bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of m6A/m5C/m1A regulated lncRNA signature for prognostic prediction, personalized immune intervention and drug selection in LUAD
Authors: Ma Chao , Gu Zhuoyu , Yang Yang
Published: April 2024

Research indicates that there are links between m6A, m5C and m1A modifications and the development of different types of tumours. However, it is not yet clear if these modifications are involved in the prognosis of LUAD. The TCGA‐LUAD dataset was used as for signature training, while the validation cohort was created by amalgamating publicly accessible GEO datasets including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081. The study focused on 33 genes that are regulated by m6A, m5C or m1A (mRG), which were used to form mRGs clusters and clusters of mRG differentially expressed genes clusters (mRG‐DEG clusters). Our subsequent LASSO regression analysis trained the signature of m6A/m5C/m1A‐related lncRNA (mRLncSig) using lncRNAs that exhibited differential expression among mRG‐DEG clusters and had prognostic value. The model's accuracy underwent validation via Kaplan–Meier analysis, Cox regression, ROC analysis, tAUC evaluation, PCA examination and nomogram predictor validation. In evaluating the immunotherapeutic potential of the signature, we employed multiple bioinformatics algorithms and concepts through various analyses. These included seven newly developed immunoinformatic algorithms, as well as evaluations of TMB, TIDE and immune checkpoints. Additionally, we identified and validated promising agents that target the high‐risk mRLncSig in LUAD. To validate the real‐world expression pattern of mRLncSig, real‐time PCR was carried out on human LUAD tissues. The signature's ability to perform in pan‐cancer settings was also evaluated. The study created a 10‐lncRNA signature, mRLncSig, which was validated to have prognostic power in the validation cohort. Real‐time PCR was applied to verify the actual manifestation of each gene in the signature in the real world. Our immunotherapy analysis revealed an association between mRLncSig and immune status. mRLncSig was found to be closely linked to several checkpoints, such as IL10, IL2, CD40LG, SELP, BTLA and CD28, which could be appropriate immunotherapy targets for LUAD. Among the high‐risk patients, our study identified 12 candidate drugs and verified gemcitabine as the most significant one that could target our signature and be effective in treating LUAD. Additionally, we discovered that some of the lncRNAs in mRLncSig could play a crucial role in certain cancer types, and thus, may require further attention in future studies. According to the findings of this study, the use of mRLncSig has the potential to aid in forecasting the prognosis of LUAD and could serve as a potential target for immunotherapy. Moreover, our signature may assist in identifying targets and therapeutic agents more effectively.
The barcode trap—Description of a new species of Microglanis, with a review of the status of Microglanis cibelae (Siluriformes: Pseudopimelodidae)
Authors: Lehmann Albornoz Pablo , Bartzen César Sá , Malabarba Luiz R.
Published: April 2024

In a recent study based on the generalized mixed Yule coalescent method for delimiting species, a threshold of 2% genetic distance using cytochrome c oxidase subunit I sequences was used to delimit the species of Microglanis. That action resulted in assembling several populations of Microglanis from Atlantic coastal rivers between Rio Grande do Sul and São Paulo states as a single species, Microglanis cottoides, including Microglanis cibelae as a junior synonym. We reexamined these populations and found three species diagnosed by their morphology and that constitute separate mtDNA lineages, including a new species. The synonym of M. cibelae and M. cottoides is reviewed and refuted based on morphological and molecular evidence. M. cibelae and the new species are sympatric and occasionally syntopic in the Tramandaí, Mampituba, and Araranguá river basins. The new species is distinguished from M. cibelae and M. cottoides by the anterior margin of the posttemporosupracleitrum narrow articulated with the epioccipital, the short mental and maxillary barbels, and depressed head and body.
Is Long‐Run Risk Really Priced? Revisiting Liu and Matthies (2022)
Authors: MAIO PAULO
Published: April 2024

The claim by Liu and Matthies (LM) that their macro news risk factor (NI) prices 51 portfolios (associated with four different portfolio groups) is not appropriate. In fact, their single‐factor model is successful only in explaining the momentum deciles, while producing strongly negative performance for the remaining groups. The pricing performance is more doubtful in the case of the alternative news factor (HNI), as the respective risk price is not identified. LM's conclusions stem from a combination of questionable empirical choices and misinterpretation of their results. Moreover, the NI model cannot explain prominent capital asset pricing model anomalies not considered in their study.
Transactive Memory Systems and Acquisition Performance: A Strategic Decision Making Process Perspective
Authors: Lou Bowen , Bauer Florian , Samba Codou , Shepherd Neil
Published: April 2024

During the pre‐merger phase of an acquisition, fundamental decisions are made concerning whether to buy, which company to buy, and how much to pay. Further, acquisitions carry significant firm‐wide implications requiring input from multiple different specializations, and hence, they are the product of the judgements, decisions, and social interactions between top managers. We focus our theory development on a pivotal yet under‐researched top management team characteristic, transactive memory system (TMS). TMS is the shared division of cognitive labour with respect to encoding, storing, and retrieving knowledge from individual areas of expertise. We theorize that TMT transactive memory directly influences the strategic decision making process, which in turn determines acquisition performance. We test our hypotheses with a sample of 109 acquisitions, combining survey and archival data. We find that TMT transactive memory increases reliance on expert intuition and procedural rationality, while reducing political behaviour; and each of these three strategic decision processes carries different implications for acquisition performance. Our study advances theory by explaining the team‐level behavioural mechanisms that underlie acquisition performance.
Unveiling the consequences of early human saliva contamination on membranes for guided bone regeneration
Authors: Kunrath Marcel F. , Giraldo‐Osorno Paula Milena , Mendes Karina , Gomes Ana T. P. C. , Rosa Nuno , Barros Marlene , Dahlin Christer
Published: April 2024

Aims

GBR membranes have various surface properties designed to elicit positive responses in regenerative clinical procedures; dental clinicians attempt to employ techniques to prevent the direct interaction of contaminated oral fluids with these biomaterials. However, saliva is uninterruptedly exhibited in oral surgical procedures applying GBR membranes, suggesting a persistent interaction with biomaterials and the surrounding oral tissues. This fundamental study aimed to investigate potential alterations in the physical, chemical, and key biological properties of membranes for guided bone regeneration (GBR) caused by isolated early interaction with human saliva.

Methods

A reproducible step‐by‐step protocol for collecting and interacting human saliva with membranes was developed. Subsequently, membranes were evaluated for their physicochemical properties, protein quantification, DNA, and 16S rRNA levels viability of two different cell lines at 1 and 7 days, and ALP activity. Non‐interacted membranes and pure saliva of donors were applied as controls.

Results

Qualitative morphological alterations were noticed; DNA extraction and 16S quantification revealed significantly higher values. Furthermore, the viability of HGF‐1 and MC3T3‐E1 cells was significantly (p < .05) reduced following saliva interaction with biodegradable membranes. Saliva contamination did not prejudice PTFE membranes significantly in any biological assay.

Conclusions

These outcomes demonstrated a susceptible response of biodegradable membranes to isolated early human saliva interaction, suggesting impairment of structural morphology, reduced viability to HGF‐1 and MC3T3‐E1, and higher absorption/adherence of DNA/16S rRNA. As a result, clinical oral procedures may need corresponding refinements.
Pulmonary dimorphic fungal infections among HIV/AIDS non‐TB patients with chronic cough in Kampala, Uganda
Authors: Kiconco Prossy , Achan Beatrice , Sanya Moses , Najjingo Irene , Okeng Alfred , Bwanga Freddie
Published: April 2024

Introduction

Dimorphic fungi cause infection following the inhalation of spores into the pulmonary system. In the lower respiratory tract, the conidia transform into yeasts, which are engulfed by alveolar macrophages and may be destroyed without disease manifestation. However, in some immunocompromised individuals, they may persist and cause active fungal disease characterized by formation of granulomas in the infected tissues, which may mimic Mycobacterium tuberculosis (MTB).

Objective

To determine the prevalence of pulmonary dimorphic fungal infections among HIV/AIDS patients with non‐TB chronic cough at Mulago National Referral and Teaching Hospital in Kampala, Uganda.

Methods

Sputum samples were collected from 175 consented HIV/AIDS patients attending the immuno‐suppression syndrome (ISS) clinic at the hospital. Upon Xpert MTB/RIF sputum testing, 21 patients tested positive for MTB, and these were excluded from further analysis. The other 154 sputum negative samples were then subjected to PCR for dimorphic fungi at MBN Clinical Laboratories. Singleplex PCR was used to detect the target sequences in selected respective genes of each dimorphic fungal species of interest. DNA amplicons were detected based on gel electrophoresis.

Results

Dimorphic fungi were detected in 16.2% (25/154) of the studied population. Of these 9.1% (14/154) had Blastomyces dermatitidis and 7.1% (11/154) had Talaromyces marneffei. The remaining 84% of the studied participants had no dimorphic fungi. Histoplasma capsulatum, Coccidioides immitis and Paracoccidioides brasiliensis were not detected in any of the participants.

Conclusion

Dimorphic fungi (B. dermatitidis and T. marneffei) were found in 16.2% of the HIV/AIDS patients with non‐TB chronic cough in Kampala, Uganda. We recommend routine testing for these pathogens among HIV/AIDS patients with chronic cough.
Do Age and Timing Influence the Outcomes of Single‐stage Reconstruction of Multiple Ligament Knee Injuries? 5‐10 Years Follow Up
Authors: He Jinwen , Geng Bin , Xu Peng , Xia Yayi
Published: April 2024

Objectives

Multiple ligament knee injuries (MLKIs) are disruptive injuries, however, there are controversies in the results of acute and delayed reconstruction. Also, clinical outcomes between patients older or younger than 40 have not been compared in MLKIs. This study was designed to investigate the influence of age and timing of reconstruction on the outcomes of single‐stage reconstruction of MLKIs.

Methods

The patients who underwent reconstruction of multiple injured ligaments because of MLKIs between May 2013 and July 2019 were added to the cohort. The postoperative complications, knee range of motion (ROM), Lysholm score, International Knee Documentation Committee (IKDC) 2000 score, Tegner activity level, patient satisfaction, and SF‐36 score were compared between young (≤ 40 years old, n = 41) and old patients (n = 61); acute (≤ 3 weeks after injury, n = 75) and delayed reconstruction (n = 27), using Mann–Whitney U test or χ2 test.

Results

A total of 102 MLKI patients managed by single‐stage multi‐ligament reconstruction were retrospectively reviewed. Patients were followed up after surgery for a mean of 7.3 years (5.2‐10.7 years). At the last follow‐up, no significant difference was found in knee ROM, functional scores, and patient‐reported outcomes between patients older or younger than 40; acute and delayed reconstruction (p > 0.05). The rate of complications in the delayed reconstruction group was higher than that of the acute reconstruction group (22.2% vs 5.3%, p < 0.05). The IKDC objective scores reached grade A in 63.7%–80.4% of patients, and grade B in 11.8%–23.5% patients.

Conclusion

The single‐stage reconstruction of MLKIs can obtain comparative long‐term functional and objective outcomes regardless of patients older or younger than 40; acute and delayed reconstruction, however, delayed reconstruction is related to a high rate of postoperative complications.
Milestone Moments: Community Violence and Women's Life‐Course Transitions in Colombia, the Dominican Republic, and Guatemala
Authors: Svallfors Signe
Published: April 2024

Deadly violence has drastically increased in Latin America, posing a serious threat to women's sexual and reproductive health. Previous research has documented both increases and declines in youth‐to‐adulthood transitions associated with exposure to violence globally. However, there has been a lack of comparative studies focusing on multiple life‐course transitions. This study investigated the impact of community violence on women's life‐course transitions in Colombia, the Dominican Republic, and Guatemala. Drawing on nationally representative surveys and homicide statistics, fixed effects models are employed to estimate the correlation between women's exposure to community violence and the intensity, timing, and sequencing of their critical life events: first cohabitation and childbirth. The results revealed that exposure to violence was associated with an increase in the quantum and tempo of transitions to first cohabitation and birth in Colombia. Competing risk models showed that community violence correlated with the sequencing of cohabitation and birth in the Dominican Republic, as identified by an increase in precohabiting fertility. There was suggestive but inconclusive evidence of an association between community violence and transitions to first birth in Guatemala. In conclusion, community violence indeed predicts women's youth‐to‐adulthood transitions in Colombia, the Dominican Republic, and potentially Guatemala, with repercussions for the subsequent life experiences of individuals and entire cohorts.
A bamboo bHLH transcription factor PeRHL4 has dual functions in enhancing drought and phosphorus starvation tolerance
Authors: Zhu Chenglei , Lin Zeming , Liu Yan , Li Hui , Di Xiaolin , Li Tiankuo , Wang Jiangfei , Gao Zhimin
Published: April 2024

ROOTHAIRLESS (RHL) is a typical type of basic helix‐loop‐helix (bHLH) transcription factor (TF), which has been reported to participate in various aspects of plant growth and in response to stress. However, the functions of RHL subfamily members in moso bamboo (Phyllostachys edulis) remain unknown. In this study, we identified 14 bHLH genes (PeRHL1–PeRHL14) in moso bamboo. Phylogenetic tree and conserved motif analyses showed that PeRHLs were clustered into three clades. The expression analysis suggested that PeRHL4 was co‐expressed with PeTIP1‐1 and PePHT1‐1 in moso bamboo. Moreover, these three genes were all up‐regulated in moso bamboo under drought stress and phosphate starvation. Y1H, DLR and EMSA assays demonstrated that PeRHL4 could activate the expression of PeTIP1‐1 and PePHT1‐1. Furthermore, overexpression of PeRHL4 could increase both drought and phosphate starvation tolerance in transgenic rice, in which the expression of OsTIPs and OsPHT1s was significantly improved, respectively. Overall, our results indicated that drought stress and phosphate starvation could induce the expression of PeRHL4, which in turn activated downstream genes involved in water and phosphate transport. Collectively, our findings reveal that PeRHL4 acting as a positive regulator contributes to enhancing the tolerance of moso bamboo under drought stress and phosphate starvation.
Coupled hydraulics and carbon economy underlie age‐related growth decline and revitalisation of sand‐fixing shrubs after crown removal
Authors: Guo Jing‐Jing , Gong Xue‐Wei , Li Xue‐Hua , Zhang Chi , Duan Chun‐Yang , Lohbeck Madelon , Sterck Frank , Hao Guang‐You
Published: April 2024

Crown removal revitalises sand‐fixing shrubs that show declining vigour with age in drought‐prone environments; however, the underlying mechanisms are poorly understood. Here, we addressed this knowledge gap by comparing the growth performance, xylem hydraulics and plant carbon economy across different plant ages (10, 21 and 33 years) and treatments (control and crown removal) using a representative sand‐fixing shrub (Caragana microphylla Lam.) in northern China. We found that growth decline with plant age was accompanied by simultaneous decreases in soil moisture, plant hydraulic efficiency and photosynthetic capacity, suggesting that these interconnected changes in plant water relations and carbon economy were responsible for this decline. Following crown removal, quick resprouting, involving remobilisation of root nonstructural carbohydrate reserves, contributed to the reconstruction of an efficient hydraulic system and improved plant carbon status, but this became less effective in older shrubs. These age‐dependent effects of carbon economy and hydraulics on plant growth vigour provide a mechanistic explanation for the age‐related decline and revitalisation of sand‐fixing shrubs. This understanding is crucial for the development of suitable management strategies for shrub plantations constructed with species having the resprouting ability and contributes to the sustainability of ecological restoration projects in water‐limited sandy lands.
The good thief: A note on revisits in long‐running ethnography
Authors: Hopper Kim
Published: April 2024

This commentary revisits Nancy Scheper‐Hughes’ Saints, Scholars and Schizophrenics ([1979] 2001) and opens up its contentious history as resented exposé, unflinching portrait of a demoralized and anomic landscape, and ethnographic test‐case of the terms of engagement. I suggest that the controversy may betoken what long‐haul ethnography in the present era might hold in store, not for individual researchers alone but for our discipline as well. Wholesale rewrites or retractions may not be in the cards, but reparation comes in many shades. At times what it creates is the necessary clearance to build out what was missed—with what may look like deliberate provocation—the first time around. The trick is not to confuse contrition with renunciation … or the space of a landing with the finality of an ending.
Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high‐quality reference transcript dataset
Authors: Wu Zhi‐Hao , He Liang‐Liang , Wang Cong‐Cong , Liang Chen , Li Han‐Ying , Zhong Dan‐Wen , Dong Zhao‐Xia , Zhang Li‐Juan , Zhang Xiang‐Qian , Ge Liang‐Fa , Chen Shu
Published: April 2024

Inadequate reference databases in RNA‐seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high‐quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely‐used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low‐temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine‐rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low‐temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low‐temperature stress, suggesting a unique co‐regulatory mechanism governing transcription and splicing in the context of low‐temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.
Impact of autologous platelet concentrates on the osseointegration of dental implants
Authors: Ivanovski Sašo , Lee Ryan S. B. , Fernandez‐Medina Tulio , Pinto Nelson , Andrade Catherine , Quirynen Marc
Published: April 2024

Osseointegration is defined as the direct deposition of bone onto biomaterial devices, most commonly composed from titanium, for the purpose of anchoring dental prostheses. The use of autologous platelet concentrates (APC) has the potential to enhance this process by modifying the interface between the host and the surface of the titanium implant. The rationale is to modify the implant surface and implant–bone interface via “biomimicry,” a process whereby the deposition of the host's own proteins and extracellular matrix enhances the biocompatibility of the implant and hence accelerates the osteogenic healing process. This review of the available evidence reporting on the effect of APC on osseointegration explores in vitro laboratory studies of the interaction of APC with different implant surfaces, as well as the in vivo and clinical effects of APC on osseointegration in animal and human studies. The inherent variability associated with using autologous products, namely the unique composition of each individual's blood plasma, as well as the great variety in APC protocols, combination of biomaterials, and clinical/therapeutic application, makes it is difficult to make any firm conclusions about the in vivo and clinical effects of APC on osseointegration. The available evidence suggests that the clinical benefits of adding PRP and the liquid form of L‐PRF (liquid fibrinogen) to any implant surface appear to be limited. The application of L‐PRF membranes in the osteotomy site, however, may produce positive clinical effects at the early stage of healing (up to 6 weeks), by promoting early implant stability and reducing marginal bone loss, although no positive longer term effects were observed. Careful interpretation and cautious conclusions should be drawn from these findings as there were various limitations in methodology. Future studies should focus on better understanding of the influence of APCs on the biomaterial surface and designing controlled preclinical and clinical studies using standardized APC preparation and application protocols.
Zinc oxide nanoparticles preserve the quality and fertility potential of rooster sperm during the cryopreservation process
Authors: Karimi‐Sabet Mohammad Javad , Khodaei‐Motlagh Mahdi , Masoudi Reza , Sharafi Mohsen
Published: April 2024

Sperm cryopreservation is one of the main methods for preserving rooster sperm for artificial insemination (AI) in commercial flocks. Yet, rooster sperm is extremely susceptible to reactive oxygen species (ROS) produced during the freezing process. Oxidative stress could be prevented by using nanoparticles containing antioxidants. The present study was conducted to investigate the effect of zinc oxide nanoparticles (ZnONP) in rooster semen freezing extender on quality parameters and fertility potential. For this aim, semen samples were collected and diluted in Lake extenders as follows: control: Lake without ZnONP, ZnO100: Lake with 100‐μg zinc oxide (ZnO), ZnONP50: Lake with 50‐μg ZnONP, ZnONP100: Lake with 100‐μg ZnONP and ZnONP200: Lake with 200‐μg ZnONP. After freezing and thawing, sperm motility, viability, membrane integrity, morphology, mitochondrial activity, acrosome integrity, DNA fragmentation, lipid peroxidation and ROS, as well as fertility and hatchability were assessed. According to the current results, higher rates of motility, membrane integrity, mitochondrial activity, acrosome integrity and live cells were detected in the ZnO100, ZnONP50 and ZnONP100 groups compared to other groups (p ≤ .05). Yet, the percentage of dead cells, DNA fragmentation, lipid peroxidation and ROS levels were lower in the mentioned groups (p ≤ .05). Furthermore, a higher percentage of fertility was observed in the ZnO100 and ZnONP100 groups than in the control group (p ≤ .05). In conclusion, the use of 100‐μg ZnO and 50‐ to 100‐μg ZnONP represents a valuable and safe additive material that could be used to improve the quality and fertility potential of rooster sperm under cryopreservation conditions.
Responsive and responsible methodologies. Emplacing care with collaborative filmmaking
Authors: Jacobs Jessica , Salimbeni Alice
Published: April 2024

This paper is a response to the call for more caring kinds of scholarly transactions that acknowledge our interdependencies. We delve into collaborative filmmaking as a method that emplaces care in a range of different ways and that highlights researcher responsibility in the fieldwork. Recognising that discussions on care and responsibility often remain abstract, we ground our exploration in a recent collaborative filmmaking research project to argue that collaborative filmmaking can challenge researcher positionality and foster a deeper understanding of power dynamics in research practice and process. Starting from existing literature that tends to oversimplify research processes due to the pressure to present ‘knowledge’, we highlight the discrepancies between polished academic presentations and the intricate and sometimes contradictory realities of fieldwork. This paper offers insights for activists and other scholars in feminist and queer geographies, emphasising the role of care in shaping academic research.
Genetic diversity, growth and heart function of Auckland Island pigs, a potential source for organ xenotransplantation
Authors: Lange Andreas , Medugorac Ivica , Ali Asghar , Kessler Barbara , Kurome Mayuko , Zakhartchenko Valeri , Hammer Sabine E. , Hauser Andreas , Denner Joachim , Dobenecker Britta , Wess Gerhard , Tan Paul L. J. , Garkavenko Olga , Reichart Bruno , Wolf Eckhard , Kemter Elisabeth
Published: April 2024

One of the prerequisites for successful organ xenotransplantation is a reasonable size match between the porcine organ and the recipient's organ to be replaced. Therefore, the selection of a suitable genetic background of source pigs is important. In this study, we investigated body and organ growth, cardiac function, and genetic diversity of a colony of Auckland Island pigs established at the Center for Innovative Medical Models (CiMM), LMU Munich. Male and female Auckland Island pig kidney cells (selected to be free of porcine endogenous retrovirus C) were imported from New Zealand, and founder animals were established by somatic cell nuclear transfer (SCNT). Morphologically, Auckland Island pigs have smaller body stature compared to many domestic pig breeds, rendering their organ dimensions well‐suited for human transplantation. Furthermore, echocardiography assessments of Auckland Island pig hearts indicated normal structure and functioning across various age groups throughout the study. Single nucleotide polymorphism (SNP) analysis revealed higher runs of homozygosity (ROH) in Auckland Island pigs compared to other domestic pig breeds and demonstrated that the entire locus coding the swine leukocyte antigens (SLAs) was homozygous. Based on these findings, Auckland Island pigs represent a promising genetic background for organ xenotransplantation.
Multi-Pass Laser Polishing of As-Built Directed Energy Deposition Surfaces
Authors: Patel Arpan , Webster Samantha , Cao Jian , Ehmann Kornel
Published: April 2024

Laser polishing (LP) provides a fast and efficient way of remelting part surfaces manufactured by additive manufacturing to alter both their geometric as well as physical properties. Depending on the laser parameters, remelted surfaces with different properties are achieved, with a majority exhibiting lower surface roughness compared to the original surface. In this study, a high-power continuous fiber laser is used to polish Inconel 718 (IN718) surfaces produced by depositing a single layer of clads on a steel substrate by the powder-blown directed energy deposition (DED) process. Polishing was performed under different sets of parameters, namely, laser power, beam diameter, feed rate or feed, hatch spacing, and the number of polishing passes. Their effects on the surface roughness profiles and the microstructural properties of the sample cross section were analyzed after one and two polishing passes. Optical microscopic images of the sample's cross sections show the presence of supersaturated γ phase particles, γ′+γ″ precipitates, Laves phases, and δ phase needles. The combined effect of high-temperature gradients and lower solidification rates in certain regions within the cross section results in undercooled regions and pseudo-heat treatment of unmelted regions close to the undercooled regions. These results are corroborated by indenting the various regions of the IN718 sample cross section with a pyramidal diamond indenter in the form of a grid, resulting in different micro-hardness values due to different densities of precipitate and phase transformed δ particles.
Lattice Boltzmann–Carleman quantum algorithm and circuit for fluid flows at moderate Reynolds number
Authors: Sanavio Claudio , Succi Sauro
Published: April 2024

We present a quantum computing algorithm for fluid flows based on the Carleman-linearization of the Lattice Boltzmann (LB) method. First, we demonstrate the convergence of the classical Carleman procedure at moderate Reynolds numbers, namely, for Kolmogorov-like flows. Then we proceed to formulate the corresponding quantum algorithm, including the quantum circuit layout, and analyze its computational viability. We show that, at least for moderate Reynolds numbers between 10 and 100, the Carleman–LB procedure can be successfully truncated at second order, which is a very encouraging result. We also show that the quantum circuit implementing the single time-step collision operator has a fixed depth, regardless of the number of lattice sites. However, such depth is of the order of ten thousands quantum gates, meaning that quantum advantage over classical computing is not attainable today, but could be achieved in the near or mid-term future. The same goal for the multi-step version remains, however, an open topic for future research.
Labor-based grading practices in the physics classroom
Authors: Wachter Jeremy M.
Published: April 2024

I describe the assessment framework of labor-based contract grading (LBCG). In a labor-based grading scheme, the time and effort (“labor”) a student spends on an assignment determines the credit they receive; the contract component requires students to design projects with clearly defined goals and deliverables, which must be satisfied to earn credit. LBCG is intended to promote student agency and engagement and to provide a more equitable assessment framework, given that students come with a wide range of prior experiences and preparation. I illustrate the LBCG framework within the context of an upper level physics course, using a particular assignment as an example; I also provide information on student experiences and engagement.
Recovering seldom-used theorems of vector calculus and their application to problems of electromagnetism
Authors: Pérez-Garrido A.
Published: April 2024

In this paper, we use differential forms to prove a number of theorems of integral vector calculus that are rarely found in textbooks. Two of them, as far as the author knows, have not been published before. Some possible applications to problems in physics are shared including a general approach for computing net forces and torques on current-carrying loops that yields insights that are not evident from the standard approach.
Paraxial and ray approximations of acoustic vortex beams
Authors: Gokani Chirag A. , Haberman Michael R. , Hamilton Mark F.
Published: April 2024

A compact analytical solution obtained in the paraxial approximation is used to investigate focused and unfocused vortex beams radiated by a source with a Gaussian amplitude distribution. Comparisons with solutions of the Helmholtz equation are conducted to determine bounds on the parameter space in which the paraxial approximation is accurate. A linear relation is obtained for the dependence of the vortex ring radius on the topological charge, characterized by its orbital number, in the far field of an unfocused beam and in the focal plane of a focused beam. For a focused beam, it is shown that as the orbital number increases, the vortex ring not only increases in radius but also moves out of the focal plane in the direction of the source. For certain parameters, it is demonstrated that with increasing orbital number, the maximum amplitude in a focused beam becomes localized along a spheroidal surface enclosing a shadow zone in the prefocal region. This field structure is described analytically by ray theory developed in the present work, showing that the spheroidal surface in the prefocal region coincides with a simple expression for the coordinates of the caustic surface formed in a focused vortex beam.
Controlling
Candida
: immune regulation of commensal fungi in the gut
Authors: Jensen Owen , Trujillo Emma , Hanson Luke , Ost Kyla S.
Published: April 2024

The intestinal microbiome harbors fungi that pose a significant risk to human health as opportunistic pathogens and drivers of inflammation. Inflammatory and autoimmune diseases are associated with dysbiotic fungal communities and the expansion of potentially pathogenic fungi. The gut is also the main reservoir for disseminated fungal infections. Immune interactions are critical for preventing commensal fungi from becoming pathogenic. Significant strides have been made in defining innate and adaptive immune pathways that regulate intestinal fungi, and these discoveries have coincided with advancements in our understanding of the fungal molecular pathways and effectors involved in both commensal colonization and pathogenesis within the gut. In this review, we will discuss immune interactions important for regulating commensal fungi, with a focus on how specific cell types and effectors interact with fungi to limit their colonization or pathogenic potential. This will include how innate and adaptive immune pathways target fungi and orchestrate antifungal immune responses, in addition to how secreted immune effectors, such as mucus and antimicrobial peptides, regulate fungal colonization and inhibit pathogenic potential. These immune interactions will be framed around our current understanding of the fungal effectors and pathways regulating colonization and pathogenesis within this niche. Finally, we highlight important unexplored mechanisms by which the immune system regulates commensal fungi in the gut.
Diagnosis, management, and outcomes of parechovirus infections in infants: an overview
Authors: Sasidharan Anjana , Harrison Christopher J. , Selvarangan Rangaraj
Published: April 2024

Parechovirus A (PeV-A) infections have been detected with increasing frequency in US infants under 6 months of age, leading to a Centers for Disease Control and Prevention (CDC) health advisory in July 2022. Clinicians are advised to consider PeV-A laboratory testing of blood and cerebrospinal fluid when infants present with unexplained fever, sepsis-like illness, or neurological issues. Clinical laboratories are encouraged to offer in-house molecular testing for PeV-A to avoid diagnostic delays, unnecessary use of antibiotics, and prolonged hospitalization of infants presenting with sepsis-like illness. While data are evolving on potential neurodevelopmental sequelae after PeV-A infant central nervous system infections, most infected infants return to baseline health for age. This review examines the PeV-A literature with a focus on PeV-A3, including aspects of epidemiology, clinical presentations/management, laboratory diagnostics, genotyping, and post-infectious sequelae related to PeV-A infections in infants.
Uncommon BK polyomaviruses detected in allogeneic hematopoietic cell transplant recipients
Authors: Chokshi Saagar M. , Odegard Elizabeth A. , Meeds Heidi L. , Kleiboeker Steven B. , Ziady Assem , Sabulski Anthony , Jodele Sonata , Seif Alix E. , Davies Stella M. , Laskin Benjamin L. , Blackard Jason T.
Published: April 2024

The role of viral diversity in the pathogenesis of BK polyomavirus (BKPyV)-associated disease is poorly understood. Here, we report near full-length BKPyV genome sequences from two allogeneic hematopoietic cell transplant recipients infected with BKPyV genotype II, which is uncommon in the USA.
Complete genome of
Vibrio harveyi
isolate K2014767 from the hepatopancreas of captive Caribbean spiny lobster (
Panulirus argus
)
Authors: Rose Divya , Bennett Hannah , Dill-Okubo Jennifer , Francis-Floyd Ruth , Camus Alvin C. , Waldbieser Geoffrey C. , Griffin Matt J.
Published: April 2024

The complete genome sequence is reported for
Vibrio harveyi
isolate K2014767, isolated from a captive Caribbean spiny lobster (
Panulirus argus
) during a species-specific mortality event in a public display aquarium in the United States.
Colon microbiota and metabolite potential impact on tail fat deposition of Altay sheep
Authors: Hou Meng , Ye Mengjun , Ma Xuelian , Sun Yawei , Yao Gang , Liu Liya , Li Xin , Hu Yan , Wang Jinquan
Published: April 2024

Tail fat deposition of Altay sheep not only increased the cost of feeding but also reduced the economic value of meat. Currently, because artificial tail removal and gene modification methods cannot solve this problem, it is maybe to consider reducing tail fat deposition from the path of intestinal microbiota and metabolite. We measured body weight and tail fat weight, collected the serum for hormone detection by enzyme-linked immunosorbent assay, and collected colon contents to 16S rRNA sequence and liquid chromotography with mass spectrometry detection to obtain colon microbiota and metabolite information, from 12 3-month-old and 6-month-old Altay sheep. Subsequently, we analyzed the correlation between colon microbiota and tail fat weight, hormones, and metabolites, respectively. We identified that the tail fat deposition of Altay sheep increased significantly with the increase of age and body weight, and the main microbiota that changed were Verrucomicrobia, Cyanobacteria,
Akkermansia
,
Bacteroides
,
Phocaeicola
,
Escherichia-Shigella
, and
Clostridium_sensu_stricto_1
. The results indicated that the diversities of metabolites in the colon contents of 3-months old and 6-months old were mainly reflected in phosphocholine (PC) and phosphatidylethanolamine (PE) in the lipid metabolism pathway. The correlations analyzed showed that Verrucomicrobia, Chlamydiae,
Akkermansia
,
Ruminococcaceae_UCG-005
,
Bacteroides
, and
Phocaeicola
were negatively correlated with tail fat deposition. Verrucomicrobia,
Akkermansia
, and
Bacteroides
were negatively correlated with growth hormone (GH). Verrucomicrobia was positively correlated with L-a-lysophosphatidylserine and PE(18:1(9Z)/0:0). Our results showed that tail fat deposition of Altay sheep was probably correlated with the abundance of Verrucomicrobia,
Akkermansia
,
Bacteroides
of colon microbiota, PC, PE of metabolites, and GH of serum.

IMPORTANCE

Excessive tail fat deposition of Altay sheep caused great economic losses, and the current research results could not solve this problem well. Now, our research speculates that the tail fat deposition of Aletay sheep may be related to the abundance of Verrucomicrobia, Akkermansia, Bacteroides, metabolites phosphocholine, phosphatidylethanolamine, and growth hormone of serum. Further investigation of the interaction mechanism between these microbiota or metabolites and tail fat deposition is helpful in reducing tail fat deposition of Altay sheep and increasing the economic benefits of breeding farms.
Evolution of Silurian to Devonian magmatism associated with the Acadian orogenic cycle in eastern and southern Newfoundland Appalachians: Evidence for a three-stage evolution characterized by episodic hinterland- and foreland-directed migration of granitoid magmatism
Authors: Wang Chaoyang , Wang Tao , van Staal C.R. , Hou Zengqian , Lin Shoufa
Published: April 2024

The migration and character of magmatism over time can provide important insights into the tectonic evolution of an orogen. We present evidence for three separate stages of compositionally distinct granitoid magmatism associated with the Acadian orogenic cycle in the eastern and southern Newfoundland Appalachians. The interpretations are based on new zircon U-Pb ages, geochemical data, and Sr-Nd-Hf-O isotopic data for 18 samples from 15 Silurian and Devonian granitoid plutons, combined with previously published data. The three stages outline hinterland- and foreland-directed migration trends and represent subduction (435–420 Ma), syncollision (415–405 Ma), and postcollision (395–370 Ma) settings in the Acadian orogenic cycle. The Silurian plutons (435–420 Ma) of the first stage consist mainly of quartz diorite, tonalite, granodiorite, monzogranite, and syenogranite, with high-K calc-alkaline and enriched Sr-Nd-Hf-O isotopic compositions (e.g., εNd[t] = −5 to −2; εHf[t] = −3 to −1; δ18O = +6‰ to +8‰). They are interpreted to record the subduction of oceanic lithosphere of the Acadian seaway that separated the leading edge of composite Laurentia, represented by the Gander margin, and Avalonia. Early Devonian plutons (415–405 Ma) of the second stage contain more voluminous monzogranite and syenogranite; they have calc-alkaline to high-K calc-alkaline features, adakite-like compositions, and more depleted Sr-Nd-Hf-O isotopic compositions (e.g., εNd[t] = −6 to 0; εHf[t] = +1 to +3; δ18O = +5‰ to +6‰). Plutons of this stage occur mostly to the northwest of the Silurian granitoids, indicating a regional-scale northwestward (hinterland-directed) migration of magmatism with a rate of >9 km/m.y. The migration is interpreted to have been related to the progressive shallow underthrusting of Avalonia beneath the Gander margin (composite Laurentia) at least as far as 90 km inboard. The Middle to Late Devonian plutons of the third stage (395–370 Ma) consist mainly of monzogranite, syenogranite, and alkali-feldspar granite, which are silica- and alkali-rich granites with large negative Eu anomalies. These rocks are concentrated along both sides of the Dover–Hermitage Bay fault zone, which represents the boundary between Avalonia and composite Laurentia, to the southeast of the Silurian and Early Devonian igneous rocks. This stage of magmatism represents a foreland-directed (retreating) migration. The Early Devonian and Middle to Late Devonian episodes of magmatism were separated by a gap between 405 Ma and 395 Ma and recorded an evolution from (high-K) calc-alkaline to alkaline compositions, ascribed to partial delamination of Avalonian lithospheric mantle in a postcollisional setting.
Bilateral quadriceps tendon rupture: two injuries 6 years apart
Authors: Street Jean-Marc , Goalan Raakesh , Kumar Anil
Published: April 2024

We present a case of a fit man in his 50s, with simultaneous bilateral quadriceps tendon repair of injuries sustained 6 years apart. Spontaneous closed ruptures of the quadriceps tendon are uncommon. Clinical data of a single case of bilateral quadriceps tendon injury with simultaneous repair was gathered via the patient, notes and surgeon. Diagnosis was primarily based on history and clinical examination. Suggestive features on the plain radiographic imaging were also present. Confirmation was attempted using ultrasonography but yielded conflicting reports. The patient was screened for any associated predisposing conditions that would preclude surgical intervention or increase risk of recurrence. Repairs were accomplished by employing a combination of suture anchors and transpatellar cerclage reinforcement. Apposition of the tendon to the superior patellar pole was successful although with decreased passive flexion on the neglected side (approximately 30°) compared with the acute (approximately 90°). Follow-up continues with postoperative rehabilitation.
Case of eccrine chondroid syringoma of the upper lip
Authors: Chon Jeewon , Laub Peter , Alhalaseh Yazan , Ogrodnik Joseph
Published: April 2024

Chondroid syringoma (CS) is a benign, slow-growing mixed tumour that arises from the sweat glands and usually presents in the head and neck area. Histopathological examination is important for proper diagnosis, as CS is often confused with epidermal cysts due to its rare presentation. This article presents a man in his 40s with a right upper lip mass that emerged 6 months prior to presentation. An intraoral surgical excision was performed and the histopathological analysis revealed solid epithelial cells that formed multiple, non-branching ducts lined by cuboidal epithelium. Cystic spaces were filled by heterogeneous eosinophilic material embedded in chondromyxoid stroma. Histopathology identified the lesion as an eccrine-variant CS. The patient recovered well.
Benign ectopic prostate—a rare differential for a presacral mass
Authors: Dsouza Royson , A Ramachandran , Mathew Aleena , Raghunath Rajat
Published: April 2024

A man in his mid-40s presented to the colorectal surgery clinic with complaints of chronic perianal pain for over 20 years. He had episodes of urinary incontinence associated with pain. There were no other symptoms to suspect bowel pathology. On examination, he was found to have a tender mass in the retro-rectal plane without any evidence of rectal mucosal irregularity. He underwent an MRI of the pelvis, which showed a well-defined T2 hyperintense partly cystic lesion in the presacral region abutting the mesorectal fascia and a normal prostate gland. With a suspicion of a tailgut cyst or a duplication cyst, he underwent an excision of the presacral mass. Intraoperatively, there was a 2 × 2 cm well-defined firm, cystic lesion anterior to the fifth sacral vertebra and coccyx. The lesion was adherent to the mesorectum and was excised. On histopathology, there were features of muscular stroma and bilayered glandular epithelium with clear cytoplasm conclusive of a benign ectopic prostate.
Hypokalaemia associated with excessive cola-flavoured drinks consumption
Authors: Baba-Aissa Sara , Cooke Lynn , Alner Victoria , Ahmed Mohamed H
Published: April 2024

We present a case involving a male patient in his 30s who was admitted to hospital due to recurrent episodes of hypokalaemia over the past 5 years. His medical history revealed hypertension, attention deficit hyperactivity disorder (ADHD), autism, and paranoia. He was taking citalopram, ramipril, amlodipine, and pramipexole. Tests indicated normal levels of aldosterone/renin ratio and plasma metanephrines. On reviewing his dietary history, it was noted that he consumed 3 to 3.5 L of cola-flavoured drinks on a daily basis. Normal potassium levels were achieved after a significant reduction in cola-flavoured drinks intake and potassium replacement. Subsequent outpatient clinic follow-up revealed that normal potassium levels were maintained even after the patient ceased taking potassium replacement tablets. Given the rarity of hypokalaemia associated with fizzy drinks, the underlying mechanism for this association remains unclear. In this case report, we attempt to provide a possible explanation for the involved mechanisms.