent versus non-operative 66.6 per cent, P <0.001). However, when the length of index admission was taken into account, patients treated non-operatively spent significantly less time admitted to hospital in the first year (median 3 days non-operative versus 6 days operative, P <0.001). On multivariable analysis, operative treatment was associated with decreased risks of recurrence (HR 0.22 (95 per cent c.i. 0.10–0.48), P <0.001) but an increased all-cause mortality rate (HR 2.48 (95 per cent c.i. 1.13–5.46), P = 0.024).

Conclusion

Operative treatment of adhesional small bowel obstruction is associated with reduced risks of recurrence but increased risk of death in the first year after admission.

Registration number

NCT04750811 (http://www.clinicaltrials.gov).prior (registration date: 11 February 2021).
Graded functional organization in the left inferior frontal gyrus: evidence from task-free and task-based functional connectivity
Authors: Diveica Veronica , Riedel Michael C , Salo Taylor , Laird Angela R , Jackson Rebecca L , Binney Richard J
Published: October 2023

The left inferior frontal gyrus has been ascribed key roles in numerous cognitive domains, such as language and executive function. However, its functional organization is unclear. Possibilities include a singular domain-general function, or multiple functions that can be mapped onto distinct subregions. Furthermore, spatial transition in function may be either abrupt or graded. The present study explored the topographical organization of the left inferior frontal gyrus using a bimodal data-driven approach. We extracted functional connectivity gradients from (i) resting-state fMRI time-series and (ii) coactivation patterns derived meta-analytically from heterogenous sets of task data. We then sought to characterize the functional connectivity differences underpinning these gradients with seed-based resting-state functional connectivity, meta-analytic coactivation modeling and functional decoding analyses. Both analytic approaches converged on graded functional connectivity changes along 2 main organizational axes. An anterior–posterior gradient shifted from being preferentially associated with high-level control networks (anterior functional connectivity) to being more tightly coupled with perceptually driven networks (posterior). A second dorsal–ventral axis was characterized by higher connectivity with domain-general control networks on one hand (dorsal functional connectivity), and with the semantic network, on the other (ventral). These results provide novel insights into an overarching graded functional organization of the functional connectivity that explains its role in multiple cognitive domains.
Prediction of misfolded proteins spreading in Alzheimer’s disease using machine learning and spreading models
Authors: Gherardini Luca , Zajdel Aleksandra , Pini Lorenzo , Crimi Alessandro
Published: October 2023

The pervasive impact of Alzheimer’s disease on aging society represents one of the main challenges at this time. Current investigations highlight 2 specific misfolded proteins in its development: Amyloid-$\beta$ and tau. Previous studies focused on spreading for misfolded proteins exploited simulations, which required several parameters to be empirically estimated. Here, we provide an alternative view based on 2 machine learning approaches which we compare with known simulation models. The first approach applies an autoregressive model constrained by structural connectivity, while the second is based on graph convolutional networks. The aim is to predict concentrations of Amyloid-$\beta$ 2 yr after a provided baseline. We also evaluate its real-world effectiveness and suitability by providing a web service for physicians and researchers. In experiments, the autoregressive model generally outperformed state-of-the-art models resulting in lower prediction errors. While it is important to note that a comprehensive prognostic plan cannot solely rely on amyloid beta concentrations, their prediction, achieved by the discussed approaches, can be valuable for planning therapies and other cures, especially when dealing with asymptomatic patients for whom novel therapies could prove effective.
Personalizing electrolytes in the dialysis prescription: what, why and how?
Authors: Dilaver R Gulsah , Ikizler T Alp
Published: October 2023

Maintenance hemodialysis patients suffer from multiple comorbidities and treatment-related complications. A personalized approach to hemodialysis prescription could reduce some of these burdens by preventing complications such as excessive changes in blood pressure, arrhythmias, post-dialysis fatigue and decreased quality of life. A patient-centered approach to dialysate electrolyte concentrations represents one such opportunity. In addition to modifications in dialysate electrolyte concentrations, consideration of individual factors such as patients’ serum concentrations, medication profiles, nutritional status and comorbidities is critical to tailoring hemodialysis prescriptions to optimize patient outcomes. The development of personalized dialysis treatment depends on the collection of comprehensive patient data, advances in technology, resource allocation and patient involvement in decision-making. This review discusses how the treatment of maintenance hemodialysis patients could benefit from individualized changes in certain dialysis fluid components.
Intraventricular haemodynamic changes caused by increased left ventricular afterload in re-coarctation of aorta: a case report
Authors: Shibagaki Yuki , Oka Hideharu , Nakau Kouichi , Takahashi Satoru
Published: October 2023

Background

Long-term re-coarctation of the aorta can cause aortic dilatation, hypertension, and cardiac dysfunction due to increased left ventricular (LV) afterload. It is difficult to detect changes in LV function due to increased afterload if the contractile force of the left ventricle is maintained. Herein, we have reported a case of re-coarctation of the aorta, for which four-dimensional (4D) flow magnetic resonance imaging (MRI) scan was obtained both before and after balloon dilatation for aortic re-coarctation. Ultimately, improvement in aortic helical flow and LV haemodynamics was observed.

Case summary

A 29-year-old female was diagnosed with coarctation of the aorta and a bicuspid aortic valve after birth and underwent surgery at 1 month. At 8 years of age, she underwent balloon dilatation for re-coarctation. At the age of 28 years, she was diagnosed with re-coarctation triggered by hypertension. She underwent balloon dilatation as her cardiac catheterization revealed a systolic pressure gradient of 40 mmHg. Pretreatment 4D flow MRI demonstrated helical flow in the ascending aorta and descending thoracic aorta and LV blood flow analysis revealed a decrease in LV kinetic energy during systole; these improved after treatment.

Discussion

The use of helical flow evaluation by 4D flow MRI for aortic re-coarctation is well known in clinical practice. However, our report is the first to evaluate intraventricular blood flow before and after the re-coarctation treatment. The MRI evaluation demonstrated that the helical flow and LV blood flow distribution improved after re-coarctation treatment due to the reduction of afterload.
Understanding the conditions included in data-driven patterns of multimorbidity: a scoping review
Authors: Sukumaran Luxsena , Winston Alan , Sabin Caroline A
Published: October 2023

Background

Despite the growing utilization of data-driven methods to investigate multimorbidity patterns, there is currently no consensus or guidance on the conditions to include when identifying patterns. This scoping review aims to systematically examine the nature of conditions included in existing studies using data-driven techniques.

Methods

A comprehensive search of three electronic databases (MEDLINE, Web of Science and Scopus) was conducted to identify relevant publications from inception to 28 February 2022 using predefined search terms and inclusion/exclusion criteria. The reference lists and citations of relevant papers were also searched.

Results

Among 7326 search results, 5444 relevant articles were identified. After screening against the eligibility criteria, 60 articles were included in the review. Half of the reviewed studies reported selection criteria for conditions, with prevalence in the population of interest being the most common criterion (40%). Most studies included at least one neurological [59 (98.3%)], musculoskeletal [58 (96.7%)], respiratory [57 (95.0%)] or mental health [56 (93.3%)] condition. In contrast, only a small proportion of studies included skin [17 (28.3%)], infections [14 (23.3%)] or autoimmune conditions [10 (16.7%)]. Nine conditions (hypertension, diabetes, cancer, arthritis, COPD, asthma, depression, stroke and osteoporosis) were included by more than half of the studies.

Conclusions

This review highlights the considerable heterogeneity among the conditions included in analyses of multimorbidity patterns. Researchers should provide a clear rationale for the selection of conditions to facilitate comparisons across studies and ensure reproducibility, as well as consider selecting a diverse range of conditions to capture the complexity of multimorbidity.
Effect of gum tragacanth–sodium alginate coatings incorporated with epigallocatechin gallate on the quality and shelf life of large yellow croaker (Larimichthys crocea) during superchilling storage
Authors: Xu Zhilong , Pei Juxin , Mei Jun , Yu Huijie , Chu Siyuan , Xie Jing
Published: October 2023

The effect of gum tragacanth (GT) and sodium alginate (SA) active coatings incorporated with epigallocatechin gallate (EGCG; 0.16%, 0.32%, and 0.64%, respectively) on the quality of large yellow croaker fillets was evaluated during superchilling storage at –3 ˚C for 42 d. The results revealed that the GT-SA-EGCG active coatings delayed microbial spoilage by reducing the total viable counts of Pseudomonas spp. and psychrophile bacteria and retarded the degradation of the physical properties of water-holding capacity, cooking loss, color, odor and texture. GT-SA-EGCG coatings could also maintain fillet freshness by maintaining lower total volatile basic nitrogen, K value, and histidine content, inhibiting myofibrillar protein degradation during superchilling storage. These results suggested that the active coatings embedded with GT-SA-EGCG could be used as a preservative to enhance the quality of large yellow croaker and prolong the shelf life by 7–14 d during superchilling storage at –3 ˚C.
Inhibitory effect of bilobalide on Staphylococcus aureus von Willebrand factor-binding protein and its therapeutic effect in mice with pneumonia
Authors: Hou Juan , Jiang Yijing , Xu Yangming , Zhao Chunhui , Cao Yali , Song Wu , Wang Bingmei
Published: October 2023

Aims

Disabling bacterial virulence with small molecules has been proposed as a potential strategy to prevent bacterial pathogenicity. The von Willebrand factor-binding protein of Staphylococcus aureus was identified previously as a key virulence determinant. Our objective was to discover a von Willebrand-factor binding protein (vWbp) inhibitor distinct from the antibiotics used to prevent infections resulting from S. aureus.

Methods and results

Using coagulation assays, we found that the sesquiterpene trilactone bilobalide blocks coagulation mediated by vWbp, but has no impact on the growth of S. aureus at a concentration of 128 μg ml−1. Moreover, a mouse model of pneumonia caused by S. aureus indicated that bilobalide could attenuate S. aureus virulence in vivo. This effect is achieved not by interfering with the expression of vWbp but by binding to vWbp, as demonstrated by western blotting, thermal shift assays, and fluorescence quenching assays. Using molecular dynamic simulations and point mutagenesis analysis, we identified that the Q17A and R453A residues are key residues for the binding of bilobalide to vWbp.

Conclusions

Overall, we tested the ability of bilobalide to inhibit S. aureus infections by targeting vWbp and explored the potential mechanism of this activity.
The effect of bone and analytical methods on the assessment of bone mineralization response to dietary phosphorus, phytase, and vitamin D in nursery pigs
Authors: Williams Hadley R , Chin Taylor E , Tokach Mike D , Woodworth Jason C , DeRouchey Joel M , Goodband Robert D , Bergstrom Jon R , Rahe Michael C , Siepker Christopher L , Sitthicharoenchai Panchan , Radke Scott L , Ensley Steve M , Gebhardt Jordan T
Published: October 2023

A total of 360 pigs (DNA 600 × 241, DNA; initially 11.9 ± 0.56 kg) were used in a 28-d trial to evaluate the effects of different bones and analytical methods on the assessment of bone mineralization response to dietary P, vitamin D, and phytase in nursery pigs. Pens of pigs (six pigs per pen) were randomized to six dietary treatments in a randomized complete block design with 10 pens per treatment. Dietary treatments were designed to create differences in bone mineralization and included: (1) 0.19% standardized total tract digestibility (STTD) P (deficient), (2) 0.33% STTD P (NRC [2012] requirement) using monocalcium phosphate, (3) 0.33% STTD P including 0.14% release from phytase (Ronozyme HiPhos 2700, DSM Nutritional Products, Parsippany, NJ), (4) 0.44% STTD P using monocalcium phosphate, phytase, and no vitamin D, (5) diet 4 with vitamin D (1,653 IU/kg), and (6) diet 5 with an additional 50 µg/kg of 25(OH)D3 (HyD, DSM Nutritional Products, Parsippany, NJ) estimated to provide an additional 2,000 IU/kg of vitamin D3. After 28 d on feed, eight pigs per treatment were euthanized for bone (metacarpal, 2nd rib, 10th rib, and fibula), blood, and urine analysis. The response to treatment for bone density and ash was dependent upon the bone analyzed (treatment × bone interaction for bone density, P = 0.044; non-defatted bone ash, P = 0.060; defatted bone ash, P = 0.068). Thus, the response related to dietary treatment differed depending on which bone (metacarpal, fibula, 2nd rib, or 10th rib) was measured. Pigs fed 0.19% STTD P had decreased (P < 0.05) bone density and ash (non-defatted and defatted) for all bones compared to 0.44% STTD P, with 0.33% STTD P generally intermediate or similar to 0.44% STTD P. Pigs fed 0.44% STTD P with no vitamin D had greater (P < 0.05) non-defatted fibula ash compared to all treatments other than 0.44% STTD P with added 25(OH)D3. Pigs fed diets with 0.44% STTD P had greater (P < 0.05) defatted second rib ash compared to pigs fed 0.19% STTD P or 0.33% STTD P with no phytase. In summary, bone density and ash responses varied depending on bone analyzed. Differences in bone density and ash in response to P and vitamin D were most apparent with fibulas and second ribs. There were apparent differences in the bone ash percentage between defatted and non-defatted bone. However, differences between the treatments remain consistent regardless of the analytic procedure. For histopathology, 10th ribs were more sensitive than 2nd ribs or fibulas for the detection of lesions.
Operative Innovation and Surgical Conservatism in Twentieth-Century Ulcer Surgery
Authors: Crenner Christopher
Published: October 2023

Peptic ulcers were a common, and seemingly intractable, problem for surgeons in the US through the early twentieth century. Initial surgical efforts reduced operative mortality and achieved short term successes but failed to establish a definitive solution. The flawed successes of early ulcer surgery drove sustained effort to improve, producing a stream of novel operations over the decades. An examination of the history of ulcer surgery confirms the recent observation that surgical operations of this period were malleable entities subject to constant tinkering and repurposing. Yet, this dynamism in surgical practice remained in tension with conservative pressures, as surgeons hung on to familiar practices and sought to codify agreement on which operation served best for which purpose. Ulcer surgery became a workshop for attempts to resolve this tension. In this context, a canon of recognized operations emerged that accommodated novelties while preserving in surgical discourse an awareness of older operations. Established operations that fell from use literally remained on the books for decades. This compromise between innovation and operative conservatism favored the creative reuse of older ulcer operations, some repurposed, and some combined with other operations in new modular configurations. Ulcer surgery demonstrated recurring patterns of operative repurposing, reconfiguration, and modular recombination. This feature of twentieth-century ulcer surgery also highlights the attachment in modern surgical culture to the historicity of their endeavor, manifested for example in the wide use of eponyms and a fondness for deep genealogies of mentoring and training.
Amoxicillin treatment of pneumococcal pneumonia impacts bone marrow neutrophil maturation and function
Authors: Mondemé Mélanie , Zeroual Yasmine , Soulard Daphnée , Hennart Benjamin , Beury Delphine , Saliou Jean-Michel , Carnoy Christophe , Sirard Jean-Claude , Faveeuw Christelle
Published: October 2023

Pneumonia caused by Streptococcus pneumoniae is a leading cause of death worldwide. A growing body of evidence indicates that the successful treatment of bacterial infections results from synergy between antibiotic-mediated direct antibacterial activity and the host's immune defenses. However, the mechanisms underlying the protective immune responses induced by amoxicillin, a β-lactam antibiotic used as the first-line treatment of S. pneumoniae infections, have not been characterized. A better understanding of amoxicillin's effects on host-pathogen interactions might facilitate the development of other treatment options. Given the crucial role of neutrophils in the control of S. pneumoniae infections, we decided to investigate amoxicillin's impact on neutrophil development in a mouse model of pneumococcal superinfection. A single therapeutic dose of amoxicillin almost completely eradicated the bacteria and prevented local and systemic inflammatory responses. Interestingly, in this context, amoxicillin treatment did not impair the emergency granulopoiesis triggered in the bone marrow by S. pneumoniae. Importantly, treatment of pneumonia with amoxicillin was associated with a greater mature neutrophil count in the bone marrow; these neutrophils had specific transcriptomic and proteomic profiles. Furthermore, amoxicillin-conditioned, mature neutrophils in the bone marrow had a less activated phenotype and might be rapidly mobilized in peripheral tissues in response to systemic inflammation. Thus, by revealing a novel effect of amoxicillin on the development and functions of bone marrow neutrophils during S. pneumoniae pneumonia, our findings provide new insights into the impact of amoxicillin treatment on host immune responses.
Prevalence of pelvic pain in transgender individuals on testosterone
Authors: Grimstad Frances W , Boskey Elizabeth R , Clark Rachael S , Ferrando Cecile A
Published: October 2023

Background

Pelvic pain has been reported in transmasculine individuals taking testosterone. There is a need for further investigation to increase understanding of the prevalence and risk factors of this pain.

Aim

We sought to determine the prevalence of pelvic pain reported by transmasculine individuals who had both a uterus and ovaries and were taking testosterone.

Methods

We conducted an institutional review board–approved retrospective study of all transmasculine individuals who had been taking testosterone for at least 1 year and had a uterus and ovaries at the time of testosterone initiation. Charts of participating patients were reviewed to determine patient characteristics, testosterone use, and pelvic pain symptoms both before and after initiation of testosterone.

Outcomes

Patients reported experiences of pelvic pain while on testosterone.

Results

Of 280 individuals who had been on testosterone for at least 1 year, 100 (36%) experienced pelvic pain while on testosterone. Of those patients, 71% (n = 71) had not experienced pelvic pain prior to starting testosterone. There were 42 patients (15%) who had pelvic pain prior to starting testosterone, 13 (31%) of whom no longer experienced pain once starting testosterone. The median (IQR) age at initiation of testosterone was 22 (19-41) years and duration of testosterone treatment was 48 (27-251) months.

Those patients who experienced pelvic pain while on testosterone were significantly more likely to have also reported pelvic pain prior to starting testosterone (29% vs 7%, P < .001). These patients were also more likely to have a pre-existing diagnosis of dysmenorrhea (27% vs 7%, P < .001), endometriosis (6% vs 2%, P = .049), or ovarian cysts and/or masses (12% vs 2% P < .001). Patients with pelvic pain were also more likely to have been on a menstrual suppression agent prior to and overlapping testosterone initiation (22% vs 12%, P = .03) and to have used menstrual suppression for longer durations (median [IQR] 18 [6-44] vs 8 [4-15] months, P = .04).

Clinical Implications

Pelvic pain is common in transmasculine individuals who are initiating testosterone treatment, although testosterone has both positive and negative effects on pelvic pain in different individuals.

Strengths and Limitations

The major strengths of this study included large numbers of patients, ability to assess for documentation of pelvic pain prior to testosterone, and ability to determine an actual prevalence of pelvic pain. Major limitations included the study being a retrospective analysis in a single tertiary care center, the limitations of clinical documentation, and the lack of a standard pelvic pain evaluation process.

Conclusion

More than one-third of transmasculine patients with a uterus and ovaries had pelvic pain while on testosterone, with the majority reporting onset of pain after initiating testosterone.
Erskine Nicol and the representation of national and religious identities in nineteenth-century Ireland
Authors: NicGhabhann Niamh
Published: October 2023

This article investigates the visual representation of Irish Catholicism in mid-nineteenth century genre painting through a close analysis of St Patrick’s Day (1856), a picturesque genre painting by the Scottish artist Erskine Nicol. In doing so, it will explore why artists like Nicol, Frederic William Burton and others chose to equate Irish rural Catholicism with romantic ideas of nature and outdoor ‘primitive’ worship. This tradition of representation will be examined in the context of contemporary Catholic institutional expansion across Ireland following the removal of the legal disabilities known as the ‘penal laws’ in 1829, and the parallel emphasis on the church building as the location of worship, the sacraments, and Catholic devotional life.

To date, scholars of Nicol’s oeuvre have tended to focus on Nicol’s representation of an Irish national ‘type’ or ‘character’. My reading of Nicol’s St Patrick’s Day, however, aims to extend the art historical investigation of the signification of the Irish stereotype in Victorian painting, and to examine Nicol’s painting within the interwoven frameworks of national identity and religious identity. This analysis of St Patrick’s Day is rooted in a consideration of both genre and historical context, facilitating new insights into ideas of ‘peasant’ or ‘primitive’ Catholicism as central to mid-Victorian representations of the Irish ‘national character’.
The gain-of-function mutation blf13 in the barley orthologue of the rice growth regulator NARROW LEAF1 is associated with increased leaf width
Authors: Jöst Moritz , Soltani Ouad , Kappel Christian , Janiak Agnieszka , Chmielewska Beata , Szurman-Zubrzycka Miriam , McKim Sarah M , Lenhard Michael
Published: October 2023

Canopy architecture in cereals plays an important role in determining yield. Leaf width represents one key aspect of this canopy architecture. However, our understanding of leaf width control in cereals remains incomplete. Classical mutagenesis studies in barely identified multiple morphological mutants, including those with differing leaf widths. Of these, we characterized the broad leaf13 (blf13) mutant in detail. Mutant plants form wider leaves due to increased post-initiation growth and cell proliferation. The mutant phenotype perfectly co-segregated with a missense mutation in the HvHNT1 gene which affected a highly conserved region of the encoded protein, orthologous to the rice NARROW LEAF1 (NAL1) protein. Causality of this mutation for the blf13 phenotype is further supported by correlative transcriptomic analyses and protein–protein interaction studies showing that the mutant HvNHT1 protein interacts more strongly with a known interactor than wild-type HvHNT1. The mutant HvHNT1 protein also showed stronger homodimerization compared with wild-type HvHNT1, and homology modelling suggested an additional interaction site between HvHNT1 monomers due to the blf13 mutation. Thus, the blf13 mutation parallels known gain-of-function NAL1 alleles in rice that increase leaf width and grain yield, suggesting that the blf13 mutation may have a similar agronomic potential in barley.
Efficacy of a membrane concentration method combined with real-time PCR for detection of Giardia and Cryptosporidium in drinking water
Authors: Jingyi Jiang , Ping Yao , Jian Xu , Jia Chen , Xujian Mao , Qiong Li , Bowen Tu , Fengming Wang
Published: October 2023

The occurrence of Giardia and Cryptosporidium (oo)cysts in drinking source water poses a serious public health risk. Here, we established a method that combines membrane concentration and real-time polymerase chain reaction (PCR) to quantify Giardia and Cryptosporidium in drinking water. The water samples were filtered through a cellulose membrane to collect Giardia and Cryptosporidium, and then nucleic acids were extracted. Specific primers and probes were designed and synthesized according to the gph gene sequence of Giardia and 18S rRNA gene sequence of Cryptosporidium. The concentrations of the two targets were determined using real-time PCR technology. The sensitivity, specificity, and stability of the method were evaluated. Our findings revealed that the detection limits of real-time PCR method for detecting Giardia and Cryptosporidium were 0.926 and 0.65 copy/µL, respectively; the spiked recovery rates were above 60% and 38%, respectively, and relative standard deviations were under 0.95% and 2.26%, respectively. Therefore, this effective procedure based on the membrane concentration method and real-time PCR will be useful for detecting Giardia and Cryptosporidium in drinking water for purpose of continuous environmental monitoring.
Constraining the FRB mechanism from scintillation in the host galaxy
Authors: Kumar Pawan , Beniamini Paz , Gupta Om , Cordes James M
Published: October 2023

Most fast radio burst (FRB) models can be divided into two groups based on the distance of the radio emission region from the central engine. The first group of models, the so-called ‘nearby’ or magnetospheric models, invoke FRB emission at distances of 109 cm or less from the central engine, while the second ‘far-away’ models involve emission from distances of 1011 cm or greater. The lateral size for the emission region for the former class of models (≲107 cm) is much smaller than the second class of models (≳109 cm). We propose that an interstellar scattering screen in the host galaxy is well-suited to differentiate between the two classes of models, particularly based on the level of modulations in the observed intensity with frequency, in the regime of strong diffractive scintillation. This is because the diffractive length scale for the host galaxy’s interstellar medium scattering screen is expected to lie between the transverse emission-region sizes for the ‘nearby’ and the ‘far-away’ class of models. Determining the strength of flux modulation caused by scintillation (scintillation modulation index) across the scintillation bandwidth (∼1/2πδts) would provide a strong constraint on the FRB radiation mechanism when the scatter broadening (δts) is shown to be from the FRB host galaxy. The scaling of the scintillation bandwidth as ∼ν4.4 may make it easier to determine the modulation index at ≳ 1 GHz.
Cosmology from LOFAR Two-metre Sky Survey Data Release 2: angular clustering of radio sources
Authors: Hale C L , Schwarz D J , Best P N , Nakoneczny S J , Alonso D , Bacon D , Böhme L , Bhardwaj N , Bilicki M , Camera S , Heneka C S , Pashapour-Ahmadabadi M , Tiwari P , Zheng J , Duncan K J , Jarvis M J , Kondapally R , Magliocchetti M , Rottgering H J A , Shimwell T W
Published: October 2023

Covering $\sim 5600\, \deg ^2$ to rms sensitivities of ∼70−100 $\mu$Jy beam−1, the LOFAR Two-metre Sky Survey Data Release 2 (LoTSS-DR2) provides the largest low-frequency (∼150 MHz) radio catalogue to date, making it an excellent tool for large-area radio cosmology studies. In this work, we use LoTSS-DR2 sources to investigate the angular two-point correlation function of galaxies within the survey. We discuss systematics in the data and an improved methodology for generating random catalogues, compared to that used for LoTSS-DR1, before presenting the angular clustering for ∼900 000 sources ≥1.5 mJy and a peak signal-to-noise ≥ 7.5 across ∼80 per cent of the observed area. Using the clustering, we infer the bias assuming two evolutionary models. When fitting angular scales of $0.5 \le \theta \lt 5{^\circ }$, using a linear bias model, we find LoTSS-DR2 sources are biased tracers of the underlying matter, with a bias of $b_{\rm C}= 2.14^{+0.22}_{-0.20}$ (assuming constant bias) and $b_{\rm E}(z=0)= 1.79^{+0.15}_{-0.14}$ (for an evolving model, inversely proportional to the growth factor), corresponding to $b_{\rm E}= 2.81^{+0.24}_{-0.22}$ at the median redshift of our sample, assuming the LoTSS Deep Fields redshift distribution is representative of our data. This reduces to $b_{\rm C}= 2.02^{+0.17}_{-0.16}$ and $b_{\rm E}(z=0)= 1.67^{+0.12}_{-0.12}$ when allowing preferential redshift distributions from the Deep Fields to model our data. Whilst the clustering amplitude is slightly lower than LoTSS-DR1 (≥2 mJy), our study benefits from larger samples and improved redshift estimates.