bluuebunny/crossref_metadata_2025 huggingface dataset:
Bearing Witness and Creative Activism
Authors: Bacharach Sondra
Published: June 2023

In this article, I explore the relationship between witness-bearing arts as a form of creative activism designed to respond to social injustices. In the first section, I present some common features of bearing witness, as conceptualized within media studies and journalism. Then I explain how artworks placed in the streets can bear witness in a similar way. I argue that witness-bearing art transmits knowledge about certain unjust and harmful events, which then places a moral burden or responsibility on the viewer. To defend this view, I offer some examples of activist art that bears witness to certain events. I suggest that witness-bearing art is placed in the streets in order to make certain truths publicly available, by offering evidence of them embedded in the artwork. The final section considers why the bearing witness is especially effective for activist art. Witness-bearing art plays a crucial knowledge-transmitting function, one which enables art to engage in creative activism. I conclude by considering how witness-bearing art offers a powerful and persuasive voice for the oppressed.
Animal Deities, Domestication, and the Purpose of Control in Contemporary Singaporean Mediumship
Authors: Strange Stuart Earle
Published: June 2023

This article considers how to study the meanings of control in religious life and multispecies relations. In it, I examine how contemporary Singaporean deity mediums, who describe themselves as subject to an absolute form of control while possessed, interpret what this control should be like. By treating mediums’ self-described subordination as analogous to that of domestic animals’ relations to humans, I explore common problems with control shared between religious and multispecies studies. In doing so, I examine core issues that point to how control can be more effectively conceptualized and analyzed by paying attention to the ways religious practices shape the interpretation of purpose. The article contends that any effective theory of control must explore how what it means to be controlled is embedded in the ways that different religious traditions perceive the purposes of the relations that make the subjects of control interpretable to themselves and others.
A snapshot of artificial intelligence research 2019–2021: is it replacing or assisting physicians?
Authors: Elmahdy Mahmoud , Sebro Ronnie
Published: June 2023

Artificial intelligence (AI) has the potential to be a disruptive technology in healthcare. Recently, there is increased speculation that AI may be used to replace healthcare providers in the future. To answer this question, we reviewed over 21 000 articles published in medical specialty journals between 2019 and 2021 to evaluate whether these AI models were intended to assist or replace healthcare providers. We also evaluated whether all Food and Drug Administration (FDA)-approved AI models were used to assist or replace healthcare providers. We find that most AI models published in this time period were intended to assist rather than replace healthcare providers, and that most of the published AI models performed tasks that could not be done by healthcare providers.
Effect of withdrawing an immunomodulatory feed additive from lactating cow diets on peripheral blood mononuclear cell proliferation
Authors: Marins Thiago N , Calix Jainer O S , Orellana Rivas Ruth M , Bernard John K , Garcia Miriam , Chapman James D , Kirk David J , Tao Sha
Published: June 2023

Supplementation of immunomodulatory feed additives, such as OmniGen AF (OG), helps to maintain immune competency; however, it is unknown if immune benefits persist in lactating cows after OG is removed from the diet. The aim of this trial was to evaluate the effect of withdrawing OG from the diet on peripheral blood mononuclear cells (PBMC) proliferation of midlactation dairy cows. Multiparous Holstein cows (N = 32), blocked by parity (2.7 ± 0.8) and days in milk (153 ± 39 d) were randomly assigned to one of the two dietary treatments within each block: diets were top dressed with either OG (56 g/d/cow) or placebo (CTL, 56 g/d/cow). Cows were housed in the same free-stall pen and individually fed once per day through Calan gates. All cows were fed the same diet containing OG for at least 1 yr before the onset of treatments. Cows were milked three time per day and milk yield was recorded at each milking. Milk samples were collected from three consecutive milkings weekly and composition analyzed. Body weight (BW) and condition score were measured weekly. Blood samples were collected at −1, 1, 3, 5, and 7 wk relative to the onset of treatments for the isolation of PBMC. The PBMC were cultured with concanavalin A (ConA) and lipopolysaccharides (LPS) for 72 h in vitro to determine proliferative responses. Prior to the experiment, cows in both treatments had similar disease incidence. During the experiment, cows did not show symptoms of disease. Withdrawing OG from the diet did not affect (P ≥ 0.20) milk yield or composition, intake, or BW. Compared with CTL, feeding OG maintained greater body condition score (2.83 vs. 2.92, P = 0.04). Regardless of time, relative to CTL, PBMC isolated from cows fed with OG had a greater proliferative rate when stimulated with LPS (stimulation index: 1.27 vs. 1.80, P = 0.05) and tended to have greater proliferation when stimulated with ConA (stimulation index: 5.24 vs. 7.80, P = 0.08). In conclusion, withdrawing OG from the diet of midlactation cows reduced proliferative response of PBMC suggesting that the immunomodulatory role of OG is lost as early as 1 wk after its withdrawal from the diet of lactating dairy cows.
A systems approach to evaluate nitrogen utilization efficiency and environmental impacts of swine growing-finishing feeding programs in U.S. pork production systems
Authors: Yang Zhaohui , Urriola Pedro E , Johnston Lee J , Shurson Gerald C
Published: June 2023

Traditionally, swine diets have been formulated to meet nutrient requirements at the lowest cost with little regard toward minimizing environmental impacts. The overall objective of this study was to evaluate the relative differences among four grower-finisher feeding programs, using precision diet formulation practices, on growth performance, carcass composition, nitrogen utilization efficiency, and environmental impacts. In experiment 1, four 4-phase growing-finishing feeding programs consisting of diets containing corn and soybean meal (CSBM), low protein CSBM supplemented with crystalline amino acids (LP), CSBM with 30% distillers dried grains with solubles (DDGS), and DDGS supplemented with crystalline Ile, Val, and Trp (DDGS + IVT) were fed to 288 mixed sex pigs (initial body weight [BW] = 36.9 ± 4.2 kg) for 12 wk to determine effects on growth performance and carcass characteristics. Pigs fed with CSBM had greater (P < 0.05) final BW than those fed with LP and DDGS, and greater gain efficiency than pigs fed with LP. Pigs fed with DDGS + IVT tended to have greater (P = 0.06) backfat depth than pigs fed with DDGS, and less (P < 0.05) loin muscle area than pigs fed with CSBM. In experiment 2, nitrogen (N) and phosphorus (P) balance of barrows (n = 32; initial BW = 59.9 ± 5.1 kg) fed with each of the phase-2 diets from experiment 1 was determined in a 12-d metabolism study (7 d adaptation and 5 d collection). Pigs fed with CSBM had a greater (P < 0.05) amount of N retained than pigs fed with other diets, but also had a greater (P < 0.05) amount of urinary N excretion and blood urea N than pigs fed with LP and DDGS + IVT diets. Pigs fed with LP tended (P = 0.07) to have the greatest N utilization efficiency but the least (P < 0.05) P retained as a percentage of P intake among dietary treatments. Diet composition and data collected from experiments 1 and 2 were used to calculate life cycle assessment environmental impacts using Opteinics software (BASF, Lampertheim, Germany). The CSBM feeding program had the least impact on climate change, marine and freshwater eutrophication, and fossil resource use. The LP feeding program had the least impact on acidification, terrestrial eutrophication, and water use, while the DDGS feeding programs had the least impact on land use. These results indicate that feeding CSBM diets optimized growth performance and carcass composition while simultaneously reducing impacts on climate change, marine and freshwater eutrophication, and fossil resource use compared with the other feeding programs evaluated.
A new genus of Madagascan freshwater crab to accommodate Hydrothelphusa vencesi Cumberlidge, Marijnissen & Thompson, 2007 (Brachyura: Potamoidea: Deckeniidae), and the description of two new congeners
Authors: Cumberlidge Neil , Soma Julia B , Leever Ellen M , Daniels Savel R
Published: June 2023

Nheena n. gen. is established to accommodate the Madagascan freshwater crab Hydrothelphusa vencesi Cumberlidge, Marijnissen & Thompson, 2007 that was formerly included in Hydrothelphusa A. Milne-Edwards, 1872. In addition, N. museonatoran. sp. and N. artiareginan. sp. are established and these new taxa are recognized based on a combination of morphological characters and previous molecular data; are all illustrated. The three species assigned to Nheenan. gen. are compared with each other and with other species of freshwater crabs found in Madagascar, and a map of their distribution is included.
Population changes of Bemisia tabaci (Hemiptera: Aleyrodidae) on different colored poinsettia leaves with different trichome densities and chemical compositions
Authors: Shi Pei-Qiong , Liu Jing , Ye Jun-Xi , Zhang Ting-Zhen , Lin Yu-Chun , Lao Qiao-Bin , Qiu Bao-Li , Zhou Hong-Kai , Xu Jin
Published: June 2023

The whitefly, Bemisia tabaci, is a destructive and invasive pest of many horticultural plants including poinsettia (Euphorbia pulcherrima). Outbreaks of B. tabaci cause serious damage by direct feeding on phloem sap, and spreading 100+ plant viruses to crops. Bemisia tabaci were observed more frequently on green than red poinsettia leaves, and the factors responsible for this are unknown. Here, we investigated the development rate, survivorship, fecundity of B. tabaci feeding on green versus red leaves, as well as the leaves’ volatiles, trichome density, anthocyanin content, soluble sugars, and free amino acids. Compared to red leaves, B. tabaci on green leaves showed increased fecundity, a higher female sex ratio, and survival rate. The green color alone was more attractive to B. tabaci than red. Red leaves of poinsettia contained more phenol, and panaginsene in their volatiles. Alpha-copaene and caryophyllene were more abundant in the volatiles of poinsettia green leaves. Leaf trichome density, soluble sugars and free amino acids were higher in green than red leaves of poinsettia, anthocyanin was lower in green than red leaves. Overall, green leaves of poinsettia were more susceptible and attractive to B. tabaci. The morphological and chemical variation between red and green leaves also differed; further investigation may reveal how these traits affect B. tabaci’s responses.
Entomopathogens infecting brown marmorated stink bugs before, during, and after overwintering
Authors: Hajek Ann E , Brandt Samuel N , González Jennifer B , Bergh J Christopher
Published: June 2023

The microsporidian, Nosema maddoxi Becnel, Solter, Hajek, Huang, Sanscrainte & Estep, infects brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), populations in North America and Asia and causes decreased fitness in infected insects. This host overwinters as adults, often in aggregations in sheltered locations, and variable levels of mortality occur over the winter. We investigated pathogen prevalence in H. halys adults before, during, and after overwintering. Population level studies resulted in detection of N. maddoxi in H. halys in 6 new US states, but no difference in levels of infection by N. maddoxi in autumn versus the following spring. Halyomorpha halys that self-aggregated for overwintering in shelters deployed in the field were maintained under simulated winter conditions (4°C) for 5 months during the 2021–2022 winter and early spring, resulting in 34.6 ± 4.8% mortality. Over the 2020–2021 and 2021–2022 winters, 13.4 ± 3.5% of surviving H. halys in shelters were infected with N. maddoxi, while N. maddoxi infections were found in 33.4 ± 10.8% of moribund and dead H. halys that accumulated in shelters. A second pathogen, Colletotrichum fioriniae Marcelino & Gouli, not previously reported from H. halys, was found among 46.7 ± 7.8% of the H. halys that died while overwintering, but levels of infection decreased after overwintering. These 2 pathogens occurred as co-infections in 11.1 ± 5.9% of the fungal-infected insects that died while overwintering. Increasing levels of N. maddoxi infection caused epizootics among H. halys reared in greenhouse cages after overwintering.
Engaging with the Nagoya Protocol on Access and Benefit-Sharing: recommendations for noncommercial biodiversity researchers
Authors: Colella Jocelyn P , Silvestri Luciana , Súzan Gerardo , Weksler Marcelo , Cook Joseph A , Lessa Enrique P
Published: June 2023

The Convention on Biological Diversity and the Nagoya Protocol on Access and Benefit-Sharing provide an international legal framework that aims to prevent misappropriation of the genetic resources of a country and ensure the fair and equitable sharing of benefits arising from their use. The legislation was negotiated at the behest of lower-income, biodiverse countries to ensure that benefits derived from research and development of genetic resources from within their jurisdictions were equitably returned and could thereby incentivize conservation and sustainable use of biodiversity. Despite good intentions, however, rapid adoption of access and benefit-sharing measures at the national level, often without participatory strategic planning, has hampered noncommercial, international collaborative genetic research with counterproductive consequences for biodiversity conservation and sustainable use. We outline how current implementation of the Convention of Biological Diversity and the Nagoya Protocol affect noncommercial research, such as that conducted in many disciplines in biology, including mammalogy. We use a case study from Brazil, an early adopter, to illustrate some current challenges and highlight downstream consequences for emerging pathogen research and public health. Most emerging pathogens colonize or jump to humans from nonhuman mammals, but noncommercial research in zoonotic diseases is complicated by potential commercial applications. Last, we identify proactive ways for the mammalogical community to engage with the Convention on Biological Diversity and the Nagoya Protocol, through sharing of nonmonetary benefits and working with local natural history collections. Leveraging international scientific societies to collectively communicate the needs of biodiversity science to policy makers will be critical to ensuring that appropriate accommodations are negotiated for noncommercial research.
Patterns of post-hibernation wing damage healing in little brown bats (Myotis lucifugus) impacted by white-nose syndrome
Authors: Ineson Katherine M , Richardson Christopher S , Looney Caitlin E , Fuller Nathan W , Reichard Jonathan D
Published: June 2023

The patterns of recovery from injury or infection are not well studied in free-ranging animals. Bats that survive the fungal disease white-nose syndrome (WNS) often emerge from hibernation suffering from skin infections and wing damage. The extent of wing damage reflects physiological and immunological responses to WNS and may impact the ability of bats to fly, forage, and reproduce. Here, we built on previous studies of wing damage in both captive and free-ranging bats to better understand the patterns and extent of wing damage healing in little brown bats (Myotis lucifugus) post-hibernation. We quantified two main types of wing damage, black necrotic dots and white spots, and used the extent of damage to assign bats 1 of 6 wing damage scores. We found that the patterns of black dots and white spots on wing membranes of free-ranging bats aligned with the patterns observed in captive bats soon after emergence from hibernation. Black dot extent was highest at the beginning of the active season in May, while white spot extent peaked 3–4 weeks later. Our study also extends our knowledge of wing damage healing throughout the active season. Wing scores of bats recaptured within the summer decreased or stayed the same and >95% had negligible signs of wing damage by August. We found that black dots were more indicative of disease status than other types of wing damage and could be consistently quantified in the field and from photographs by multiple observers. These results suggest that black dots and our wing damage scoring system can be used to better understand the patterns of post-hibernation healing in little brown bats impacted by WNS.
Data at the Ballet
Authors: Matiussi Adam , Shaw Joseph
Published: June 2023

Ballet isn’t the first thing that springs to mind when you think of data analytics. But those tasked with taking care of dancers’ health and well-being depend heavily on statistics to make the best decisions. Adam Matiussi and Joseph Shaw of The Royal Ballet explain
The law of small numbers: When statistics and psychology go to war
Authors: Shatz Itamar
Published: June 2023

Humans have innate biases when it comes to probability, leading to poor decision-making. Itamar Shatz looks at a bias that affects disinformation-spreaders and statisticians alike
When numbers lie: A good bad example
Authors: Ditlevsen Susanne , Poulsen Rolf
Published: June 2023

When the Danish government was awarding a new DAB radio licence in 2019, taxpayers assumed the selection process would be fair and mathematically rigorous. However, Susanne Ditlevsen and Rolf Poulsen show how badly handled data led to a biased decision
In the best light? Road safety and public spending
Authors: Marchant Paul , Norman Paul
Published: June 2023

How do different types of street light affect road safety? Paul Marchant and Paul Norman call for more rigorous statistical work to be carried out before local authorities make expensive changes
Dragons and data
Authors: Christofides Sarah
Published: June 2023

How do you convince the maths-anxious that statistics can be fun? Sarah R. Christofides shows how she uses simulated data to fire up her introductory statistics classes
Predicting cancer incidence in regions without population-based cancer registries using mortality
Authors: Retegui Garazi , Etxeberria Jaione , Riebler Andrea , Ugarte María Dolores
Published: June 2023

Cancer incidence numbers are routinely recorded by national or regional population-based cancer registries (PBCRs). However, in most southern European countries, the local PBCRs cover only a fraction of the country. Therefore, national cancer incidence can be only obtained through estimation methods. In this paper, we predict incidence rates in areas without cancer registry using multivariate spatial models modelling jointly cancer incidence and mortality. To evaluate the proposal, we use cancer incidence and mortality data from all the German states. We also conduct a simulation study by mimicking the real case of Spain considering different scenarios depending on the similarity of spatial patterns between incidence and mortality, the levels of lethality, and varying the amount of incidence data available. The new proposal provides good interval estimates in regions without PBCRs and reduces the relative error in estimating national incidence compared to one of the most widely used methodologies.
Rare case of retroperitoneal mitotically active leiomyoma in a postmenopausal woman
Authors: Doita Susumu , Taniguchi Fumitaka , Mouri Kengo , Miyake Eiki , Hatono Minami , Kajioka Hiroki , Ogawa Toshihiro , Watanabe Megumi , Arata Takashi , Katsuda Kou , Tanakaya Kouji , Aoki Hideki
Published: June 2023

Leiomyomas are benign smooth muscle tumors, and retroperitoneal leiomyomas without coexisting uterine leiomyomas are extremely rare. Mitotically active leiomyomas, which are leiomyomas with increased mitotic activity, are rarely observed in postmenopausal women, except under the influence of exogenous hormones. This report presents a rare case of a retroperitoneal mitotically active leiomyoma in a postmenopausal woman. The patient presented with an abdominal mass and underwent surgical resection of the retroperitoneal tumor. Pathological examination revealed a mitotically active retroperitoneal leiomyoma with 31 mitotic figures per 10 high-power fields. The patient did not experience recurrence during the 2-year follow-up period. This case highlights the need to consider retroperitoneal mitotically active leiomyomas in postmenopausal women and suggests that myomectomy can prevent their recurrence.
JustRNA: a database of plant long noncoding RNA expression profiles and functional network
Authors: Tseng Kuan-Chieh , Wu Nai-Yun , Chow Chi-Nga , Zheng Han-Qin , Chou Chin-Yuan , Yang Chien-Wen , Wang Ming-Jun , Chang Song-Bin , Chang Wen-Chi
Published: June 2023

Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. This study developed JustRNA, an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species. In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw.
The swansong of petal cell death: insights into the mechanism and regulation of ethylene-mediated flower senescence
Authors: Parveen Shazia , Altaf Foziya , Farooq Sumira , Lone Mohammad Lateef , ul Haq Aehsan , Tahir Inayatullah
Published: June 2023

Flower senescence is a fundamental aspect of the developmental trajectory in flowers, occurring after the differentiation of tissues and maturation of petals, and preceding the growth and development of seeds. It is accompanied by various alterations at the cytological, physiological, and molecular levels, similar to other forms of programmed cell death (PCD). It involves an intricate interplay of various plant growth regulators, with ethylene being the key orchestrator in ethylene-dependent petal senescence. Petal senescence mediated by ethylene is marked by various changes such as petal wilting, amplified oxidative stress, degradation of proteins and nucleic acids, and autophagy. Ethylene crosstalks with other growth regulators and triggers genetic and/or epigenetic reprogramming of genes during senescence in flowers. While our understanding of the mechanism and regulation of petal senescence in ethylene-sensitive species has advanced, significant knowledge gaps still exist, which demand critical reappraisal of the available literature on the topic. A deeper understanding of the various mechanisms and regulatory pathways involved in ethylene-dependent senescence has the capacity to facilitate a more precise regulation of the timing and site of senescence, thus leading to optimized crop yields, enhanced product quality, and extended longevity.
The flavour of grape colour: anthocyanin content tunes aroma precursor composition by altering the berry microenvironment
Authors: Rodríguez-Lorenzo Maite , Mauri Nuria , Royo Carolina , Rambla José L , Diretto Gianfranco , Demurtas Olivia , Hilbert Ghislaine , Renaud Christel , Tobar Vanessa , Huete Joaquín , Delrot Serge , Granell Antonio , Martínez-Zapater José Miguel , Carbonell-Bejerano Pablo
Published: June 2023

Anthocyaninless (white) instead of black/red (coloured) fruits develop in grapevine cultivars without functional VviMYBA1 and VviMYBA2 genes, and this conditions the colour of wines that can be produced. To evaluate whether this genetic variation has additional consequences on fruit ripening and composition, we performed comparisons of microenvironment, transcriptomics, and metabolomics of developing grapes between near-isogenic white- and black-berried somatic variants of Garnacha and Tempranillo cultivars. Berry temperature was as much as 3.5 ºC lower in white- compared to black-berried Tempranillo. An RNA-seq study combined with targeted and untargeted metabolomics revealed that ripening fruits of white-berried variants were characterized by the up-regulation of photosynthesis-related and other light-responsive genes and by their higher accumulation of specific terpene aroma precursors, fatty acid-derived aldehyde volatiles, and phenylpropanoid precursor amino acids. MYBA1-MYBA2 function proved essential for flavonol trihydroxylation in black-berried somatic variants, which were also characterized by enhanced expression of pathogen defence genes in the berry skin and increased accumulation of C6-derived alcohol and ester volatiles and γ-aminobutyric acid. Collectively, our results indicate that anthocyanin depletion has side-effects on grape composition by altering the internal microenvironment of the berry and the partitioning of the phenylpropanoid pathway. Our findings show how fruit colour can condition other fruit features, such as flavour potential and stress homeostasis.
A dynamical survey of the trans-Neptunian region − II. On the nature of chaotic diffusion
Authors: Kővári E , Forgács-Dajka E , Kovács T , Kiss Cs , Sándor Zs
Published: June 2023

On long enough time-scales, chaotic diffusion has the potential to significantly alter the appearance of a dynamical system. The Solar system is no exception: diffusive processes take part in the transportation of small bodies and provide dynamical pathways even for the distant trans-Neptunian objects to reach the inner Solar system. In this letter, we carry out a thorough investigation of the nature of chaotic diffusion. We analyse the temporal evolution of the mean squared displacement of 10 000 ensembles of test particles and quantify in each case the diffusion exponent (enabling the classification between normal, sub-, and superdiffusion), the generalized diffusion coefficient, and a characteristic diffusion time-scale, too. This latter quantity is compared with an entropy-based time-scale, and the two approaches are studied in light of direct computations as well. Our results are given in the context of two-dimensional maps, thereby facilitating the understanding of the relationship between the typical phase space structures and the properties of chaotic diffusion.
IXPE and NICER view of black hole X-ray binary 4U 1630–47: First significant detection of polarized emission in thermal state
Authors: Kushwaha Ankur , Jayasurya Kiran M , Agrawal Vivek K , Nandi Anuj
Published: June 2023

We present a detailed spectro-polarimetric study of black hole X-ray binary 4U 1630−47 during its 2022 outburst with IXPE and NICER observations. The source is observed in disc dominated thermal state (kTin ≈ 1.4 keV) with clear detection of absorption features at 6.69 ± 0.01 keV and 6.97 ± 0.01 keV from both NICER as well as IXPE spectra, likely indicating a coupling of disc-wind. A significant degree of polarization (PD) $= 8.33\pm 0.17~{{\ \rm per\ cent}}$ and polarization angle (PA) =17.78° ± 0.60° in the energy range of 2 − 8 keV are measured with IXPE. PD is found to be an increasing function of energy whereas PA remains roughly same within the energy range. Simultaneous energy spectra from NICER in the range of 0.5 − 12 keV are modelled to study the spectral properties. Furthermore, the spin parameter of the black hole is estimated with spectro-polarimetric data as a$_{\ast }=0.920\pm 0.001\, (1\sigma)$ which is corroborated by NICER observations. Finally, we discuss the implications of our findings.
GRACE: a comprehensive web-based platform for integrative single-cell transcriptome analysis
Authors: Yu Hao , Wang Yuqing , Zhang Xi , Wang Zheng
Published: June 2023

Large-scale single-cell RNA sequencing (scRNA-seq) has emerged as a robust method for dissecting cellular heterogeneity at single-cell resolution. However, to meet the increasingly high computational demands of non-programming experts, a user-friendly, scalable, and accessible online platform for analyzing scRNA-seq data is urgently needed. Here, we have developed a web-based platform GRACE (GRaphical Analyzing Cell Explorer) (http://grace.flowhub.com.cn or http://grace.jflab.ac.cn:28080) that enables online massive single-cell transcriptome analysis, improving interactivity and reproducibility using high-quality visualization frameworks. GRACE provides easy access to interactive visualization, customized parameters, and publication-quality graphs. Furthermore, it comprehensively integrates preprocessing, clustering, developmental trajectory inference, cell-cell communication, cell-type annotation, subcluster analysis, and pathway enrichment. In addition to the website platform, we also provide a Docker version that can be easily deployed on private servers. The source code for GRACE is freely available at (https://github.com/th00516/GRACE). Documentation and video tutorials are accessible from website homepage (http://grace.flowhub.com.cn). GRACE can analyze massive scRNA-seq data more flexibly and be accessible to the scientific community. This platform fulfills the major gap that exists between experimental (wet lab) and bioinformatic (dry lab) research.
EPIC-0307-mediated selective disruption of PRADX–EZH2 interaction and enhancement of temozolomide sensitivity to glioblastoma via inhibiting DNA repair and MGMT
Authors: Xin Lei , Tan Yanli , Zhu Yuanxue , Cui Xiaoteng , Wang Qixue , Zhao Jixing , Tian Shaohui , Xu Can , Xiao Menglin , Hong Biao , Xu Jianglong , Yuan Xiaoye , Wang Changsheng , Kang Chunsheng , Fang Chuan
Published: June 2023

Background

Temozolomide (TMZ) treatment efficacy in glioblastoma (GBM) has been limited by resistance. The level of O-6-methylguanine-DNA methyltransferase (MGMT) and intrinsic DNA damage repair factors are important for the TMZ response in patients. Here, we reported a novel compound, called EPIC-0307, that increased TMZ sensitivity by inhibiting specific DNA damage repair proteins and MGMT expression.

Methods

EPIC-0307 was derived by molecular docking screening. RNA immunoprecipitation (RIP), and chromatin immunoprecipitation by RNA (ChIRP) assays were used to verify the blocking effect. Chromatin immunoprecipitation (ChIP) and co-immunoprecipitation (Co-IP) assays were performed to explore the mechanism of EPIC-0307. A series of in vivo and in vitro experiments were designed to evaluate the efficacy of EPIC-0307 in sensitizing GBM cells to TMZ.

Results

EPIC-0307 selectively disrupted the binding of PRADX to EZH2 and upregulated the expression of P21 and PUMA, leading to cell cycle arrest and apoptosis in GBM cells. EPIC-0307 exhibited a synergistic inhibitory effect on GBM when combined with TMZ by downregulating TMZ-induced DNA damage repair responses and epigenetically silencing MGMT expression through modulating the recruitment of ATF3-pSTAT3-HDAC1 regulatory complex to the MGMT promoter. EPIC-0307 demonstrated significant efficacy in suppressing the tumorigenesis of GBM cells, restoring TMZ sensitivity.

Conclusion

This study identified a potential small-molecule inhibitor (SMI) EPIC-0307 that selectively disrupted the PRADX–EZH2 interaction to upregulate expressions of tumor suppressor genes, thereby exerting its antitumor effects on GBM cells. EPIC-0307 treatment also increased the chemotherapeutic efficacy of TMZ by epigenetically downregulating DNA repair-associate genes and MGMT expression in GBM cells.
Full-parameter omnidirectional transformation optical devices
Authors: Gao Yuan , Luo Yu , Zhang Jingjing , Huang Zhengjie , Zheng Bin , Chen Hongsheng , Ye Dexin
Published: June 2023

Transformation optics (TO) provides an unprecedented technique to control electromagnetic (EM) waves by engineering the constitutive parameters of the surrounding medium through a proper spatial transformation. In general, ideal transformation optical devices require simultaneous electric and magnetic responses along all three dimensions. To ease the practical implementation, previous studies usually made use of reduced parameters or other simplified approaches, which inevitably introduce extra reflection or unwanted phase shift. Up to today, experimental realizations of full-parameter transformation optical devices in free space are still quite limited. Here, a general design strategy is proposed to solve this problem. As a specific example, a full-parameter spatial-compression TO medium with constitutive parameters taking the diagonal form diag(a, a, 1/a) for the TM wave incidence was designed and realized experimentally. Such spatial-compression TO media were then applied to the implementation of an ideal omnidirectional invisibility cloak capable of concealing a large-scale object over a wide range of illumination angles. Both the simulation and experiment confirm that the cloak allows for nearly unity transmission of EM waves in the forward direction without introducing extra scattering or phase shift. This work constitutes an important stepping stone for future practical implementation of arbitrary full-parameter omnidirectional transformation optical devices.
Prototheca Infection: A Descriptive Study
Authors: Cullen Grace D , Yetmar Zachary A , Fida Madiha , Abu Saleh Omar M
Published: June 2023

Prototheca is a microalgae known to cause infections in humans, with protothecosis most commonly presenting as olecranon bursitis or localized soft tissue infection. Disseminated disease can be seen in immunocompromised patients. In this retrospective single-institution case series, we describe our experience with 7 patients with Prototheca infections.
Poor Sensitivity of Stool Culture Compared to Polymerase Chain Reaction in Surveillance for Vibrio cholerae in Haiti, 2018–2019
Authors: Guillaume Yodeline , Debela Meti , Slater Damien , Vissieres Kenia , Ternier Ralph , Franke Molly F , Harris Jason B , Ivers Louise C
Published: June 2023

We report on the sensitivity and specificity of stool culture compared to polymerase chain reaction for detecting Vibrio cholerae in Haiti during the waning period of the initial outbreak in 2018–2019. We found that stool culture (with a sensitivity of 33.3% and specificity of 97.4%) may not be sufficiently robust in this context.
Optimizing the Use of Beta-Lactam Antibiotics in Clinical Practice: A Test of Time
Authors: Tilanus Alwin , Drusano George
Published: June 2023

Despite their limitations, the pharmacokinetics (PK) and pharmacodynamics (PD) indices form the basis for our current understanding regarding antibiotic development, selection, and dose optimization. Application of PK-PD in medicine has been associated with better clinical outcome, suppression of resistance, and optimization of antibiotic consumption. Beta-lactam antibiotics remain the cornerstone for empirical and directed therapy in many patients. The percentage of time of the dosing interval that the free (unbound) drug concentration remains above the minimal inhibitory concentration (MIC) (%fT > MIC) has been considered the PK-PD index that best predicts the relationship between antibiotic exposure and killing for the beta-lactam antibiotics. Time dependence of beta-lactam antibiotics has its origin in the acylation process of the serine active site of penicillin-binding proteins, which subsequently results in bacteriostatic and bactericidal effects during the dosing interval. To enhance the likelihood of target attainment, higher doses, and prolonged infusion strategies, with/or without loading doses, have been applied to compensate for subtherapeutic levels of antibiotics related to PK-PD changes, especially in the early phase of severe sepsis. To minimize resistance and maximize clinical outcome, empirical therapy with a meropenem loading dose followed by high-dose-prolonged infusion should be considered in patients with high inoculum infections presenting as severe (Gram negative) sepsis. Subsequent de-escalation and dosing of beta-lactam antibiotics should be considered as an individualized dynamic process that requires dose adjustments throughout the time course of the disease process mediated by clinical parameters that indirectly assess PK-PD alterations.
Prognostic Value of ctDNA Detection in Patients With Locally Advanced Rectal Cancer Undergoing Neoadjuvant Chemoradiotherapy: A Systematic Review and Meta-analysis
Authors: Chang Lele , Zhang Xuemei , He Lei , Ma Qian , Fang Tianyuan , Jiang Chengzhi , Ma Zhigang , Li Qingwei , Wu Chunlong , Tao Ji
Published: June 2023

Background

Circulating tumor DNA (ctDNA) is increasingly used as a biomarker for metastatic rectal cancer and has recently shown promising results in the early detection of recurrence risk.

Methods

We conducted a systematic review and meta-analysis to explore the prognostic value of ctDNA detection in LARC patients undergoing neoadjuvant chemoradiotherapy (nCRT). We systematically searched electronic databases for observational or interventional studies that included LARC patients undergoing nCRT. Study selection according to the PRISMA guidelines and quality assessment of the REMARK tool for biomarker studies. The primary endpoint was the impact of ctDNA detection at different time points (baseline, post-nCRT, post-surgery) on relapse-free survival (RFS) and overall survival (OS). The secondary endpoint was to study the association between ctDNA detection and pathological complete response(pCR) at different time points.

Results

After further review and analysis of the 625 articles initially retrieved, we finally included 10 eligible studies. We found no significant correlation between ctDNA detection at baseline and long-term survival outcomes or the probability of achieving a pCR. However, the presence of ctDNA at post-nCRT was associated with worse RFS (HR = 9.16, 95% CI, 5.48-15.32), worse OS (HR = 8.49, 95% CI, 2.20-32.72), and worse pCR results (OR = 0.40, 95%CI, 0.18-0.89). The correlation between the presence of ctDNA at post-surgery and worse RFS was more obvious (HR = 14.94; 95% CI, 7.48-9.83).

Conclusions

Our results suggest that ctDNA detection is a promising biomarker for the evaluation of response and prognosis in LARC patients undergoing nCRT, which merits further evaluation in the following prospective trials.
Drastic reduction of the population distribution of White Storks predicted in absence of landfills
Authors: López-García Alejandro , Gil-Tapetado Diego , Aguirre José I
Published: June 2023

Organic waste production has greatly increased following human sprawl and led to the development of landfills in recent decades. This abundant and reliable anthropogenic food source has favored several species, some of which consequently became overabundant. Landfills present hazards to wildlife, which may suffocate on plastic materials, tangle on cords, and get exposed to pollutants and pathogens. In response to environmental and public health concerns over the maintenance of landfills, the European Commission proposed to close the landfills. Our objective was to determine the impact of Landfill European Directive on the White Stork (Ciconia ciconia) whose population recovery and growth was linked to landfill exploitation. We implemented species distribution models to project future distribution in the absence of landfills in the Community of Madrid (Spain). Habitat suitability was estimated based on nest occurrence and we included data from land cover types, human population density, and two different climate change scenarios (i.e. emissions in low and high shared socioeconomic pathways). Given that protection measures, particularly implemented in protected areas, were associated with population recovery, we also evaluated the overlapping degree between protected areas and projected distribution. Our models predicted a sharp decline in breeding population distribution with landfill closure, reaching values similar to the 1984 breeding census when the species was categorized as threatened. Our results also suggest a decrease in maximum habitat suitability. Climate change also contributed to a reduction in breeding population distribution given model predictions for the extreme emission pathway (ssp5). Measures such as gradual change in landfill management, continuous monitoring of breeding populations, and evaluation of the White Stork use of natural feeding areas before and after landfill closure, should be considered.
Low temperature-induced regulatory network rewiring via WRKY regulators during banana peel browning
Authors: Zhu Wenjun , Li Hua , Dong Pengfei , Ni Xueting , Fan Minlei , Yang Yingjie , Xu Shiyao , Xu Yanbing , Qian Yangwen , Chen Zhuo , Lü Peitao
Published: June 2023

Banana (Musa spp.) fruits, as typical tropical fruits, are cold sensitive, and lower temperatures can disrupt cellular compartmentalization and lead to severe browning. How tropical fruits respond to low temperature compared to the cold response mechanisms of model plants remains unknown. Here, we systematically characterized the changes in chromatin accessibility, histone modifications, distal cis-regulatory elements, transcription factor binding, and gene expression levels in banana peels in response to low temperature. Dynamic patterns of cold-induced transcripts were generally accompanied by concordant chromatin accessibility and histone modification changes. These upregulated genes were enriched for WRKY binding sites in their promoters and/or active enhancers. Compared to banana peel at room temperature, large amounts of banana WRKYs were specifically induced by cold and mediated enhancer–promoter interactions regulating critical browning pathways, including phospholipid degradation, oxidation, and cold tolerance. This hypothesis was supported by DNA affinity purification sequencing, luciferase reporter assays, and transient expression assay. Together, our findings highlight widespread transcriptional reprogramming via WRKYs during banana peel browning at low temperature and provide an extensive resource for studying gene regulation in tropical plants in response to cold stress, as well as potential targets for improving cold tolerance and shelf life of tropical fruits.
RiceTFtarget: A rice transcription factor–target prediction server based on coexpression and machine learning
Authors: Zhang Baoyi , Zhu Xueai , Chen Zixin , Zhang Hongsheng , Huang Junxian , Huang Ji
Published: June 2023

The online webserver RiceTFtarget realizes rice transcription factor–target prediction based on coexpression, pattern matching, and machine learning.
Simulation study of ultrahigh-precision single-ion extraction from a linear Paul trap
Authors: Muroo Kento , Okamoto Hiromi , Miyawaki Nobumasa , Yuri Yosuke
Published: June 2023

A detailed simulation study is conducted to explore the possibility of transporting a single ion precisely along a particular design orbit. As a practically useful example, we consider nitrogen ions sympathetically cooled with ultracold calcium ions produced in a linear Paul trap (LPT) by the Doppler laser-cooling technique. A single nitrogen almost completely frozen in the laboratory frame is extracted from the LPT by manipulating the axial potential barriers. A similar idea was recently implemented by Groot-Berning et al. [New J. Phys. 23, 063067 (2021)] to create nitrogen-vacancy centers in diamond as a platform for some important quantum technologies. We here perform systematic 3D simulations taking a standard LPT structure into account and figure out the necessary conditions to achieve the ultrahigh-precision irradiation of a single nitrogen onto any target. In addition to the string Coulomb crystal used in the previous work above, we show that even the shell crystalline structure can be employed for our purpose. When several specific conditions are satisfied, a normalized root-mean-squared emittance of ejected nitrogen ions can be made of the order of 10−16 m·rad in transverse dimensions perpendicular to the design orbit.
Knowledge level of medical students about ionising radiation used for diagnostic purpose in radiology: a survey study
Authors: Demirtaş Meryem , Turan Arzu , Akpunar Sinan , Tafralı Şeyma , Doğan Emre , Çeliker Fatma B
Published: June 2023

People exposed to ionising radiation may develop harmful somatic and genetic effects in their anatomical structures. Technological advancements, particularly in radiological devices, research and examinations result in a significant increase in the number of radiological investigations. This large number of radiological examinations increased the number of patients affected by ionising radiation. This study aims to evaluate the medical students’ knowledge of ionising radiation and, examine the level of knowledge of medical students on the awareness and safety of ionising radiation exposure, emphasises the importance of radiation curricula internship programmes. This study is a survey application. The chi-square test is used. As a result, the intern’s knowledge of ionising radiation increased significantly after the internship in a radiology unit. Although it has been significantly increased, it is still insufficient. This gap can be filled by incorporating radiology unit internship programmes into the curriculum of medical faculty education programmes.
‘Its many workers and subscribers feel that their services can still be of benefit’: Hospital Leagues of Friends in the English West Midlands, c. 1948–1998
Authors: Millward Gareth
Published: June 2023

Leagues of Friends are charities that provide ‘personal service to patients’ and ‘supply hospitals with equipment not likely to come from the budgeting of authorities’. Hundreds continue to exist, and many trace their origins to before the NHS’s foundation in 1948. Despite the rich and growing historiographies of voluntarism and the NHS, Leagues have received little attention. This article uses case studies of Leagues in the English West Midlands to show how ‘friendship’ symbolised the relationship between local NHS institutions and the communities they served. The cases show that voluntarism in British healthcare has not always been based around activism and consumerism, two areas that recent scholarship has rightly highlighted, especially from the 1960s. This allows historians to interrogate the regional and local differences within, ostensibly, a highly centralised national health system.
Going Up in Smoke: Tobacco and Government Policy in the Age of Austerity, 1945–50
Authors: Singleton John
Published: June 2023

This article examines the Attlee government’s performance as a crisis manager in relation to tobacco policy in the years prior to the publication in 1950 of research linking smoking and cancer. Health concerns played no role in tobacco policy before 1950, and the government hoped more teenagers would take up smoking and pay tobacco duty. Tobacco took on added significance as an economic issue because policy-makers had so little room for manoeuvre. Their task was to balance the desire of consumers to smoke as much as they liked at a reasonable price, the exchequer’s need to raise revenue from tobacco duties, and the imperative to conserve scarce dollars. Tobacco was an economic and financial rather than a health issue in the late 1940s and the authorities juggled competing demands creditably. This article examines previously neglected but important aspects of the histories of tobacco and of the Attlee government’s economic policies.