bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of testing rate on biomechanical measurements related to stalk lodging
Authors: Tabaracci Kaitlin , Vos Jacques , Robertson Daniel J.
Published: August 2024

Background

Stalk lodging (the premature breaking of plant stalks or stems prior to harvest) is a persistent agricultural problem that causes billions of dollars in lost yield every year. Three-point bending tests, and rind puncture tests are common biomechanical measurements utilized to investigate crops susceptibility to lodging. However, the effect of testing rate on these biomechanical measurements is not well understood. In general, biological specimens (including plant stems) are well known to exhibit viscoelastic mechanical properties, thus their mechanical response is dependent upon the rate at which they are deflected. However, there is very little information in the literature regarding the effect of testing rate (aka displacement rate) on flexural stiffness, bending strength and rind puncture measurements of plant stems.

Results

Fully mature and senesced maize stems and wheat stems were tested in three-point bending at various rates. Maize stems were also subjected to rind penetration tests at various rates. Testing rate had a small effect on flexural stiffness and bending strength calculations obtained from three-point bending tests. Rind puncture measurements exhibited strong rate dependent effects. As puncture rate increased, puncture force decreased. This was unexpected as viscoelastic materials typically show an increase in resistive force when rate is increased.

Conclusions

Testing rate influenced three-point bending test results and rind puncture measurements of fully mature and dry plant stems. In green stems these effects are expected to be even larger. When conducting biomechanical tests of plant stems it is important to utilize consistent span lengths and displacement rates within a study. Ideally samples should be tested at a rate similar to what they would experience in-vivo.
How to customize common data models for rare diseases: an OMOP-based implementation and lessons learned
Authors: Ahmadi Najia , Zoch Michele , Guengoeze Oya , Facchinello Carlo , Mondorf Antonia , Stratmann Katharina , Musleh Khader , Erasmus Hans-Peter , Tchertov Jana , Gebler Richard , Schaaf Jannik , Frischen Lena S. , Nasirian Azadeh , Dai Jiabin , Henke Elisa , Tremblay Douglas , Srisuwananukorn Andrew , Bornhäuser Martin , Röllig Christoph , Eckardt Jan-Niklas , Middeke Jan Moritz , Wolfien Markus , Sedlmayr Martin
Published: August 2024

Background

Given the geographical sparsity of Rare Diseases (RDs), assembling a cohort is often a challenging task. Common data models (CDM) can harmonize disparate sources of data that can be the basis of decision support systems and artificial intelligence-based studies, leading to new insights in the field. This work is sought to support the design of large-scale multi-center studies for rare diseases.

Methods

In an interdisciplinary group, we derived a list of elements of RDs in three medical domains (endocrinology, gastroenterology, and pneumonology) according to specialist knowledge and clinical guidelines in an iterative process. We then defined a RDs data structure that matched all our data elements and built Extract, Transform, Load (ETL) processes to transfer the structure to a joint CDM. To ensure interoperability of our developed CDM and its subsequent usage for further RDs domains, we ultimately mapped it to Observational Medical Outcomes Partnership (OMOP) CDM. We then included a fourth domain, hematology, as a proof-of-concept and mapped an acute myeloid leukemia (AML) dataset to the developed CDM.

Results

We have developed an OMOP-based rare diseases common data model (RD-CDM) using data elements from the three domains (endocrinology, gastroenterology, and pneumonology) and tested the CDM using data from the hematology domain. The total study cohort included 61,697 patients. After aligning our modules with those of Medical Informatics Initiative (MII) Core Dataset (CDS) modules, we leveraged its ETL process. This facilitated the seamless transfer of demographic information, diagnoses, procedures, laboratory results, and medication modules from our RD-CDM to the OMOP. For the phenotypes and genotypes, we developed a second ETL process. We finally derived lessons learned for customizing our RD-CDM for different RDs.

Discussion

This work can serve as a blueprint for other domains as its modularized structure could be extended towards novel data types. An interdisciplinary group of stakeholders that are actively supporting the project's progress is necessary to reach a comprehensive CDM.

Conclusion

The customized data structure related to our RD-CDM can be used to perform multi-center studies to test data-driven hypotheses on a larger scale and take advantage of the analytical tools offered by the OHDSI community.
Associating transcription factors to single-cell trajectories with DREAMIT
Authors: Maulding Nathan D. , Seninge Lucas , Stuart Joshua M.
Published: August 2024

Inferring gene regulatory networks from single-cell RNA-sequencing trajectories has been an active area of research yet methods are still needed to identify regulators governing cell transitions. We developed DREAMIT (Dynamic Regulation of Expression Across Modules in Inferred Trajectories) to annotate transcription-factor activity along single-cell trajectory branches, using ensembles of relations to target genes. Using a benchmark representing several different tissues, as well as external validation with ATAC-Seq and Perturb-Seq data on hematopoietic cells, the method was found to have higher tissue-specific sensitivity and specificity over competing approaches.
Design and validation of an instrument to evaluate Person-Centered care in health services
Authors: Lehmann-Mendoza Rodolfo , Cortés-Moreno Gabriela Yanet , Sarabia-González Odet , Figuerola-Escoto Rosa Paola , Luna David , González-Mundo Ilicia , Caselín-Ledezma Rubén , Vázquez-Dávila Roberto Arturo , Martínez-Arredondo Hilario Ascención
Published: August 2024

Background

The concept of quality in health care has evolved, placing greater importance on the patient’s needs, culture, and social context, as well as their participation in clinical decision-making, as highlighted by Mead and Bower’s Person-Centered Care Model. The aim of the present study was to design and validate an instrument to assess the extent to which healthcare services provided by PEMEX (Petróleos Mexicanos) offer person-centered care according to user perceptions.

Methods

The first phase comprised the development of 57 items based on the analysis of responses from an open-ended questionnaire administered to 30 users of Pemex healthcare services. This questionnaire was designed considering the four factors of the person-centered care model, however, the high correlation between the 4 factors (i.e., r ≥ .80) indicated an overfactoring effect and consequently an increase in the risk of overfitting. Therefore, an exhaustive analysis of the instrument was performed, starting with the review of the individual behavior of each item, and carrying out exploratory and confirmatory factor analysis. Using a sample of 330 individuals, an exploratory factor analysis was perfomed. Afterward, a confirmatory factorial analysis was carried out with 335 participants. Finally, a new confirmatory factorial analysis included 130 participants due to the refinements made in the previous phase. Internal consistency was assessed using Cronbach’s α and McDonald’s ω at every phase.

Results

The exploratory factor analysis retained 35 items in a single factor that accounted for 49% of the variance with an internal consistency of Cronbach’s α and McDonald’s ω = 0.97. Because the factorial structure by confirmatory factorial analysis was unsatisfactory, the initial model was refined, leading to the retention of 11 items and a final model with adjustment index of χ2 = 127.53, χ2/gl = 2.89, RMSEA = 0.07, IC RMSEA 0.06 to 0.09, TLI = 0.95 and CFI = 0.96, with an internal consistency of Cronbach’s α and McDonald’s ω = 0.93. Due to the refinements, a new confirmatory factorial analysis was conducted with suitable goodness-of-fit criteria in most items (χ2 = 151.44, χ2/gl = 3.43, RMSEA = 0.13, IC RMSEA 0.11 to 0.16, TLI = 0.93 and CFI = 0.94), resulting in a Cronbach’s α and McDonald’s ω = 0.98.

Conclusions

The instrument exhibits suitable psychometric properties to be employed to measure the degree to which medical care is patient centered. This instrument represents a strategy for promoting an innovative healthcare model.
The western extension of the Balantak Fault revealed by the 2021 earthquake cascade in the central arm of Sulawesi, Indonesia
Authors: Simanjuntak Andrean V. H. , Palgunadi Kadek H. , Supendi Pepen , Muksin Umar , Gunawan Endra , Widiyantoro Sri , Rawlinson Nicholas , Daryono Mudrik R. , Daryono D. , Karnawati Dwikorita , Hanifa Nuraini R. , Pratama Cecep , Ida Rachmah
Published: August 2024

Two shallow earthquakes of moment magnitude 6.2 and 5.8 occurred in the central arm of Sulawesi on 26 July 2021 and 26 August 2021, respectively. The fault responsible for the earthquake had previously only been partially mapped, thus making further analysis of its characteristics crucial for the assessment of seismic hazard. In this study, we exploit data from a regional seismic network, relocate the associated seismicity using the double difference method with an updated velocity model, determine focal mechanisms from full-waveform inversion, and analyze the static stress changes caused by the mainshock. Our relocated hypocenters and focal mechanism solutions reveal two earthquake clusters, one at the Central Balantak Fault that exhibits normal slip on a SE–NW trending rupture, and the other at the West Balantak Fault, which exhibits dextral strike-slip motion on a SE–NW trending rupture. The additional static stress increase transferred by the Mw 6.2 mainshock may have triggered the subsequent Mw 5.8 event. A detailed assessment of previously unmapped faults in Central Sulawesi is essential for a more comprehensive understanding of seismic hazard in the region.
Seismogenic structures along the deformation front from onshore to offshore SW Taiwan
Authors: Wu Wen-Nan , Lin Jing-Yi , Doo Wen-Bin , Lo Chung-Liang , Hsu Shu-Kun
Published: August 2024

Accurately imaging seismogenic structures is crucial for seismic hazard assessment. This is especially important around the deformation front (DF) region off SW Taiwan, where seismic potential is high but the fault structure and seismic activity are still poorly understood. Here, we present a comprehensive delineation of seismogenic structures along the onshore and offshore DF of SW Taiwan, utilizing hypocenter relocations and first-motion focal mechanism solutions from January 1991 to March 2019. Five distinctive seismogenic structures are delineated. Particularly, the energetic seismic activity initialled after the 2017 Mw5.3 Tainan earthquake and migrated northeastward along the western side of the DF. The offshore trace of the DF could serve as a boundary delimiting the seismic activity driven by the flexural stress of the subducted Eurasia Plate to the west of the DF. This observation could constrain the magnitude estimation of future earthquakes offshore SW Taiwan. Meanwhile, the areas with higher seismic moment release are located near the DF rather than known faults, indicating that the DF may dominate the seismic moment release. However, further study is warranted into the intricate relationship among seismic strain variation, the structure of DF, and seismic activity to further understand the seismic potential. Our first-motion focal mechanism solutions show that several earthquakes in SW Taiwan were characterized by P-axis orientations parallel to the strike of the Taiwan orogeny. Those events are preferably explained by the lateral compression induced by the ongoing collision between the Eurasia and Philippine Sea plates.
Dissecting reactive astrocyte responses: lineage tracing and morphology-based clustering
Authors: Delgado-García Lina M. , Ojalvo-Sanz Ana C. , Nakamura Thabatta K. E. , Martín-López Eduardo , Porcionatto Marimelia , Lopez-Mascaraque Laura
Published: August 2024

Brain damage triggers diverse cellular and molecular events, with astrocytes playing a crucial role in activating local neuroprotective and reparative signaling within damaged neuronal circuits. Here, we investigated reactive astrocytes using a multidimensional approach to categorize their responses into different subtypes based on morphology. This approach utilized the StarTrack lineage tracer, single-cell imaging reconstruction and multivariate data analysis. Our findings identified three profiles of reactive astrocyte responses, categorized by their effects on cell size- and shape- related morphological parameters: “moderate”, “strong,” and “very strong”. We also examined the heterogeneity of astrocyte reactivity, focusing on spatial and clonal distribution. Our research revealed a notable enrichment of protoplasmic and fibrous astrocytes within the “strong” and “very strong” response subtypes. Overall, our study contributes to a better understanding of astrocyte heterogeneity in response to an injury. By characterizing the diverse reactive responses among astrocyte subpopulations, we provide insights that could guide future research aimed at identifying novel therapeutic targets to mitigate brain damage and promote neural repair.

Graphical Abstract
Selective embolisation of an idiopathic bronchial artery pseudoaneurysm presenting with recurrent laryngeal nerve palsy: a case report
Authors: Copping R. , Ng N. , Osman S.
Published: August 2024

Background

Bronchial artery pseudoaneurysms (BAP) or aneurysms (BAA) are rare, potentially life-threatening and remain poorly understood. They are most commonly idiopathic but may be associated with a number of other disease processes. Bronchial artery embolisation (BAE) is considered the first line treatment while surgical techniques are reserved for patients with a clear contraindication to embolisation or where anatomical factors preclude an endovascular approach.

Case presentation

We present an interesting case of a 56 year-old male presenting with an idiopathic unruptured right BAP causing clinical and radiological signs of left recurrent laryngeal nerve (RLN) palsy. He was otherwise clinically well with no other reported symptoms and no significant past medical history. There were no significant findings on work-up and investigation. He was ultimately treated successfully with selective transarterial coil embolization of the right bronchial artery. This is an atypical presentation of a rare clinical entity and has not previously been published in the literature to our knowledge.

Conclusions

BAPs and BAAs are highly variable in their presentation, ranging from incidental asymptomatic findings to catastrophic haemorrhage, depending on their location and if they are contained or ruptured. Timely diagnosis and referral to facilitate urgent embolisation is essential to prevent potentially serious clinical sequelae. Endovascular treatment in the form of BAE is considered first line.
Proposals for consideration at IMC12 to modify provisions related solely to fungi in Chapter F of the International Code of Nomenclature for algae, fungi, and plants
Authors: May Tom W. , Hawksworth David L.
Published: August 2024

Seven proposals or sets of proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) have been received. These proposals are formally presented together here. The topics addressed relate to: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. In addition, a suggestion is included to update the mention of the World Directory of Culture Collections in Article 40.7 Note 4. A Synopsis of the formal proposals will be provided in early July 2024, and the mycological community will be invited to provide a guiding vote on the proposals with a closing date of 2 August 2024. Final decisions on the proposals will be made following debate at the Fungal Nomenclature Session of IMC12 in August 2024.
Local community engagement and gazettement approach in managing and conserving Pangani historic town in Tanzania
Authors: Chami Maximilian Felix , Mjema Elinaza
Published: August 2024

Pangani is a historic coastal Swahili town situated at the mouth of the Pangani River, which empties its waters into the Indian ocean. Archaeologists have traced the origins of this town back to the seventh century through evidence from material cultures found in this area. Despite its historical importance and archaeological interest, Pangani faces substantial conservation and management challenges, primarily due to low awareness levels among its local community. These residents are largely unaware of the town’s historical value and of the impact of factors such as climate change, stone quarrying, wave erosion, and development pressures, so effective conservation plans are lacking. In finding the best practices for managing and conserving this historic town, a critical question remains as to how to rescue the town's significance and value from these challenges. This paper proposes a gazettement approach for managing and conserving Pangani, emphasising a bottom-up approach that involves local communities and other stakeholders in the conservation process.
Separation of microplastics from deep-sea sediment using an affordable, simple to use, and easily accessible density separation device
Authors: Shaw Katherine R. , Sandquist Rachel , Fairclough Cameron , Black Jesse , Fitzgerald Alexandra , Shaw Jaxson T. , Gallager Scott , Lynch Jennifer
Published: August 2024

Microplastics accumulate in the environment but methods to extract particles from sediment for quantification and identification often lack accuracy and reproducibility. Existing methods vary greatly and many do not achieve adequate microplastic separation. During method development for extraction procedures, spike-recovery experiments (positive controls) are essential to ensure accurate and reproducible results from each sample matrix. Furthermore, the large variability in grain size and organic matter can affect the extraction of microplastics from the matrix. Scientists have used density separation to separate microplastics from matrices for decades, but apparatuses are often made of plastic, need to be custom made, and require multiple sample transfers from one apparatus to another. This study presents an affordable, easily accessible, and simple to use Density Separation Device (DSD) to remove plastics from deep-sea sediments. Eight polymers were spiked into replicates of environmental sediment, including six fragments: high density polyethylene (HDPE), polypropylene (PP), polyvinyl chloride (PVC), polystyrene (PS), nylon (PA6), and crumb rubber (CR) and two fibers: cellulose acetate (CA) and polyester (PEST). Two size classes of polymers were used: 100 μm to 300 μm and > 300 μm. Using a sodium polytungstate solution at a density of 1.9 g/mL and reflectance FTIR microscopy for particle identification, mean recoveries of all fragments exceeded 78% (CR: 92.7% ± 30.8%, PP: 78.4% ± 34.0%, HDPE: 93.8% ± 13.5%, PS: 86.9% ± 25.7%, PA6: 98.4% ± 63.2%, PVC: 100.0% ± 12.4%). Fiber recovery was much lower (PEST: 28.1% ± 28.1% and CA: 25.9% ± 17.3%) because they aggregated, passed through sieves vertically, or were obscured under other particles. The fragment recovery success, accessibility (available online, all parts under $200) and ease of use of this DSD should facilitate widespread use, thus helping to standardize sample preparation methods for microplastic metrology.
Assessment of Hearing Dysfunction in Patients With Graves’ Disease and Thyroid Eye Disease Without or With Teprotumumab
Authors: Smith Terry J , Holt Robert J , Fu Qianhong , Qashqai Anahita , Barretto Naina , Conrad Elizabeth , Brant Jason A
Published: August 2024

Context

Thyroid eye disease (TED) negatively affects quality of life. TED occurs predominantly in Graves’ disease (GD). Teprotumumab improves TED but concern for hearing adverse events (AEs) has emerged. Hearing dysfunction is reported in thyroid autoimmune disease but the background prevalence in GD/TED without teprotumumab remains uncertain.

Objective

This work aimed to quantify ear-related diagnostic codes/hearing AEs in GD, TED, and patients receiving teprotumumab by examining medical claims and clinical trials.

Methods

Deidentified claims for ear/labyrinth-related International Classification of Disorders, Tenth Revision codes (KOMODO) were examined in GD patients without TED, and TED patients without/with teprotumumab treatment. Hearing AE incidence/severity was evaluated in teprotumumab clinical trials. Graves’ Ophthalmopathy Quality of Life questionnaire (GO-QOL) scores were compared in teprotumumab TED trial patients without/with hearing AEs.

Results

GD (469 720), TED (38 566) and teprotumumab-treated (967) patients were identified in the claims database. Ear-related codes (including those not specific for hearing) occurred in 24% GD, 33% TED, and 32% teprotumumab-treated patients. “Sensorineural hearing loss bilateral” was most frequent: 7% (32 961/469 720) GD, 11.1% (4279/38 566) TED, and 10.8% (104/967) teprotumumab patients. Before teprotumumab use, 17.1% (165) patients had ear-related codes, while 10.1% (98) had new ear-related codes post treatment.

Eight teprotumumab oncology trials revealed 8.1% (51/633) had ear/labyrinth disorders with 2.1% (13) considered study-drug-related and 3.8% (24) hearing impairment/tinnitus-related AEs with 1.3% (8) considered study-drug-related. Similar rates occurred in TED trials.

GO-QOL improved in teprotumumab-treated patients without/with hearing AEs. Incidence/severity was consistent across patients with chronic and acute TED.

Conclusion

These analyses indicate similar prevalence of hearing claims in patients with GD/TED alone as following teprotumumab treatment. Future analyses of incremental hearing risk from teprotumumab should use a priori study designs accounting for background hearing dysfunction in patients with GD/TED.
Compensation of gene dosage on the mammalian X
Authors: Cecalev Daniela , Viçoso Beatriz , Galupa Rafael
Published: August 2024

Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.
Compromised COPII vesicle trafficking leads to glycogenic hepatopathy
Authors: Yang Yuxi , Zhang Xue , Zhao Qingshun , Zhang Jingzi , Lou Xin
Published: August 2024

Being a vital cellular process, coat protein complex II (COPII) vesicle trafficking has been found to play a crucial role in liver metabolism. However, its functions and the underlying mechanisms in systemic metabolic homeostasis have not been fully understood. Here, with a newly identified gene trap zebrafish line (sec31anju221), we show that compromised COPII vesicle trafficking leads to biphasic abnormal hepatic metabolism. During the larval stage, deficiency of COPII-mediated trafficking leads to activation of the unfolded protein response and the development of hepatic steatosis. By using epistasis analysis, we found that the eIF2α–ATF4 pathway serves as the primary effector for liver steatosis. In adult sec31anju221 fish, the hepatosteatosis was reversed and the phenotype switched to glycogenic hepatopathy. Proteomic profiling and biochemical assays indicate that sec31anju221 fish are in a state of hypothyroidism. Moreover, our study shows that thyroid hormone treatment alleviates the metabolic defects. This study provides insights into processes of liver diseases associated with vesicle trafficking impairments and expands our understanding of the pathological interplay between thyroid and liver.
Computational modeling establishes mechanotransduction as a potent modulator of the mammalian circadian clock
Authors: Francis Emmet A. , Rangamani Padmini
Published: August 2024

Mechanotransduction, which is the integration of mechanical signals from the external environment of a cell to changes in intracellular signaling, governs many cellular functions. Recent studies have shown that the mechanical state of the cell is also coupled to the cellular circadian clock. To investigate possible interactions between circadian rhythms and cellular mechanotransduction, we have developed a computational model that integrates the two pathways. We postulated that translocation of the transcriptional regulators MRTF (herein referring to both MRTF-A and MRTF-B), YAP and TAZ (also known as YAP1 and WWTR1, respectively; collectively denoted YAP/TAZ) into the nucleus leads to altered expression of circadian proteins. Simulations from our model predict that lower levels of cytoskeletal activity are associated with longer circadian oscillation periods and higher oscillation amplitudes, which is consistent with recent experimental observations. Furthermore, accumulation of YAP/TAZ and MRTF in the nucleus causes circadian oscillations to decay in our model. These effects hold both at the single-cell level and within a population-level framework. Finally, we investigated the effects of mutations in YAP or lamin A, the latter of which result in a class of diseases known as laminopathies. In silico, oscillations in circadian proteins are substantially weaker in populations of cells with mutations in YAP or lamin A, suggesting that defects in mechanotransduction can disrupt the circadian clock in certain disease states; however, reducing substrate stiffness in the model restores normal oscillatory behavior, suggesting a possible compensatory mechanism. Thus, our study identifies that mechanotransduction could be a potent modulatory cue for cellular clocks and that this crosstalk can be leveraged to rescue the circadian clock in disease states.
Hominini-specific regulation of the cell cycle by stop codon readthrough of FEM1B
Authors: Akhtar Md Noor , Singh Anumeha , Manjunath Lekha E. , Dey Dhruba , Kumar Sangeetha Devi , Vasu Kirtana , Das Arpan , Eswarappa Sandeep M.
Published: August 2024

FEM1B is a substrate-recognition component of the CRL2 E3 ubiquitin-protein ligase. This multi-protein complex targets specific proteins for ubiquitylation, which leads to their degradation. Here, we demonstrate the regulation of FEM1B expression by stop codon readthrough (SCR). In this process, translating ribosomes readthrough the stop codon of FEM1B to generate a C-terminally extended isoform that is highly unstable. A total of 81 nucleotides in the proximal 3′UTR of FEM1B constitute the necessary and sufficient cis-signal for SCR. Also, they encode the amino acid sequence responsible for the degradation of the SCR product. CRISPR-edited cells lacking this region, and therefore SCR of FEM1B, showed increased FEM1B expression. This in turn resulted in reduced expression of SLBP (a target of FEM1B-mediated degradation) and replication-dependent histones (target of SLBP for mRNA stability), causing cell cycle delay. Evolutionary analysis revealed that this phenomenon is specific to the genus Pan and Homo (Hominini). Overall, we show a relatively recently evolved SCR process that relieves the cell cycle from the negative regulation by FEM1B.
Considering ultraviolet radiation in experimental biology: a neglected pervasive stressor
Authors: Hird Coen , Lundsgaard Niclas U. , Downie Adam T. , Cramp Rebecca L. , Franklin Craig E.
Published: August 2024

Ultraviolet radiation (UVR) is a pervasive factor that has shaped the evolution of life on Earth. Ambient levels of UVR mediate key biological functions but can also cause severe lethal and sublethal effects in a wide range of organisms. Furthermore, UVR is a powerful modulator of the effects of other environmental factors on organismal physiology, such as temperature, disease, toxicology and pH, among others. This is critically important in the context of global change, where understanding the effects of multiple stressors is a key challenge for experimental biologists. Ecological physiologists rarely afford UVR discussion or include UVR in experimental design, even when it is directly relevant to their study system. In this Commentary, we provide a guide for experimental biologists to better understand if, when, and how UVR can be integrated into experimental designs to improve the ecological realism of their experiments.
The genome sequence of a tephritid fruit fly, Merzomyia westermanni Meigen 1826
Authors: Falk Steven , Crowley Liam M. , Medd Nathan C. ,   University of Oxford and Wytham Woods Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: August 2024

We present a genome assembly from an individual Merzomyia westermanni (a tephritid fruit fly; Arthropoda; Insecta; Diptera; Tephritidae). The genome sequence spans 986.20 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,765 protein-coding genes.
Case Article–Forecasting at FoodMart: A Case on Cultural Diversity in Supply Chain Management
Authors: David Amy
Published: August 2024

This case focuses on forecasting a number of grocery items from the perspective of a demand planner who notices that the items have irregular patterns in the seasonality of their historical sales. It introduces students to the need for diverse cultural knowledge in forecasting certain consumer products and provides instructors with a starting point for discussing the business case for diversity and the value of diverse teams in a supply chain management context. This case is recommended for use in an undergraduate-level course in supply chain management, operations management, or business analytics. Learning goals are for students to identify irregular patterns in historical sales data and determine their root causes, evaluate a statistical forecast created without human intervention, and explain how culturally diverse teams can be valuable in a forecasting process.

Supplemental Material: The Teaching Note and grocery forecasting Excel spreadsheet are available at https://www.informs.org/Publications/Subscribe/Access-Restricted-Materials .
Mycophenolate mofetil for the treatment of warm autoimmune haemolytic anaemia post-rituximab therapy: a case series
Authors: Borja-Montes Oscar F. , Toro-Pedroza Alejandro , Horton Darrell D. , Andritsos Leslie A. , Ebaid Ala
Published: August 2024

Background: Warm autoimmune haemolytic anaemia (wAIHA) is an acquired haemolytic disorder most commonly treated with a combination of corticosteroids, rituximab and/or splenectomy. Third-line therapies for refractory cases include immunosuppressive agents. Mycophenolate mofetil is frequently used in these scenarios, although its use is supported by small studies and anecdotal evidence rather than large-scale data. Case description: We describe three cases of refractory warm autoimmune haemolytic anaemia successfully treated with mycophenolate mofetil. Case 1: A persistent case of autoimmune haemolytic anaemia in a 56-year-old was ultimately managed with mycophenolate mofetil, leading to successful steroid tapering and stable haemoglobin levels without relapse. Case 2: A woman with a complex oncological history, including lymphoma and breast cancer, achieved remission with mycophenolate therapy, maintaining stability post-steroid treatment. Case 3: Mycophenolate proved effective for a 63-year-old with cirrhosis after recurrent autoimmune anaemia and deep vein thrombosis, enabling cessation of steroids and maintaining remission. Conclusion: Management of this condition can be challenging and balancing the available treatments is crucial to reduce potential complications from long-term therapies that appear to be ineffective. Our case series demonstrates anecdotal experience on successful use of mycophenolate mofetil for complex refractory cases of wAIHA.
An intimate relationship lies between the appendix and the colon: a case report of colitis cystica profunda post-laparoscopic appendectomy
Authors: Chebbo Houssein , Yazbak Amer , Saleh Sarah , Karam Karam , Azizi Lamia , Fiani Elias
Published: August 2024

Cystica profunda is a rare benign finding of mucous-filled cysts in the submucosa of the gastrointestinal tract, more commonly found in the rectum and colon. Risk factors include rectal prolapse, inflammatory bowel diseases, pelvic radiation and being post-appendectomy. We present a case of a female patient presenting with rectorrhagia, found to have sigmoidal colitis cystica profunda (CCP) six months post-appendectomy. This case is one of the few in medical literature to highlight the direct association between laparoscopic appendectomy and CCP, previously discussed in the literature as a complication post-appendectomy in the American Journal of Gastroenterology.
Nurses with dyslexia: overcoming challenges and thriving in the profession
Authors: Butler Sarah
Published: August 2024

Dyslexia is a specific learning difficulty impacting reading, writing and spelling. Practising nursing requires a unique set of skills that encompass effective communication, critical thinking, and organisational skills. This article focuses on the experiences of nurses with dyslexia, shedding light on the distinct challenges they encounter and the resilient strategies they employ to navigate their roles and excel in the health profession.
Is patient safety in the NHS fundamentally broken?
Authors: Tingle John
Published: August 2024

John Tingle, Associate Professor, Birmingham Law School, University of Birmingham, discusses the state of patient safety in the NHS and several key reports
An updated checklist of the jewel beetles (Coleoptera: Buprestidae) of Peru
Authors: JUÁREZ-NOÉ GINO , GONZÁLEZ-CORONADO UZBEKIA
Published: August 2024

Compilation of data from bibliographic records and revision of specimens deposited in institutions and private collections, an updated checklist of the jewel beetles (Coleoptera: Buprestidae) of Peru is presented. The updated checklist includes 4 subfamilies, 14 tribes, 37 genera and 214 species-group taxa (199 species and 15 subspecies). The subfamily Agrilinae and the genus Agrilus are most species-rich, while 50 species are known only from Peru. Agrilus (Agrilus) auratolineatus Curletti & Brûlé, 2011, Amorphosoma penicillatum (Klug, 1827), Conognatha (Conognatha) clara Erichson, 1848, Leiopleura gemma Obenberger, 1936, L. trochilus Kerremans, 1896, Lius elongatus Kerremans, 1896, Pachyschelus bolivianus Obenberger, 1925, P. nemoralis Obenberger, 1925, Taphrocerus catacaustus Obenberger, 1941, T. scutellatus Obenberger, 1934, T. subauratus Marek, 2017 and T. zikani Obenberger, 1924 are new country records, while Chrysobothris (Chrysobothris) fallax Juárez-Noé & González-Coronado, 2023, C. (C.) requensis Juárez-Noé, Barboza & Perales, 2023 and Lasionota (Nelsonozodes) oberthuri (Kerremans, 1897) present new regional records. Each species listed includes its current name, synonyms, and regional/provincial distribution data. Additionally, photographs of some species are provided.
Ultrafast dynamics and internal processing mechanism of silica glass under double-pulse femtosecond laser irradiation
Authors: Ren Guoqi , Ito Yusuke , Yoshizaki Reina , Sun Huijie , Hattori Junya , Sugita Naohiko
Published: August 2024

Femtosecond laser-induced plasma filaments have potential for various applications including attosecond physics, spectroscopy, and microprocessing. However, the use of plasma filaments to generate high-aspect-ratio internal modifications remains low-efficiency. Here, we experimentally demonstrated high-efficiency internal processing using plasma filaments induced by a double-pulse femtosecond laser. The processing mechanism was revealed through an investigation of the ultrafast dynamics of plasma filaments in experiments and simulations. We found that the excitation region of the first pulse (P1) exerted a temporal effect on the propagation and absorption of the second pulse (P2) due to the evolution of excited electrons, thus resulting in different processing characterizations. At a smaller inter-pulse delay (IPD), electrons and self-trapped excitons induced by P1 improved the absorption of P2 in the shallow region. Consequently, the main excitation regions of P1 and P2 were separated, resulting in a lower density of energy deposition and weak modifications. Whereas, at a larger IPD, P2 penetrated a deeper region with the relaxation of electrons and excitons induced by P1, leading to a better overlap of excitation regions between P2 and P1, thus improving the density of energy deposition and achieving efficient microprocessing. Besides, at an infinite IPD, P2 behaved like P1, but no modification was obtained owing to the complete energy diffusion of P1. Therefore, controlling the electron dynamic and energy diffusion contributes to the improvement of modification efficiency. Furthermore, the distribution of electron densities on the cross section was estimated to precisely analyze the microprocessing. These results are expected to aid in a better understanding of the interaction mechanism between dielectrics and intense ultrafast lasers and be useful for microprocessing applications.
Analysis and enhancement for ultra-large depth-of-field light field display based on MEMS laser scanning projection arrays
Authors: Yu Haiyang , Yan Xingpeng , Yan Zhiqiang , Chen Zhuo , Liu Jing , Jiang Xiaoyu
Published: August 2024

This study systematically analyzes factors limiting the depth of field in projection-based light field display systems, pinpointing two primary contributors: the blurring caused by traditional lens imaging principles at non-focus planes, and the increased light reconstruction errors induced by large-angle light diffusing devices. MEMS laser scanning projectors are employed as light sources to enable accurate focusing of reconstructed light at any distance. Furthermore, cylindrical lens compound diffusers with smaller diffusing angles are utilized to minimize the direction deviation of reconstructed light. Complemented by enhancing the density of the projection arrangements, the system–composed of 108 MEMS projectors–achieves substantial 3-meter depth of field and a frame size of 1.30 m × 0.75 m, delivering clear light field reconstruction around the diffusing devices. Corresponding experiments validate the theoretical analysis, demonstrating tremendous innovation and application value.
SSCDN: a spatial-spectral collaborative network for hyperspectral image denoising
Authors: Li Kaixiang , Li Renjian , Li Guiye , Liu Shaojun , He Zhengdi , Zhang Meng , Chen Lingling
Published: August 2024

Hyperspectral imaging provides the full spectrum at each point of the whole field-of-view, and thus is being extensively employed in remote sensing, surveillance, medical diagnostics and biological research. However, the intrinsically limited photons for each spectral band and the inevitable noise during acquisition result in complex degradation of hyperspectral images (HSIs) that adversely impacts the subsequent data analysis. Yet, it remains challenging for current HSI denoising methods to effectively address HSI datasets that are significantly contaminated by complex noise, especially in terms of spectral recovery. In this paper, we propose a spatial-spectral collaborative denoising network (SSCDN) that makes full use of spatial-spectral correlation information for HSI denoising. Through the combination of attention mechanism and specifically designed spatial-spectral collaborative attention module along with a multi-loss joint optimization strategy, the proposed model achieves superior denoising performance while well-preserving spectral and spatial features for complex degradation. Extensive experimental results on simulated and real data for remote sensing and biomedical applications demonstrate that the proposed SSCDN outperforms other state-of-the-art competitive HSI denoising methods under various noise settings, especially in terms of structural-spectral fidelity and the model robustness against noise.
Ultrawideband 3-bit multifunctional metasurfaces by completely spin-decoupled meta-atom
Authors: Zhang Jingwei , Chen Wenqiong , Qi Buxiong , Feng Junlang , Niu Tiaoming , Mei Zhonglei
Published: August 2024

The achievement of distinct wavefront reconstruction for orthogonally polarized electromagnetic (EM) waves in a broadband frequency range is extremely important in modern wireless communications. However, the development of circularly polarized wavefront modulation devices is hindered by conjugate symmetric phase responses introduced by the rotation-induced geometric phase. Herein, a spin-decoupled meta-atom with a novel structure is designed to independently tailor left-hand and right-hand circularly polarized incident waves over a broadband range of 12–28 GHz with a fractional bandwidth of 80%. By incorporating diagonal curvature-induced and conventional geometric phases, spin-dependent phase modulation covering the entire 2π range can be obtained. As a proof of concept, three prototypes are designed and manufactured. In addition, a four-channel imaging method is proposed to enhance the information capacity of the meta-hologram. Furthermore, the applications of the proposed spin-decoupled method are also investigated in metalens and orbital angular momentum. Both the calculation and experimentation demonstrate the feasibility of the proposed spin-decoupled phase modulation strategy, which has potential applications in information metasurfaces, metalens, wireless communications, and other fields.
Low-complexity adaptive multipath interference and channel noise mitigation scheme based on optimized detection for bandwidth-limited IM/DD systems
Authors: Xie Fei , Huang Xiaoqian , Qiao Yaojun
Published: August 2024

In this Letter, we propose a low-complexity adaptive multipath interference (MPI) and channel noise mitigation (AMCM) scheme in the receiver digital signal processing (DSP) for bandwidth-limited intensity modulation and direct detection (IM/DD) transmission systems. Following channel equalization, MPI and channel noise are distributed in the low- and high-frequency parts, respectively, and exhibit the characteristics of bandstop filtering. The proposed AMCM is designed based on optimized detection, which incorporates an adaptive bandpass filter (BPF) and a log-maximum a posteriori estimation with a lookup table-based fixed number of surviving states (LUT-based FS-MAP) decoder. The adaptive BPF is capable of mitigating the MPI and channel noise based on spectral distribution. Moreover, the LUT-based FS-MAP decoder can eliminate intersymbol interference (ISI) introduced by the BPF. The proposed AMCM is implemented in an O-band 56-Gbaud IM/DD optical 4-level pulse amplitude modulation (PAM-4) system with a 10.7-GHz bandwidth over a 10-km standard single-mode fiber with different linewidths. The results demonstrate that the proposed AMCM scheme can enhance signal-to-interference ratio (SIR) tolerance to 11 dB with only three real-valued multiplications per symbol, achieving a 7% hard-decision forward error correction threshold. To the best of our knowledge, for the first time, this represents the inaugural instance of optimized detection being employed for MPI mitigation.
GRK2 kinases in the primary cilium initiate SMOOTHENED-PKA signaling in the Hedgehog cascade
Authors: Walker Madison F. , Zhang Jingyi , Steiner William , Ku Pei-I , Zhu Ju-Fen , Michaelson Zachary , Yen Yu-Chen , Lee Annabel , Long Alyssa B. , Casey Mattie J. , Poddar Abhishek , Nelson Isaac B. , Arveseth Corvin D. , Nagel Falko , Clough Ryan , LaPotin Sarah , Kwan Kristen M. , Schulz Stefan , Stewart Rodney A. , Tesmer John J. G. , Caspary Tamara , Subramanian Radhika , Ge Xuecai , Myers Benjamin R.
Published: August 2024

During Hedgehog (Hh) signal transduction in development and disease, the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO) communicates with GLI transcription factors by binding the protein kinase A catalytic subunit (PKA-C) and physically blocking its enzymatic activity. Here, we show that GPCR kinase 2 (GRK2) orchestrates this process during endogenous mouse and zebrafish Hh pathway activation in the primary cilium. Upon SMO activation, GRK2 rapidly relocalizes from the ciliary base to the shaft, triggering SMO phosphorylation and PKA-C interaction. Reconstitution studies reveal that GRK2 phosphorylation enables active SMO to bind PKA-C directly. Lastly, the SMO-GRK2-PKA pathway underlies Hh signal transduction in a range of cellular and in vivo models. Thus, GRK2 phosphorylation of ciliary SMO and the ensuing PKA-C binding and inactivation are critical initiating events for the intracellular steps in Hh signaling. More broadly, our study suggests an expanded role for GRKs in enabling direct GPCR interactions with diverse intracellular effectors.
Aboveground and belowground biodiversity have complementary effects on ecosystem functions across global grasslands
Authors: Martins Catarina S. C. , Delgado-Baquerizo Manuel , Jayaramaiah Ramesha H. , Tao Dongxue , Wang Jun-Tao , Sáez-Sandino Tadeo , Liu Hongwei , Maestre Fernando T. , Reich Peter B. , Singh Brajesh K.
Published: August 2024

Grasslands are integral to maintaining biodiversity and key ecosystem services and are under threat from climate change. Plant and soil microbial diversity, and their interactions, support the provision of multiple ecosystem functions (multifunctionality). However, it remains virtually unknown whether plant and soil microbial diversity explain a unique portion of total variation or shared contributions to supporting multifunctionality across global grasslands. Here, we combine results from a global survey of 101 grasslands with a novel microcosm study, controlling for both plant and soil microbial diversity to identify their individual and interactive contribution to support multifunctionality under aridity and experimental drought. We found that plant and soil microbial diversity independently predict a unique portion of total variation in above- and belowground functioning, suggesting that both types of biodiversity complement each other. Interactions between plant and soil microbial diversity positively impacted multifunctionality including primary production and nutrient storage. Our findings were also climate context dependent, since soil fungal diversity was positively associated with multifunctionality in less arid regions, while plant diversity was strongly and positively linked to multifunctionality in more arid regions. Our results highlight the need to conserve both above- and belowground diversity to sustain grassland multifunctionality in a drier world and indicate climate change may shift the relative contribution of plant and soil biodiversity to multifunctionality across global grasslands.