bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrodynamic adjustment of mean flow and turbulence around a sinking boulder during local scouring
Authors: Ye Chen , Zhang Qing-Yu , Wang Xie-Kang , Lei Ming , Gomes Pattiyage , Yan Xu-Feng
Published: May 2024

The fact that on a live bed, boulders tend to sink during scouring is usually ignored, weakening the true understanding of hydrodynamics in boulder beds. In this paper, flume experiments were conducted to investigate the hydrodynamics around a boulder over a movable bed with a particle tracking velocimetry (PTV) system. By measuring the velocity field, the major flow characteristics, such as velocity distribution, turbulent kinetic energy (TKE) and bed shear stress, were analyzed. The results show that the sinking boulder apparently mediates the local flow structure and turbulence pattern. The near wake region is located in the range of 2D (D is the particle size of the boulder) downstream of the boulder. There is a near-bed countercurrent in the near-wake region, the TKE increase sharply, and the velocity distribution deviates from the logarithmic distribution. Compared with the flat bed, the turbulent kinetic energy extreme point of the boulder riverbed in the near wake area deviate from the bed surface to the water depth at the top of the boulder, and the direction reversal and extreme point appear at the top of the boulder. The bed shear stress increases sharply in the near-wake region of 1.5 ~ 2D.
RETRACTED: The Influence of Tobacco Use, Hazardous Drinking, and Other Risk Factors on HPV-Associated Oropharyngeal Cancer Risk and Screening Perceptions among Gay and Bisexual Men: A Cross-sectional Study
Authors: Zoschke I. Niles , Bennis Sarah L. , Tang Yi , Wilkerson J. Michael , Stull Cynthia L. , Nyitray Alan G. , Khariwala Samir S. , Nichols C. Mark , Rosser B. R. Simon , Flash Charlene , Ross Michael W.
Published: May 2024

The authors have requested that this preprint be removed from Research Square.
Parameter Optimization Methodology of Modular EIT System for Noninvasive Imaging
Authors: Sharma Vaishali , Goswami Mayank
Published: May 2024

This work presents an empirically obtained novel mutual relation between the hardware design and operating parameters, namely: (a) molarity of the coupling media, (b) scanning duration, (c) size of the object, and parameters defining the size of the scanning assembly (d) Number of electrodes, (e) the area of the vessel, and (f) the percentage periphery covered by the electrodes, affecting its performance. The expression suggests that by maintaining these six parameters within a specified range, it's anticipated that the reconstruction error can be limited to less than 10%. The minimum root mean square error between the experiment values and predicted values from the presented equation is 1.4053. Additionally, the parameter selection and optimization are done using the help of the obtained relation. The capability of discriminating Impedance profiles in recovery is around 73%. However, similar to other modalities, EITs’ performance depends on its hardware design, operating parameters and recovery algorithm. It is observed that scanning time significantly affects the recovery process compared to other optimizing parameters thus characterizing dynamically varying profile imaging. The accepted molarity value for the presented system is also found to be 0.5M.
Clinicopathological characteristics and outcome analysis of patients with double primary ovarian cancer and endometrial cancer
Authors: Li Fangyu , Guo Yongzhen , Zhang Xiwen , Dong Xing , Pei Xiaoyin , Ban Zhenying
Published: May 2024

Ovarian cancer (OC) and endometrial cancer (EC) are two female reproductive system tumors with high incidence rates. However, the clinicopathological characteristics of double primary OC and EC have been less studied. In this study, we aimed to identify some predictive and prognostic factors for synchronous endometrial and ovarian cancer (SEOC) by comparing survival outcomes between SEOC and single-primary OC patients.Clinical data were collected from 447 patients in the Surveillance, Epidemiology, and End Results (SEER) database who were diagnosed with OC as the first primary tumor and EC (8380/3, 8382/3, 8383/3) as the second primary tumor from 2010 to 2015. Survival outcome was estimated using Kaplan-Meier survival curves and compared using the log-rank test. Univariate and multivariate analyses were conducted utilizing COX models to identify their independent prognostic factors. A total of 447 SEOC patients and 20,769 single primary OC patients between 2010 and 2015 were included in this study. dual-primary group has more survival benefits than single-primary group. Age, marital status, histological typing, tumor size and tumor SEER stage and AJCC stage were independent factors affecting the prognosis of patients with double primary. Our study demonstrated that the clinicopathologic features of OC patients in the dual-primary group were young (43–55 years old), highly/moderately differentiated endometrioid ovarian cancer, and early-stage tumors. The prognosis of these patients was better than that of the single-primary group. These findings contribute to a better understanding of the differences between SEOC and single primary OC, and can help inform the development of more precise treatment guidelines to improve prognosis.
Patterns of male-female and male-male social bonds within Rwenzori Angolan colobus monkey core units
Authors: Adams Frances Victoria , Mujjuzi Edward , Teichroeb Julie Annette
Published: May 2024

Understanding the evolution of multilevel societies is important for elucidating our own social evolution. The Rwenzori Angolan colobus (Colobus angolensis ruwenzorii) multilevel society is unique in its high prevalence of multi-male/multi-female core units and rare occurrence of all-male units. However, little is known about male-male social behaviour within multi-male core units or how male-female bonds are distributed among the males. We used social network analysis to examine spatial-proximity networks for identifiable colobus within eight multi-male/multi-female core units at Nabugabo, Uganda. Over a 12-month period, we found variation in the structure of male-female relationships, showing one of three patterns; (1) one male was preferred by females while others remained peripheral to the network (N = 3 units), (2) males and females were divided into social clusters where each male monopolized the social relationships of two to three females (N = 2 units), (3) all males invested equally in their associations with females and more significantly in each other (N = 3 units). Importantly, each of these social structures showed evidence of strong male-male bonds. Pairing these data with co-residency and parallel dispersal data from five subsequent years showed that males with more equitable patterns of proximity to females stayed together significantly longer and transferred together more in the future. We conclude that the variation in social network structure between core units reflects different strategies used by males to access the benefits of group-living and defend resources, mates, and offspring. Our study demonstrates that male Rwenzori colobus form lasting bonds that can transcend multiple dispersals between units.
Unique continuation at the boundary for divergence form elliptic equations on quasiconvex domains
Authors: Cai Yingying
Published: May 2024

Let Ω ⊂ Rd be a quasiconvex Lipschitz domain and A(x) be a d × d uniformly eliiptic, symmetric matrix with Lipschitz coefficients. Assume nontrivial u solves −∇ · (A(x)∇u) = 0 in Ω, and u vanishes on Σ = ∂Ω ∩ B for some ball B. The main contribution of this paper is to demonstrate the existence of a countable collection of open balls (Bi)i such that the restriction of u to Bi ∩ Ω maintains a consistent sign. Furthermore, for any compact subset K of Σ, the set difference K\ Ui Bi is shown to possess a Minkowski dimension that is strictly less than d−1−ϵ. As a consequence, we prove Lin’s conjecture in quasiconvex domains.
Fever and Hypotension Vs. Frank Septic Shock: Elderly Patients Taking Vasodilators Who Present with Fever and Hypotension Have a Higher Incidence of Negative Blood Cultures. A Retrospective Analysis of 3,726 Patients.
Authors: Dumanis Guy , Vaisman Adva , Issawy Mariana , Gilboa Mayan , Zenilman Chava Landau , Itelman Edward , Segal Gad
Published: May 2024

Background. Septic shock is a leading cause of mortality. Yet, blood cultures are negative in many cases, questioning the diagnosis. In the quest for characterization of “culture negative septic shock”, the impact of chronic vasodilating medications was questioned.
Methods. This was a retrospective analysis of patients with vital signs compatible with septic shock (fever > 37.9 or < 36ºC and systolic blood pressure < 90 mmHg).
Results. The study included 3,726 patients (ages 65 to 90). Of these, 1,382 (37.1%) took chronic vasodilators. This group of patients had a lower rate of positive blood cultures compared to the group that did not receive vasodilators (28.5% vs. 32%; P = 0.026). They were older (median 80 vs. 78 years; P = 0.001), and their background included more cardiovascular diseases (P < 0.001). Their total length of hospital stay was shorter (median 4 vs. 6 days; P < 0.001) yet, they had a higher risk of in-hospital mortality (39% vs. 35.1%; P = 0.019). Taking chronic vasodilators was associated with decreased risk for bacteremia by 16% (P = 0.023). Older age, positive bacterial culture, and chronic vasodilation treatment were independently associated with increased risk for in-hospital mortality by 3% (P < 0.001), 36% (P < 0.001), and 21% (P = 0.009) respectively.
Conclusion. Chronic use of vasodilators amongst elderly patients presenting with fever and hypotension is associated with a higher incidence of negative blood cultures. We suggest these patients exhibit a combination of sepsis and shock rather than frank septic shock.
Association of eGFR slopes with Cardiorenal outcomes in Chronic kidney disease patients before and after Multidisciplinary education
Authors: Matsui Masaru , Kokubu Maiko , Nishimoto Masatoshi , Kosugi Takaaki , Eriguchi Masahiro , Samejima Ken-ichi , Tsuruya Kazuhiko
Published: May 2024

Multidisciplinary education has been shown to slow the progression of chronic kidney disease (CKD) and reduce cardiovascular (CV) risk, although its effects depend partly on patient characteristics. The aim of this study was to assess how patients categorized on the basis of estimated glomerular filtration rate (eGFR) responded to multidisciplinary education in terms of cardiorenal outcomes. In this retrospective cohort study, we included 447 CKD patients who received multidisciplinary education between January 1, 2013, and December 31, 2020, at Nara Prefecture General Medical Center. Exposure was four categories according to eGFR slopes before and after multidisciplinary education. The primary outcomes were renal events defined as the composite of dialysis initiation, transplantation, and 30% eGFR decline, and CV events defined as the composite of heart failure requiring hospitalization, coronary or leg revascularization, cardiac sudden death, and stroke. Multidisciplinary education decreased the median eGFR slope from − 5.00 to − 0.65 mL/min/1.73 m2/year. In fully adjusted models, the hazard ratios (95% confidence intervals) for total renal events relative to slow–slow eGFR decline were 1.02 (0.50–2.06) for fast–slow decline, 5.30 (2.82–9.97) for slow–fast decline, and 7.53 (4.02–14.1) for fast–fast decline. Only fast–fast eGFR decline was associated with a high risk of CV events. Subgroup analyses showed similar trends. Fast decline after education was independently associated with increased proteinuria and decreased hemoglobin levels. Fast eGFR decline after but not before multidisciplinary education was significantly associated with renal and CV events in CKD patients. Attention should be paid to CKD patients with limited benefit from multidisciplinary education.
Unveiling the Distinctive Mechanical and Thermal Properties of γ-GeSe
Authors: Park Jinsub , Je Yugyeong , Kim Joonho , Park Je Myoung , Jung Joong-Eon , Cheong Hyeonsik , Lee Sang Wook , Kim Kwanpyo
Published: May 2024

γ-GeSe is a newly identified polymorph among group-IV monochalcogenides, characterized by a distinctive interatomic bonding configuration. Despite its promising applications in electrical and thermal domains, the experimental verification of its mechanical and thermal properties remains unreported. Here, we experimentally characterize the in-plane Young’s modulus (E) and thermal conductivity (\(\kappa\)) of γ-GeSe. The mechanical vibrational modes of freestanding γ-GeSe flakes are measured using optical interferometry. Nano-indentation via atomic force microscopy is also conducted to induce mechanical deformation and to extract the E. Comparison with finite-element simulations reveals that the E is 97.3\(\pm\)7.5 GPa as determined by optical interferometry and 109.4\(\pm\)13.5 GPa as established through the nano-indentation method. Additionally, optothermal Raman spectroscopy reveals that γ-GeSe has a lattice thermal conductivity of 2.3\(\pm\)0.4 Wm−1K−1 and a total thermal conductivity of 7.5\(\pm\)0.4 Wm−1K−1 in the in-plane direction at room temperature. The notably high \(E/\kappa\) ratio in γ-GeSe, compared to other layered materials, underscores its distinctive structural and dynamic characteristics.
A Simulation Study for Optimal Pinhole Collimator Design in Gamma Camera Systems
Authors: Ghoneim M. A. , Elsharkawy Wafaa B.
Published: May 2024

A pinhole collimator was designed and simulated to achieve the desired level of resolution and sensitivity in a gamma camera by utilizing a CdTe semiconductor detector. To conduct this objective, a simulation toolkit based on the Geant4 Application for Tomographic Emission (GATE) was employed. The image capabilities of the proposed system were assessed by varying the magnification factor and pinhole diameter to estimate spatial resolution and sensitivity. Moreover, a hot rod phantom was designed to evaluate the system's overall imaging functionality. Results revealed that an increase in the pinhole diameter was correlated with an increase in sensitivity, while the spatial resolution was decreasing. There were distinct variations in sensitivity and spatial resolution depending on changes in the magnification factor as well. Finally, by analyzing trade-off curves, 1.38 ± 0.081 mm was approximately the optimal pinhole diameter for our proposed system.
The Positive Effect of Retirement Pensions on Mental Health in Older Adults A nationally representative cross-sectional survey
Authors: zuo xinyi , chen yifang
Published: May 2024

Background: Nowadays, there are 95 million people have symptoms of depression in China, and the rate of the old adults is 25.55%. Over the years, the Chinese government has introduced numerous social security programs including the social pension.Retirement pensions have been widely applied for older adults. To date, no evidence regarding the correlation between retirement pensions and depression in older adults in China has been published.
Objective: This cross-sectional survey aimed to examine the relationship between retirement pensions and depression in older people.
Methods: Province-level socioeconomic characteristics were merged with microdata for respondents over 60 years from the 2020 China Health and Retirement Longitudinal Study(CHARLS2020) Wave 5 (N = 8692). Respondents were asked if they were received retirement pension. Mental health was assessed using the 10-item Center for Epidemiological Studies Depression Scale. The chi-square test was used to explore whether retirement pensions were associated with mental health status. A binary logistic regression model was used to evaluate this association further after controlling for confounding factors.
Results: Overall, 81% (7039/8692) of the participants over 60 years had retirement pensions. Regression analyses revealed that older adults with retirement pensions (OR = 0.677, 95% CI: 0.563–0.815, p < .001) had a lower risk of depression than did those without retirement pensions. In addition, older adults who were female, single, illiterate, and living in rural areas, had 2 chronic diseases and had very poor self-related health(SRH) had a greater risk of depression. For province-level characteristics, older adults living in provinces in the first quartile of the number of beds per 10,000 persons in medical institutions were more likely to experience depressive symptoms, while there was no significant effect(OR = 0.822, 95% CI: 0.664–1.018, p = .072) (OR = 0.752, 95% CI: 0.594–0.953, p = .018)(OR = 0.877, 95% CI: 0.703–1.093, p = .242) of GDP on depression.
Conclusions: Retirement pensions had a positive effect on the mental health of older adults who participated in this study. Older adults with a retirement pension have a lower risk of depression than those without a retirement pension. However, the ownership rate of retirement pensions remains low among older Chinese people. Therefore, the retirement pension penetration rate should be a priority.
Study of Amino-Modified Resorcinol-Formaldehyde Aerogels for Odorous Gas Removal
Authors: Zhu Xingna , Liu Yuan , Wu Xueling , Wang Xiaodong , Zhang Zhihua , Shen Jun
Published: May 2024

When it comes to owning pets, pet odor is a major concern for many individuals. Ammonia (NH3) and hydrogen sulfide (H2S) are the primary odor components that have negative effects on human life. Therefore, there is an urgent need to develop a deodorizing material with high NH3 and H2S adsorption capacity. In this study, Resorcinol-formaldehyde (RF) aerogels containing amine groups (RF-Mx) were prepared using the sol-gel method and atmospheric pressure drying technique. Melamine was used as a modifier. The specific surface area of the modified aerogel was 119 m2/g with an average pore size of 12 nm when the melamine addition was 20%. The adsorption capacity of RF-M20 for odor was the highest (NH3: 593.8 mg/g, H2S: 640 mg/g), which was significantly superior to the unmodified sample. In addition, the adsorption capacity of RF-M20 for H2S exceeded that of commercial activated carbon. The results concluded that the introduction of amine groups and the higher microporous specific surface area benefited the chemical and physical adsorption of gases, effectively improving the adsorbent's capacity to capture NH3 and H2S. The preparation method is not only efficient in enhancing the odor adsorption capacity but also simple and cost-effective to operate, showing promising potential for industrial applications.
Application of water pollution virtual disposal cost approach for environmental damage value quantification of oil removal and cleaning wastewater.
Authors: Zhang Yuxuan , Liu Yunfang , Hong Wei , Wen Jing , Hua Feng , Liu Wenhua , Wang Zhen
Published: May 2024

Many countries’ laws stipulate compensation from responsible parties for environmental damage events, while the amount of environmental damage is commonly determined through environmental damage valuation. For cases where the environmental damage facts are unclear, or the ecological environment has naturally recovered, or the cost of restoration projects far exceeds their benefits, China implemented Technical Guidelines for Identification and Assessment of Ecological Environment Damage Part 2: Water Pollution Virtual Disposal Cost Approach (GB/T 39793.2–2020) in 2021, using the water pollution virtual disposal cost approach to calculate the amount of damage to surface water environments. However, problems such as inconsistent scope of application, inaccurate calculation of unit treatment costs, and biased parameter selection still exist in current practical applications. Therefore, this study, based on GB/T 39793.2–2020, combined with a case of illegal discharge of oil removal and cleaning wastewater, illustrated how to avoid common mistakes in the application of the water pollution virtual disposal cost approach and calculated the amount of environmental damage, providing a new method for calculating unit treatment costs. The results showed that the unit treatment cost of oil removal and cleaning wastewater was around 74.1 yuan/ton, and the environmental damage caused by the illegal discharge of oil removal and cleaning wastewater amounted to 186031.8 yuan. This study will advance the research progress of the virtual disposal cost approach for water pollution and provide crucial technical references for future ecological environment damage assessment.
Association Between Physical Activity, Performance Scores, and Clinical Trial Enrollment in Cancer Survivors
Authors: Maslana Kelsey E , Burns Ryan D , Estabrooks Paul A , Playdon Mary C , Shaw Janet M , Akerley Wallace , Coletta Adriana M
Published: May 2024

To investigate the association between patient-reported habitual physical activity (PA) and physician-assessed physical performance scores, specifically the Eastern Cooperative Oncology Group (ECOG) score, and experimental therapeutic clinical trial enrollment in adult cancer survivors. This was a retrospective analysis of patient-reported and clinical cancer data from the Total Cancer Care (TCC) cohort at the Huntsman Cancer Institute between 2016 and 2022. Patients completed a modified Godin questionnaire to assess average weekly PA (METhrs/week) for the previous 12 months. A demographics questionnaire collected information on sex, race, ethnicity, education level, and income status. ECOG performance scores were retrieved from the medical record and classified as either “Good” (ECOG of 0 or 1) or “Poor” (ECOG of 2, 3 or 4) physical function. Binary logistic regressions were used to assess the relationship between PA levels (total PA, moderate-vigorous PA, and light PA) and ECOG ratings, and PA levels and clinical trial enrollment (yes/no). Models were adjusted for demographics and cancer characteristics. Patients who completed the TCC questionnaire packet (n = 603) were primarily female (51%), non-Hispanic (95%), white (95%) with an average age of 61.9 ± 15.5 years. The top three cancer types represented were Head and Neck (30%), Thyroid (24%), and Lung (24%); all cancer stages were represented. Higher PA levels were linked with increased odds of having a good ECOG rating in unadjusted models (OR 1.01, 95% CI 1.00 to 1.02), but not in adjusted models (OR 1.01, 95% CI .99 to 1.03). Higher levels of light PA were linked with greater odds of having good ECOG rating in unadjusted and adjusted models (OR 1.05, 95% CI 1.00 to 1.11; OR 1.072, 95% CI 1.01 to 1.13; respectively). Statistically significant associations were not observed between moderate-vigorous PA and ECOG rating, and PA and clinical trial enrollment. Patient-reported light PA may serve utility in physician decision making of ECOG rating. More work is needed identifying patient centered subjective and objective tools to complement physician-assessed ECOG scores considering the implications of ECOG in cancer treatment decisions and eligibility for clinical trials.
ALZET pump implantation in mice for chronic drug delivery to the cochlea
Authors: Depreux Frederic , Whitlon Donna , Richter Claus-Peter
Published: May 2024

Drugs, chemical compounds, and other elements are often delivered to the ears of experimental animals to manipulate cochlear function, study how the ear works, identify drugs that prevent hearing loss, and test for ototoxicity. Delivery procedures for acute studies have been described in the literature. However, detailed information on methods that allow weeks of continuous drug delivery to mice cochleae is sparse. This paper describes a method for chronic drug delivery to the mouse cochlea. We illustrate the steps for the surgical implantation of an ALZET infusion pump and the placement of its catheter. We propose a ventral approach to the cochlea, using a surgical laser to make the cochleostomy and the placement of the pumps’ delivery ports into scala tympani or scala vestibuli. Depending on the experimental questions to be tested, the catheter can be directed toward the cochlear base, the vestibular system, or the cochlear apex.
Analysis of differential expression and functional annotation of non-coding RNAs in the blood transcriptome of male and female Yangtze finless porpoise (Neophocaena asiaeorientalis)
Authors: Que Jianglong , Liu Fangning , Yu Jinxiang , Dai Yingen , Chen Shiwei , Huang Yi , Tian Zhen , Rao Rongcheng , Min Jianlin , Yang Ying
Published: May 2024

The Yangtze finless porpoise (Neophocaena asiaeorientalis, YFP) is the only extant cetacean in the Yangtze River, and is listed as critically endangered species in the IUCN Red List. There are significant differences in growth and development between male and female YFPs. In order to reveal the potential mechanism of non-coding RNA (ncRNA) involved in this phenomenon, this study took female and male YFP blood as experimental samples, built a database for RNA transcriptome sequencing, and detected ncRNA gene expression profiles such as circRNA, miRNA and lncRNA, and screened differentially expressed genes (DEGs), and performed GO and KEGG functional annotation analysis on DEGs. A total of 205 differentially expressed circRNAs were detected, 87 up-regulated and 118 down-regulated in female YFPs, and the enriched items mainly included energy metabolism and nutritional development of nerves. There were 122 differentially expressed lncRNAs, 54 up-regulated and 68 down-regulated in female YFPs, and the enriched items mainly included heme synthesis and metabolism, immune regulation and immune function. There were 48 differentially expressed miRNAs, 32 up-regulated and 16 down-regulated in female YFPs, and the enriched items mainly included cancer occurrence, energy metabolism and signal transduction. Real-time PCR verified the expression levels of MAPK1, IRS1, ALAD and CIQC were consistent with the sequencing results. This study revealed that ncRNA differentially expressed genes may be involved in the mechanism of sex differences in growth through metabolism, immunity and signal transduction, which provides a new perspective for explaining the growth differences between male and female YFPs, and provides a scientific reference for the protection of YFPs.
Transcriptome analysis of sugar beet in response to the pathogenic oomycete Aphanomyces cochlioides
Authors: Rossi Valentina , Holmquist Louise , Alexandersson Erik , Grenville-Briggs Laura
Published: May 2024

Background
Aphanomyces root rot is one of the most severe diseases in sugar beet (Beta vulgaris L.), resulting in drastic losses of sugar yield and plant degeneration. The causal agent is the soil-borne pathogen Aphanomyces cochlioides, a phytopathogenic oomycete able to infect sugar beet roots from the seedling stage until harvest. Reliable control measures and fully resistant varieties to prevent the disease on mature roots are currently not available. Furthermore, the quantitative nature of the resistance mechanisms to the root rot disease remains unclear. With the aim to identify key genes involved in plant defense responses against the root rot, we performed a transcriptome analysis of sugar beet interaction with A. cochlioides. The transcriptome responses of two partially resistant and two susceptible sugar beet breeding lines, inoculated with three A. cochlioides isolates with different geographical origins have been investigated in this study.
Results
The results showed that the transcriptional responses to A. cochlioides infection were mainly genotype-dependent. Comparisons of transcriptome profiles of partially resistant and susceptible breeding lines revealed the presence of differentially expressed genes that play a key role in defense mechanisms during the initial stages of infection. Gene Ontology (GO) categories associated with hydrogen peroxide (H2O2) metabolism, detoxification and cell wall organization were significantly enriched in the differentially expressed gene set from the two partially resistant lines, while photosynthesis-related GO terms were significantly enriched in the two susceptible lines. Transcription factors belonging to the WRKY and ERF families were up-regulated in all genotypes. Furthermore, increased expression of genes encoding for disease resistant proteins have been identified in the two partially resistant genotypes.
Conclusions
This research offers new insights into the transcriptomic events that regulate the sugar beet defense responses to A. cochlioides infection. The findings of this study, combined with the genome mapping of the candidate genes reported here, can be used to improve future breeding and to assist in the development of resistant cultivars.
A Classical Chiral Spin Liquid from Chiral Interactions on the Pyrochlore Lattice
Authors: Lozano-Gómez Daniel , Vojta Matthias , Iqbal Yasir
Published: May 2024

Classical spin liquids are paramagnetic phases that feature nontrivial patterns of spin correlations within their ground-state manifold whose degeneracy scales with system size. Often they harbor fractionalized excitations, and their low-energy fluctuations are described by emergent gauge theories. In this work, we discuss a model composed of chiral three-body spin interactions on the pyrochlore lattice that realizes a novel classical chiral spin liquid whose excitations are fractonalized while also displaying a fracton-like behavior. We demonstrate that the ground-state manifold of this spin liquid is given by a subset of the so-called color-ice states. We demonstrate that the low-energy states are captured by an effective gauge theory which possesses a divergence-free condition and an additional chiral term that constrains the total flux of the fields through a single tetrahedron. The divergence-free constraint on the gauge fields results in two-fold pinch points in the spin structure factor and the identification of bionic charges as excitations of the system.
Influencing factors of fertilization failure during in vitro fertilization
Authors: Shi Hongzhi , Liu Jiajia , Liu Rongrong , Li Chen , Song Qi
Published: May 2024

Objective: To explore the influencing factors of fertilization failure (FF) during in vitro fertilization (IVF) to prevent and manage it in clinical practice and improve treatment efficiency.
Methods: IVF cycles were included and grouped according to the fertilization rate. There were 75 cycles with a fertilization rate of 0, i.e., complete FF, and 98 cycles with a fertilization rate of <30%, i.e., partial FF, and these cycles were included in the FF group; and there were 2301 cycles with a fertilization rate of ≥30%, and included in the normal fertilization(NF) group. Sperm quality of males, basic conditions of females, clinical ovulation induction and laboratory fertilization were compared between the two groups, and no differences were observed. Multivariate logistic regression analysis was performed using FF in the IVF process as the dependent variable, and the indicators with statistically significant differences in the univariate analysis as independent variables to screen the independent risk factors for FF in IVF.
Results: There were significant differences in female age, infertile duration, initial dose of Gn, Gn dose/egg, sperm concentration before treatment, sperm motility, percentage of normal sperm morphology, sperm concentration after treatment, and fertilization concentration(10,000 sperms/ml), and the differences were statistically significant(all P<0.05). Multivariate logistic regression analysis showed that a high percentage of primary infertility, a low percentage of tubal factors, a low percentage of normal sperm morphology, and low sperm concentration after treatment were independent risk factors for FF, and the differences were statistically significant (all P<0.05). Logistic binary regression fitting was used to construct a ROC curve prediction model for combined prediction of fertilization failure using various indicators, and the AUC was 74.6%.
Conclusion: A high percentage of primary infertility, a low percentage of tubal factors, a low percentage of normal sperm morphology, and low sperm concentration after treatment are independent risk factors for FF. The ROC curve model using combined indicators to predict FF constructed by logistic binary regression fitting is valuable in FF prediction.
Transcriptome analysis reveals candidate genes and provides insights in resistance to European canker in apple
Authors: Karlström Amanda , Gómez-Cortecero Antonio , Connell John , Nellist Charlotte Florence , Ordidge Matthew , Dunwell Jim M. , Harrison Richard Jonathan
Published: May 2024

Background
The fungal pathogen Neonectria ditissima causes wood cankers on a wide range of dicotyledonous species, and is a major disease threat to apple production globally. However, understanding of host response and genetic mechanisms underlying resistance remains limited. A transcriptome analysis of RNA sequencing data from infected apple stems was used to assess the response of apple to a single isolate of N. ditissima. The analysis was performed on two partially resistant cultivars; the scion variety ‘Golden Delicious’ and the rootstock cultivar ‘M9 EMLA’. Furthermore, we conducted a comparative transcriptome analysis of full-sibling apple genotypes carrying partial resistant (QTL-R) and susceptible (QTL-S) alleles at six resistance quantitative trait loci (QTL) to study the genetic mechanisms underlying quantitative resistance to this wood pathogen.
Results
The transcriptome profiling of ‘Golden Delicious’ and ‘M9 EMLA’ trees during infection with N. ditissima show that >5,000 genes were differentially expressed in the two cultivars during fungal infection. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG) and protein family (PFAM) enrichment analyses of the differentially regulated genes suggest that secondary metabolism, hormone signalling, pathogen recognition, and metabolism of sugar and carbon are involved in the response to infection. The comparative transcriptome analysis of QTL-R/QTL-S progeny revealed differential expression of genes functioning in pathogen recognition, secondary metabolism, and detoxification within the QTL intervals.
Notable candidate genes encompass putative 4-Coumarate-CoA Ligases (4CL) located within the QTL on chromosome 16, as well as clusters of putative Wall Associated Kinases (WAK) and Wall Associated Kinase Like (WAKL) situated within the QTLs on chromosomes 10 and 2, respectively.
Conclusion
Our study indicate that the host's reaction to N. ditissima involves both intracellular and extracellular immune receptors and that the presence of the pathogen triggers hormone signalling and modifies the metabolism of sugars, carbon, and secondary metabolites. The exploration of candidate genes within resistance QTL highlighted genes that can be used in marker development for breeding. Our findings identifies candidate genes associated with partial resistance to European canker that exhibit a broad impact on pathogen interaction, potentially extending their role to confer resistance against other apple diseases.
Intrusion Detection Using Statistical Classifier Based on Packet Header Analysis
Authors: S Vishnu Prasad , Malarkodi B , KG Michael Kutty , Dhruw Shiv Kumar
Published: May 2024

From a network perspective, any attack that can prevent a network or system from performing its tasks can be considered an intrusion. Network intrusions pose a significant threat, potentially leading to damage, modification, or data loss. An Intrusion Detection System (IDS) can detect intrusions into a network. Multiple techniques have been designed to detect intrusions into a network, such as signature-based and anomaly-based techniques. Machine Learning (ML) techniques can also be used for intrusion detection, but their reliance on traffic flow parameters can introduce prediction delays. This work presents a novel statistical classifier for anomaly-based IDS that uses features extracted from packet headers to make predictions, thus avoiding such delays. The proposed technique is designed by modifying the conventional Packet Header Anomaly Detection (PHAD). In PHAD, packet headers are used to generate scores, which are compared to a threshold to make predictions. Conventional packet header-based anomaly detection techniques have the demerit of generating a lot of false alarms. The proposed approach utilizes a comprehensive set of statistical features from the scores generated by the packet header anomaly detection technique to make predictions. The proposed classifier was tested using publicly available intrusion detection datasets, and the results show that the proposed classifier can make more accurate predictions than conventional PHAD techniques without high false alarms. The proposed classifier performance was also compared and cross-verified with other techniques from the literature, and it performed better than those techniques, showcasing its superior performance in accurately classifying network attacks while minimizing false alarms.
Improving Hydrocolloid Dental Impressions: Assessing the Influence of Environmentally Friendly Nanoparticles and Syzygium aromaticum/Zingiber officinale Plant Extracts
Authors: Beuter Leonie , Bourauel Christoph , Singer Lamia
Published: May 2024

Background
Impression materials can harbour microorganisms from saliva and blood, posing cross-contamination risks. However, post-setting disinfection might compromise the dimensional accuracy and mechanical properties of alginates. Hence, it was the aim of this research to assess the detail reproduction, tear strength, elastic recovery, and surface quality of the gypsum model of newly developed dental alginates with inherent antimicrobial properties.
Methods
Three dental alginate groups with antimicrobial alterations were formulated. One group replaced water with 0.2% chlorhexidine solution (CHX group), while the other two utilized water-based extracts of Syzygium aromaticum (clove) or Zingiber officinale (ginger) to reduce silver nitrate, resulting in two silver nanoparticles (AgNPs)/extract (clove or ginger) mixture solutions. These mixture solutions were employed for the preparation of dental alginate yielding the SA + AgNP and ZO + AgNPs groups. All modified groups were compared to an unmodified control group that used water for mixing. Elastic recovery, detail reproduction, and tear strength were assessed following the ISO 21563:2021 standard. The surface roughness of plaster models was analysed using the optical profilometer. Elastic recovery was assessed by applying and then releasing load on alginate specimens to measure their ability to recover from deformation. Detail reproduction was evaluated by observing the reproducibility of a 50 µm line in a metallic mold using a light microscope, while tear strength was determined by stretching the specimens until failure at a constant speed of 500 mm/min.
Results
All tested groups exhibited elastic recovery values meeting ISO standards for hydrocolloid impression materials. Regarding detail reproduction, both the control and modified alginates successfully reproduced the 50-µm line without interruption in all specimens. Tear strength values for all tested groups remained within the acceptable documented ranges, surpassing the minimum requirement of 0.38 N/mm as mandated by ISO 21563:2021. The ZO + AgNPs (0.94 ± 0.17 N/mm) demonstrated significantly higher tear strength values and surface roughness values compared to the other tested groups.
Conclusions
Chlorhexidine, Syzygium aromaticum, and Zingiber officinale green-synthesized silver nanoparticles are promising, cost-effective alternatives for disinfecting alginate impressions without compromising performance. Green nanoparticle synthesis is a safe, efficient, and non-toxic method, potentially synergizing metal ions with plant extract.
Synergistic antidepressant-like effects of biotics and n-3 polyunsaturated fatty acids on dopaminergic pathway through the brain-gut axis in rats exposed to chronic mild stress
Authors: Cho Hyunji , Park Yongsoon
Published: May 2024

Probiotics, postbiotics, and n-3 polyunsaturated fatty acids (PUFA) have antidepressant-like effects. However, the underlying mechanisms of the dopaminergic pathway are unclear. The present study investigated the hypothesis that probiotics and postbiotics combined with n-3 PUFA synergistically improve depression by modulating the dopaminergic pathway through the brain-gut axis. Rats were randomly divided into seven groups: non-chronic mild stress (CMS) with n-6 PUFA, and CMS with n-6 PUFA, n-3 PUFA, probiotics, postbiotics, probiotics combined with n-3 PUFA, and postbiotics combined with n-3 PUFA. Probiotics, postbiotics, and n-3 PUFA improved depressive behaviors, decreased blood concentrations of corticosterone, interferon-γ, and interleukin-1β, and increased the brain and gut concentrations of short chain fatty acids and dopamine. Moreover, probiotics, postbiotics, and n-3 PUFA increased the brain and gut expression of glucocorticoid receptor, tyrosine hydroxylase, and occludin; brain expression of l-type amino acid transporter 1 and dopamine receptor (DR) D1; and gut expression of DRD2. The expression of phosphorylated protein kinase A/protein kinase A and phosphorylated cAMP response element-binding protein/cAMP response element-binding protein increased in the brain, however, decreased in the gut by the supplementation of probiotics, postbiotics, and n-3 PUFA. There was synergistic effect of probiotics and postbiotics combined with n-3 PUFA on the depressive behaviors and dopaminergic pathway in blood, brain, and gut. Moreover, no significant difference in the dopaminergic pathways between the probiotics and postbiotics was observed. In conclusion, probiotics and postbiotics, combined with n-3 PUFA have synergistic antidepressant-like effects on the dopaminergic pathway through the brain-gut axis in rats exposed to CMS.
Natural Selection Primarily Shaping Codon Usage Bias in Glycine max (soybean) WRKY Genes
Authors: Sinha Krishnendu , Jana Sourav , Pramanik Payel , Bera Bithika
Published: May 2024

Background: Codon usage biases in genomes emerge from the interaction of two prominent evolutionary factors: mutational pressure and natural selection. Studying codon usage bias facilitates the understanding of the fundamental evolutionary mechanisms influencing genetic structure. Glycine max (soybean) holds considerable agricultural and industrial significance as a widely cultivated crop. Despite the pivotal role of WRKY transcription factors in plant regulation and stress responses, investigations of these transcription factors in Glycine max are limited, providing an opportunity to probe evolutionary trends within this gene family.
Results: Examination of the base composition of the Glycine max WRKY genes revealed an average GC content of 44.85% and an average GC3 content of 42.01%, indicating a preference for A/T(U)-ending codons. Relative synonymous codon usage (RSCU) analysis identified 27 codons with RSCU > 1, predominantly ending with A and U bases. The effective number of codons (NC) ranged from 42.17 to 61, with codon adaptation index (CAI) values ranging from 0.713 to 0.904, suggesting a phenomenon of weak codon bias yet high expression levels in WRKY genes. Neutrality analysis indicated a significantly weak correlation between GC12 and GC3, while NC plot analysis revealed the predominant role of natural selection in shaping the codon usage pattern. Parity rule 2 plot (PR2) analysis highlighted disproportionate usage of AT and GC bases. One optimal codon was identified.
Conclusion: Natural selection is the primary driving force of codon usage preferences in Glycine max WRKY genes. These findings provide new insights into the genetic landscape and evolutionary mechanisms of translational efficiency in Glycine max, contributing to the enhancement of genetic resources in soybeans.
The Slow Clock is the Master
Authors: Oliveira Henrique M. , Perestrelo Sara
Published: May 2024

We investigate the synchronization and stability of mutually coupled oscillators through small impacts and explore both master-master and master-slave synchrony. The synchronization behaviour between two oscillators, one operating at a frequency ω and the other at a frequency near a multiple of the first one, nω where n is an integer greater than 1, is investigated. It is observed that such systems tend to exhibit a consistent pattern of master-slave relationship. This phenomenon is geometrically elucidated by considering the interaction dynamics: while the multiple bursts of the faster oscillator tend to cancel each other out upon impacting the slower oscillator, the single burst of the slower oscillator on the faster has a secular effect. We propose that this synchronization pattern, arising from perturbative impacts, is prevalent across various physical systems. Further experimental validation of these findings could contribute to a deeper understanding of synchronization phenomena and their implications in natural and technological domains.
2020 Mathematics Subject Classification. Primary 34D06, Secondary 37E30.
Neuro-intestinal Acetylcholine Signalling Regulates the Mitochondrial Stress Response
Authors: Pocock Roger , Cornell Rebecca , Cao Wei , Harradine Bernie , Handley Ava , Godini Rasoul
Published: May 2024

Neurons coordinate inter-tissue protein homeostasis to systemically manage cytotoxic stress. In response to neuronal mitochondrial stress, specific neuronal signals coordinate the systemic mitochondrial unfolded protein response (UPRmt) to promote organismal survival. Yet, whether chemical neurotransmitters are sufficient to control the UPRmt in physiological conditions is not well understood. Here, we show that gamma-aminobutyric acid (GABA) inhibits, and acetylcholine (ACh) promotes the UPRmt in the Caenorhabditis elegans intestine. GABA controls the UPRmt by regulating extra-synaptic ACh release through metabotropic GABAB receptors GBB-1/2. We find that elevated ACh levels in animals that are GABA-deficient or lack ACh-degradative enzymes induce the UPRmt through ACR-11, an intestinal nicotinic a7 receptor. This neuro-intestinal circuit is critical for non-autonomously regulating organismal survival of oxidative stress. These findings establish chemical neurotransmission as a crucial regulatory layer for nervous system control of systemic protein homeostasis and stress responses.
Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity
Authors: Baker Brian , Ma Jiaqi , Ayres Cory , Brambley Chad , Chandran Smita , Rosales Tatiana , Corcelli Steven , Kovrign Evgenii , Klebanoff Christopher
Published: May 2024

The inherent cross-reactivity of the T cell receptor (TCR) is balanced by high specificity, which often manifests in confounding ways not easily interpretable from static structures. We show here that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen derived from mutant PIK3CA and its wild-type (WT) counterpart emerges from motions within the HLA binding groove that vary with the identity of the peptide’s first primary anchor. The motions form a dynamic gate that in the complex with the WT peptide impedes a large conformational change required for TCR binding. The more rigid neoantigen is insusceptible to this limiting dynamic, and with the gate open, is able to transit its central tryptophan residue underneath the peptide backbone to the contralateral side of the HLA-A3 peptide binding groove, facilitating TCR binding. Our findings reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I complexes, with implications for resolving long-standing and often confounding questions about the determinants of T cell specificity.