bluuebunny/crossref_metadata_2025_split huggingface dataset:
An alternative and effective method for extracting skeletal organic matrix adapted to the red coral Corallium rubrum
Authors: Ganot Philippe , Loentgen Guillaume , Marin Frédéric , Plasseraud Laurent , Allemand Denis , Tambutté Sylvie 
Published: September 2022

ABSTRACT
Skeleton formation in corals is a biologically controlled process in which an extracellular organic matrix (OM) is entrapped inside the calcified structure. The analysis of OM requires a time-consuming and tedious extraction that includes grinding, demineralization, multiple rinsing and concentration steps. Here we present an alternative and straightforward method for the red coral Corallium rubrum that requires little equipment and saves steps. The entire skeleton is directly demineralized to produce a tractable material called ghost, which is further rinsed and melted at 80°C in water. The comparative analysis of the standard and alternative methods by electrophoresis, western blot, and FTIR of C. rubrum OM, shows that the ‘alternative OM’ is of higher quality. Advantages and limitations of both methods are discussed.
The RNA ligase RNA terminal phosphate cyclase B regulates mRNA alternative splicing and is required for mouse oocyte development and maintenance
Authors: Zhang Hua , Jiang Jun-Chao , Wu Yun-Wen , Yu Yuan-Song , Wang Hua-Nan , Ding Nai-Zheng , Fan Heng-Yu 
Published: September 2022

ABSTRACT
Recent large-scale mRNA sequencing has shown that introns are retained in 5-10% of mRNA, and these events are named intron retention (IR). IR has been recognized as a key mechanism in the regulation of gene expression. However, the role of this mechanism in female reproduction in mammals remains unclear. RNA terminal phosphate cyclase B (RTCB) is a RNA ligase; we found that RTCB conditional knockout mice have premature ovarian failure and that RTCB plays a crucial role in follicular development. RTCB regulated the splicing of transcripts related to DNA methylation and DNA damage repair. In addition, it regulated the resumption of oocyte meiosis by affecting CDK1 activation. Moreover, the loss of RTCB suppressed zygotic genome activation (ZGA) and decreased translation at the global level. In addition, Rtcb deletion resulted in the accumulation of maternal mRNAs containing unspliced introns and in a decline in the overall level of transcripts. As a result, the Rtcb−/− females were sterile. Our study highlights the important role of RTCB-regulated noncanonical alternative splicing in female reproduction.
Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus
Authors: Conde Daniel , Triozzi Paolo M. , Pereira Wendell J. , Schmidt Henry W. , Balmant Kelly M. , Knaack Sara A. , Redondo-López Arturo , Roy Sushmita , Dervinis Christopher , Kirst Matias 
Published: September 2022

ABSTRACT
Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials – a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of the epidermis, leaf mesophyll and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we applied a pipeline for interspecific single-cell gene expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the principles underlying cell division and differentiation conserved between herbaceous and perennial species while also allowing us to examine species-specific differences at single-cell resolution.
Biomechanical behaviour of lizard osteoderms and skin under external loading
Authors: Kéver Loïc , Olivier Damien , Marghoub Arsalan , Evans Susan E. , Vickaryous Matthew K. , Moazen Mehran , Herrel Anthony 
Published: September 2022

ABSTRACT
Many species of lizards are partially enveloped by a dermal armour made of ossified units called osteoderms. Lizard osteoderms demonstrate considerable species-specific variation in morphology and histology. Although a physical/protective role (against predators, prey, conspecifics and impact loading during falls) is frequently advanced, empirical data on the biomechanics of lizard osteoderms are scarce, limiting our understanding of form–function relationships. Here, we report deformation recorded at the surface of temporal osteoderms during controlled external loading of preserved specimens of 11 lizard species (Tiliqua rugosa, Tiliqua scincoides, Corucia zebrata, Pseudopus apodus, Timon lepidus, Matobosaurus validus, Broadleysaurus major, Tribolonotus gracilis, Tribolonotus novaeguineae, Heloderma horridum and Heloderma suspectum). Based on the strain recorded in situ and from isolated osteoderms, the skin of the species investigated can be ranked along a marked stiffness gradient that mostly reflects the features of the osteoderms. Some species such as T. rugosa and the two Heloderma species had very stiff osteoderms and skin while others such as T. lepidus and P. apodus were at the other end of the spectrum. Histological sections of the osteoderms suggest that fused (versus compound) osteoderms with a thick layer of capping tissue are found in species with a stiff skin. In most cases, loading neighbouring osteoderms induced a large strain in the instrumented osteoderm, attesting that, in most species, lizard osteoderms are tightly interconnected. These data empirically confirm that the morphological diversity observed in lizard osteoderms is matched by variability in biomechanical properties.
Laboratory protocol for the digital multiplexed gene expression analysis of nasopharyngeal swab samples using the NanoString nCounter system
Authors: García Aranda Marilina , López-Rodríguez Inmaculada , García-Gutiérrez Susana , Padilla-Ruiz Maria , de Luque Vanessa , Hortas Maria Luisa , Diaz Tatiana , Álvarez Martina , Barragan-Mallofret Isabel , Redondo Maximino ,   Research Network on Health Services in Chronic Diseases (Red de Investigación en Servicios Sanitarios y Enfermedades Crónicas, REDISSEC)
Published: September 2022

This paper describes a laboratory protocol to perform the NanoString nCounter Gene Expression Assay from nasopharyngeal swab samples. It is urgently necessary to identify factors related to severe symptoms of respiratory infectious diseases, such as COVID-19, in order to assess the possibility of establishing preventive or preliminary therapeutic measures and to plan the services to be provided on hospital admission. At present, the samples recommended for microbiological diagnosis are those taken from the upper and/or the lower respiratory tract. The NanoString nCounter Gene Expression Assay is a method based on the direct digital detection of mRNA molecules by means of target-specific, colour-coded probe pairs, without the need for mRNA conversion to cDNA by reverse transcription or the amplification of the resulting cDNA by PCR. This platform includes advanced analysis tools that reduce the need for bioinformatics support and also offers reliable sensitivity, reproducibility, technical robustness and utility for clinical application, even in RNA samples of low RNA quality or concentration, such as paraffin-embedded samples. Although the protocols for the analysis of blood or formalin-fixed paraffin-embedded samples are provided by the manufacturer, no corresponding protocol for the analysis of nasopharyngeal swab samples has yet been established. Therefore, the approach we describe could be adopted to determine the expression of target genes in samples obtained from nasopharyngeal swabs using the nCOUNTER technology.
Case Report: Nasopharyngeal carcinoma has metastasis to the orbit, consequences in anaemia: A paediatric unusual case of Bangladesh.
Authors: Amin Mohammad Ashraful , Nahin Sabrina , Bonna Atia Sharmin , Hawlader Mohammad Delwer Hossain 
Published: September 2022

Background: Although nasopharyngeal carcinoma (NPC) has a significant risk of spreading to other parts of the body early, orbital and ocular surrounding tissues metastases are uncommon. Case Report: This paper described a 16-year-old patient diagnosed with a locally advanced NPC and ocular metastasis and was treated with neoadjuvant chemotherapy treatment. One of the rare early presentations is orbital metastases with vision problems. Discussion: Orbital metastases in children are considerably more uncommon. Cachexia and malnutrition are prevalent problems in people with cancer, affecting life and longevity. Anaemia is a severe issue for nasopharyngeal cancer patients undergoing chemotherapy or radiotherapy. Conclusion: Orbital metastases frequently arise in advanced stages of the disease and in the scenario of many metastases the persistence of therapy and the nasopharyngeal cancer patient's standard of living is linked to the occurrence of anaemia.
Putting youth at the centre: co-design of a community-based intervention to improve HIV outcomes among youth in Zimbabwe
Authors: Mackworth-Young Constance RS. , Dringus Stefanie , Dauya Ethel , Dziva Chikwari Chido , Mavodza Constancia , Tembo Mandikudza , Doyle Aoife , McHugh Grace , Simms Victoria , Wedner-Ross Maurice , Apollo Tsitsi , Mugurungi Owen , Ferrand Rashida A. , Bernays Sarah 
Published: September 2022

Abstract Background Youth have disproportionately poor HIV outcomes. We aimed to co-design a community-based intervention with youth to improve HIV outcomes among 16-24 year-olds, to be trialled in Zimbabwe. Methods We conducted 90 in-depth interviews with youth, family members, community gatekeepers and healthcare providers to understand the barriers to uptake of existing HIV services. The interviews informed an outline intervention, which was refined through two participatory workshops with youth, and subsequent pilot-testing. Results Participants considered existing services inaccessible and unappealing: health facilities were perceived to be for ‘sick people’, centred around HIV and served by judgemental providers. Proposed features of an intervention to overcome these barriers included: i) delivery in a youth-only community space; ii) integration of HIV services with broader health services; iii) non-judgemental skilled healthcare providers; iv) entertainment to encourage attendance; and v) tailored timings and outreach. The intervention framework stands on three core pillars, based on optimising access (community-based youth-friendly settings); uptake and acceptability (service branding, confidentiality, and social activities); and content and quality (integrated HIV care cascade, high quality products, and trained providers). Conclusions Ongoing meaningful youth engagement is critical to designing HIV interventions if access, uptake, and coverage is to be achieved.
Effectiveness of seasonal malaria chemoprevention administered in a mass campaign in the Kedougou region of Senegal in 2016: a case-control study
Authors: Manga Isaac Akhenaton , Tairou Fassiatou , Seck Amadou , Kouevidjin Ekoue , Sylla Khadime , Sow Doudou , Gueye Alioune Babara , Ba Mady , Ndiaye Magatte , Tine Roger Clément Kouly , Gaye Omar , Faye Babacar , Ndiaye Jean Louis Abdourahim 
Published: September 2022

Background: Seasonal malaria chemoprevention (SMC) with sulfadoxine-pyrimethamine plus amodiaquine (SPAQ) is a malaria prevention strategy recommended since 2012 by the World Health Organization (WHO) for children under 5 years. In Senegal, the scaling up of SMC started in 2013 in the south-eastern regions of the country with an extension of the target to 10 years old children. The scaling up of SMC requires regular evaluation of the strategy as recommended by the WHO. This study was conducted to evaluate the effectiveness of SMC. Methods: A case-control study was conducted in some villages of the health districts of Saraya and Kedougou in the Kedougou region from July to December 2016. A case was a sick child, aged 3 months to 10 years, seen in consultation and with a positive malaria rapid diagnostic test (RDT). The control was a child of the same age group with a negative RDT and living in the same compound as the case or in a neighbouring compound. Each case was matched with two controls. Exposure to SMC was assessed by interviewing the mothers/caretakers and by checking the SMC administration card. Results: Overall, 492 children, including 164 cases and 328 controls, were recruited in our study. Their mean ages were 5.32 (+/- 2.15) and 4.44 (+/-2.25) years for cases and controls, respectively. The number of boys was higher in both cases (55.49%; CI 95%=47.54-63.24%) and controls (51,22%; CI 95%=45.83-56.58%). Net ownership was 85.80% among cases and 90.85% among controls (p=0,053). The proportion of controls who received SMC was higher than that of cases (98.17% vs 85.98% and p=1.10-7). The protective effectiveness of SMC was 89% (OR= 0.12 (CI 95%=0.04-0.28)). Conclusions: SMC is an effective strategy in the control of malaria in children. Case-control studies are a good approach for monitoring the efficacy of drugs administered during SMC.
A Polyhedral Study on Fuel-Constrained Unit Commitment
Authors: Pan Kai , Zhao Ming , Li Chung-Lun , Qiu Feng 
Published: September 2022

The electricity production of a thermal generator is often constrained by the available fuel supply. These fuel constraints impose a maximum bound on the energy output over multiple time periods. Fuel constraints are increasingly important in electricity markets because of two main reasons. First, as more natural gas-fired generators join the deregulated market, there is often competition for natural gas supply from other sectors (e.g., residential and manufacturing heating). Second, as more environmental and emission regulations are being placed on fossil fuel-fired generators, fuel supply is becoming more limited. However, there are few studies that consider the fuel constraints in the unit commitment problem from the perspective of computational analysis. To address the challenge faced by an independent power producer with a limited fuel supply, we study a fuel-constrained self-scheduling unit commitment (FSUC) problem where the production decisions are coupled across multiple time periods. We provide a complexity analysis of the FSUC problem and conduct a comprehensive polyhedral study by deriving strong valid inequalities. We demonstrate the effectiveness of our proposed inequalities as cutting planes in solving various multistage stochastic FSUC problems. History: Accepted by Pascal Van Hentenryck, Area Editor for Computational Modeling: Methods & Analysis. Funding: K. Pan was supported in part by the Research Grants Council of Hong Kong [Grant 15501920]. F. Qiu was supported in part by the U.S. Department of Energy Advanced Grid Modeling Program [Grant DE-OE0000875]. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplementary Information [ https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2022.1235 ] or is available from the IJOC GitHub software repository ( https://github.com/INFORMSJoC ) at [ http://dx.doi.org/10.5281/zenodo.6896199 ].
Stability Representations of Many-to-One Matching Problems: An Integer Optimization Approach
Authors: Wiratchotisatian Pitchaya , Atef Yekta Hoda , Trapp Andrew C. 
Published: September 2022

We consider integer optimization models for finding stable solutions to many-to-one, utility-weighted matching problems with incomplete preference lists and ties. Whereas traditional algorithmic approaches for the stable many-to-one matching problem, such as the deferred acceptance algorithm, offer efficient performance for the strict problem setting, adaptation to alternative settings often requires careful customization. Optimization-based approaches are free of the need to create customized algorithms for each unique context and can readily accommodate such extensions as (incomplete) preference lists with ties, alternative and nontraditional objective functions, and side constraints including those that ensure stable matching outcomes free of waste. We explore the flexibility of optimization-based approaches in several ways. First, we introduce four new constraint sets that prevent justified envy and a new system of constraints that prevents waste; taken together, they jointly ensure stable matching outcomes. Second, we create two algorithms to accelerate the generation of our proposed constraints. Third, we construct aggregate objective functions to reflect multiple hierarchical emphases by imposing a strict lexicographical order on the individual components. Fourth, we conduct comprehensive experiments to study the computational performance of our proposed optimization models and compare them with models from the extant literature under a variety of problem attributes. Our experiments reveal the circumstances under which each stability representation excels in terms of optimality criteria and computational efficiency on a variety of real and synthetic data sets. One such setting in which our proposed stability representations excel includes the important context of when sufficient seats exist for applicants, such as school choice problems and hospital residency matching. History: Accepted by Pascal Van Hentenryck, Area Editor for Computational Modeling: Methods & Analysis. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplementary Information [ https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2022.1237 ] or is available from the IJOC GitHub software repository ( https://github.com/INFORMSJoC ) at [ http://dx.doi.org/10.5281/zenodo.6892615 ].
A Sensitivity Analysis of the Price of Anarchy in Nonatomic Congestion Games
Authors: Wu Zijun , Möhring Rolf H. 
Published: September 2022

The price of anarchy (PoA) is a standard measure to quantify the inefficiency of equilibria in nonatomic congestion games. Most publications have focused on worst-case bounds for the PoA. Only a few have analyzed the sensitivity of the PoA against changes of the demands or cost functions, although that is crucial for empirical computations of the PoA. We analyze the sensitivity of the PoA with respect to (w.r.t.) simultaneous changes of demands and cost functions. The key to this analysis is a metric for the distance between two games that defines a topological metric space consisting of all games with the same combinatorial structure. The PoA is then a locally pointwise Hölder continuous function of the demands and cost functions, and we analyze the Hölder exponent for different classes of cost functions. We also apply our approach to the convergence analysis of the PoA when the total demand tends to zero or infinity. Our results further develop the recent seminal work on the sensitivity of the PoA w.r.t. changes of only the demands under special conditions. Funding: This work was supported by the Science Foundation of Anhui Science and Technology Department [Grant 1908085QF262]; Science Foundation of the Anhui Education Department [Grant KJ2019A0834]; National Science Foundation of China [Grants 61906062, 72271085]; Talent Foundation of Hefei University [Grant 1819RC29].
The Impacts of Algorithmic Work Assignment on Fairness Perceptions and Productivity: Evidence from Field Experiments
Authors: Bai Bing , Dai Hengchen , Zhang Dennis J. , Zhang Fuqiang , Hu Haoyuan 
Published: September 2022

Problem definition: We study how algorithmic (versus human-based) task assignment processes change task recipients’ fairness perceptions and productivity. Academic/practical relevance: Since algorithms are widely adopted by businesses and often require human involvement, understanding how humans perceive algorithms is instrumental to the success of algorithm design in operations. Particularly, the growing concern that algorithms may reproduce inequality historically exhibited by humans calls for research about how people perceive the fairness of algorithmic decision making (relative to traditional human-based decision making) and, consequently, adjust their work behaviors. Methodology: In a 15-day-long field experiment with Alibaba Group in a warehouse where workers pick products following orders (or “pick lists”), we randomly assigned half of the workers to receive pick lists from a machine that ostensibly relied on an algorithm to distribute pick lists, and the other half to receive pick lists from a human distributor. Results: Despite that we used the same underlying rule to assign pick lists in both groups, workers perceive the algorithmic (versus human-based) assignment process as fairer by 0.94–1.02 standard deviations. This yields productivity benefits: receiving tasks from an algorithm (versus a human) increases workers’ picking efficiency by 15.56%–17.86%. These findings persist beyond the first day when workers were involved in the experiment, suggesting that our results are not limited to the initial phrase when workers might find algorithmic assignment novel. We replicate the main results in another field experiment involving a nonoverlapping sample of warehouse workers. We also show via online experiments that people in the United States also view algorithmic task assignment as fairer than human-based task assignment. Managerial implications: We demonstrate that algorithms can have broader impacts beyond offering greater efficiency and accuracy than humans: introducing algorithmic assignment processes may enhance fairness perceptions and productivity. This insight can be utilized by managers and algorithm designers to better design and implement algorithm-based decision making in operations. Supplemental Material: The e-companion is available at https://doi.org/10.1287/msom.2022.1120 .