bluuebunny/crossref_metadata_2025 huggingface dataset:
Corrections to recent changes in the taxonomy of the Sordariales
Authors: Marin-Felix Yasmina , Miller Andrew N.
Published: July 2022

The classification of taxa belonging to the Sordariales has been problematic over the years. With the beginning of the DNA era, ascospore morphology, which was the main criterium for the delimitation of taxa in the Sordariales, was demonstrated to not be useful for inferring taxonomic relationships especially at the genus level. In the past decades, the combination of both morphological and molecular data allowed the reclassification of these taxa. Recently, a study of some often overlooked Diaporthomycetidae and Sordariomycetidae included a new taxonomic classification for members of the Sordariales, many of which were based on nomenclatural errors or which lacked sufficient data to support their hypotheses. The authors did not contribute any new DNA sequences, but instead relied on datasets generated by previous authors in their published phylogenetic studies. Surprisingly, different results were obtained contradicting these previous studies and, in an act of taxonomic vandalism, five new families were introduced without performing further molecular analyses to verify the incongruencies with these previous studies. Three of these new families, which we consider doubtful, are Bombardiaceae, Lasiosphaeridaceae and Zygospermellaceae. The family Strattoniaceae is here considered superfluous since it was introduced to accommodate only a single genus and delimited based on a species that is not the type species of Strattonia. The Neoschizotheciaceae was erected based on the new genus Neoschizothecium, which was introduced to accommodate members of Schizothecium since Huang et al. (2021) considered Schizothecium as a synonym of Podospora after misinterpreting their type species as the same. However, Schizothecium and Podospora have been two independent genera based on two different type species for half a century, making Neoschizothecium and Neoschizotheciaceae superfluous. Moreover, they proposed 32 new combinations, 16 of which are now superfluous or doubtful. Most of these taxonomic errors could have been avoided if a proper literature review had been performed. Two examples are the new superfluous combinations of Triangularia tarvisina and Cladorrhinum olerum, because the former is considered conspecific with Triangularia setosa, and the latter conspecific with Cladorrhinum foecundissimum, the anamorph of Arnium olerum. The focus of the current review is to provide a scientifically responsible alternative to the erroneous novelties proposed at the family, genus and species level in the recent classification of Sordariales.
Arthrostoma leucurus sp. n. (Nematoda: Ancylostomatidae), A New Hookworm Species Isolated from Asian Badger in China
Authors: Liu Gang , Wang Shiyi , Liang Weihua , Hornok Sándor , Zhao Shanshan , Tan Wenbo , Liu Zhiqiang , Gu Xinli , Wang Yuanzhi
Published: July 2022

Purpose

To date, ten validated Arthrostoma species were reported. Here, a new hookworm species was found from Asian badger (Meles leucurus).

Methods

Nineteen hookworms (9 males and 10 females) were collected from the small intestine of two Asian badgers in Xinjiang Uygur Autonomous Region, northwestern China. The hookworms were morphologically examined according to key taxonomic characters, such as anterior extremity direction, structures of oral opening (cutting plates or teeth), vulva location, buccal capsule anatomy (integrated or formed by articulating plates), the length of spicule and gubernaculum, number of plates of buccal capsule, and presence or absence of vulvar papillae.

Results

The hookworm species from Asian badger, here named as Arthrostoma leucurus sp. n., was different from the previously described ten Arthrostoma species. The phylogenetic tree based on the cox1 gene showed that Arthrostoma leucurus sp. n. formed a separate clade, as a sister group to Ancylostoma and Uncinaria species.

Conclusion

Arthrostoma leucurus sp. n., the eleven validated Arthrostoma species, was identified from Asian badger in China.
Extracellular Adenosine (eAdo) - A2B Receptor Axis Inhibits in Nlrp3 Inflammasome-dependent Manner Trafficking of Hematopoietic Stem/progenitor Cells
Authors: Thapa Arjun , Abdelbaset-Ismail Ahmed , Chumak Vira , Adamiak Mateusz , Brzezniakiewicz-Janus Katarzyna , Ratajczak Janina , Kucia Magdalena , Ratajczak Mariusz Z.
Published: July 2022

We postulated that mobilization, homing, and engraftment of hematopoietic stem/progenitor cells (HSCPs) is facilitated by a state of sterile inflammation induced in bone marrow (BM) after administration of pro-mobilizing drugs or in response to pre-transplant myeloablative conditioning. An important role in this phenomenon plays purinergic signaling that by the release of extracellular adenosine triphosphate (eATP) activates in HSPCs and in cells in the hematopoietic microenvironment an intracellular pattern recognition receptor (PPR) known as Nlrp3 inflammasome. We reported recently that its deficiency results in defective trafficking of HSPCs. Moreover, it is known that eATP after release into extracellular space is processed by cell surface expressed ectonucleotidases CD39 and CD73 to extracellular adenosine (eAdo) that in contrast to eATP shows an anti-inflammatory effect. Based on data that the state of sterile inflammation promotes trafficking of HSPCs, and since eAdo is endowed with anti-inflammatory properties we become interested in how eAdo will affect the mobilization, homing, and engraftment of HSPCs and which of eAdo receptors are involved in these processes. As expected, eAdo impaired HSPCs trafficking and this occurred in autocrine- and paracrine-dependent manner by direct stimulation of these cells or by affecting cells in the BM microenvironment. We report herein for the first time that this defect is mediated by activation of the A2B receptor and a specific inhibitor of this receptor improves eAdo-aggravated trafficking of HSPCs. To explain this at the molecular level eAdo-A2B receptor interaction upregulates in HSPCs in NF-kB-, NRF2- and cAMP-dependent manner heme oxygenase-1 (HO-1), that is Nlrp3 inflammasome inhibitor. This corroborated with our analysis of proteomics signature in murine HSPCs exposed to eAdo that revealed that A2B inhibition promotes cell migration and proliferation. Based on this we postulate that blockage of A2B receptor may accelerate the mobilization of HSPCs as well as their hematopoietic reconstitution and this approach could be potentially considered in the future to be tested in the clinic.

Graphical Abstract
Performing a ‘Returnee’ in Benin City, Nigeria
Authors: Shaidrova Mariia
Published: July 2022

Over recent years, with the support of international NGOs, many thousands of irregular migrants were ‘returned’ to West Africa from Libyan detention centres. Through extensive ethnographic fieldwork with different groups of returnees in Benin City, Nigeria, I studied the establishment and evolution of the ‘returnee’ identity. Making use of labelling, social identity and performativity theories, I found that the performance of the returnee identity for Western donors, researchers and the media creates opportunities for the returnees to regain respect in their communities. Emphasising the role of performativity in identity formation, I use the metaphor of a theatrical play. Initially scripted by the EU border-externalisation policies, the return-migration play has evolved to fit in local political realities. On the frontstage, returnees were adjusting to the EU counter-migration agenda, testifying about the risks of irregular migration. Backstage, however, they kept pursuing their migration aspirations, also using the returnee identity to establish themselves in the city and gain some level of political recognition.
Informal Caregivers of Patients with Disorders of Consciousness: a Qualitative Study of Communication Experiences and Information Needs with Physicians
Authors: Boegle Karoline , Bassi Marta , Comanducci Angela , Kuehlmeyer Katja , Oehl Philipp , Raiser Theresa , Rosenfelder Martin , Sitt Jaco Diego , Valota Chiara , Willacker Lina , Bender Andreas , Grill Eva
Published: July 2022

Due to improvements in medicine, the figures of patients with disorders of consciousness (DoC) are increasing. Diagnostics of DoC and prognostication of rehabilitation outcome is challenging but necessary to evaluate recovery potential and to decide on treatment options. Such decisions should be made by doctors and patients’ surrogates based on medico-ethical principles. Meeting information needs and communicating effectively with caregivers as the patients´ most common surrogate-decision makers is crucial, and challenging when novel tech-nologies are introduced. This qualitative study aims to explore information needs of informal DoC caregivers, how they manage the obtained information and their perceptions and experiences with caregiver-physician communication in facilities that implemented innovative neurodiagnostics studies. In 2021, we conducted semi-structured interviews with nine caregivers of clinically stable DoC patients in two rehabilitation centers in Italy and Germany. Participants were selected based on consecutive purposeful sampling. Caregivers were recruited at the facilities after written informed consent. All interviews were recorded, transcribed verbatim and translated. For analysis, we used reflexive thematic analysis according to Braun & Clarke (2006). Caregivers experienced the conversations emotionally, generally based on the value of the information provided. They reported to seek positive information, comfort and empathy with-in the communication of results of examinations. They needed detailed information to gain a deep understanding and a clear picture of their loved-one’s condition. The results suggest a mismatch between the perspectives of caregivers and the perspectives of medical profession-als, and stress the need for more elaborate approaches to the communication of results of neu-rodiagnostics studies.
The Capability Approach and Child Well-Being: A Systematic Literature Review
Authors: Domínguez-Serrano Mónica , del Moral-Espín Lucía
Published: July 2022

Child well-being is a dynamic concept currently under revision due to its complexity and the need to incorporate traditionally overlooked perspectives. An essential aspect of this revision is considering children as active agents in defining the concept itself and incorporating new elements that enrich the more traditional economics-based and adult-centred conceptualisation. In these regards, the capability approach (CA) provides valuable theoretical support for an expanded understanding of child well-being. Therefore, this article aims to offer a systematised review of the literature from the last two decades that uses this approach in examining children and childhood. To do so, the authors examined the main international databases and conducted relevant additional searches, identifying 63 journals that have published capabilitarian articles over the last two decades. Our findings show that most publications concentrate on recent years, with an expansion of the methodologies used and the contexts addressed. Although education seems to be one of the primary interests of this literature, there has also been an increasing range of children’s realities and topics observed that we summarised in 10 categories. Between then, we dig deeper into the subsegment that specifically addresses the category of child well-being. Our review reveals that quantitative approaches and European contexts are predominant within these papers, and we analyse how they concern different spaces, well-being dimensions and intersectionalities.
Designing multi-purpose devices to enhance users’ perception of haptics
Authors: Galdieri Riccardo , Camardella Cristian , Carrozzino Marcello , Frisoli Antonio
Published: July 2022

While Virtual Reality has slowly become a common sight, haptics is still struggling to appeal to the general public. We argue that one of the possible reasons is that while VR is designed to be as easily adaptable as possible to many different contexts, haptics is often designed to fulfil a specific purpose and fails to present itself as a tool that can be exploited by designers. To test our hypothesis, we created a VR game where a wrist exoskeleton was used to interact with the environment. The game was composed of multiple levels, some of which also featured a metaphorical interaction through the same haptic device, and was tested by expert haptics scholars during a conference. Preliminary results suggest that by showing multiple potential usages of an exoskeleton, it was possible to enhance users’ interest towards the haptic device and the game.
Absolute Continuity of the Harmonic Measure on Low Dimensional Rectifiable Sets
Authors: Feneuil Joseph
Published: July 2022

In the past decades, we learnt that uniform rectifiability is often a right candidate to go past Lipschitz boundaries in boundary value problems. If $$\Omega $$
Ω
is an open domain in $$\mathbb {R}^n$$

R

n

with mild topological conditions, we can even characterize the $$n-1$$

n
-
1

dimensional uniformly rectifiability of the boundary $$\partial \Omega $$

∂
Ω

by the $$A_\infty $$

A
∞

-absolute continuity of the harmonic measure on $$\partial \Omega $$

∂
Ω

with respect to the surface measure. In low dimension ($$d<n-1$$

d
<
n
-
1

), David and Mayboroda tackled one direction of the above characterization, i.e. proved that if $$\Gamma $$
Γ
is a d-dimensional uniformly rectifiable set, then the harmonic measure (associated to an suitable degenerate elliptic operator) on $$\Gamma $$
Γ
is $$A_\infty $$

A
∞

-absolutely continuous with respect to the d-dimensional Hausdorff measure. In the present article, we use a completely new approach to give an alternative and significantly shorter proof of David and Mayboroda’s result.
Enabling AI and Robotic Coaches for Physical Rehabilitation Therapy: Iterative Design and Evaluation with Therapists and Post-stroke Survivors
Authors: Lee Min Hun , Siewiorek Daniel P. , Smailagic Asim , Bernardino Alexandre , Badia Sergi Bermúdez i
Published: July 2022

Artificial intelligence (AI) and robotic coaches promise the improved engagement of patients on rehabilitation exercises through social interaction. While previous work explored the potential of automatically monitoring exercises for AI and robotic coaches, the deployment of these systems remains a challenge. Previous work described the lack of involving stakeholders to design such functionalities as one of the major causes. In this paper, we present our efforts on eliciting the detailed design specifications on how AI and robotic coaches could interact with and guide patient’s exercises in an effective and acceptable way with four therapists and five post-stroke survivors. Through iterative questionnaires and interviews, we found that both post-stroke survivors and therapists appreciated the potential benefits of AI and robotic coaches to achieve more systematic management and improve their self-efficacy and motivation on rehabilitation therapy. In addition, our evaluation sheds light on several practical concerns (e.g. a possible difficulty with the interaction for people with cognitive impairment, system failures, etc.). We discuss the value of early involvement of stakeholders and interactive techniques that complement system failures, but also support a personalized therapy session for the better deployment of AI and robotic exercise coaches.
Weathering phenomena, rock physical properties and long-term restoration intervention: a case study from the St. Johannis Chapel of Lütgenrode (Lower Saxony, Germany)
Authors: Siegesmund Siegfried , Wiese Frank , Klein Calvin , Huster Ulrich , Pötzl Christopher
Published: July 2022

Small historical churches in rural villages are mainly functional buildings, lacking spectacular architectural or ornamental features. This is also true for the St. Johannis Chapel Lütgenrode near Göttingen (Lower Saxony, Germany), which dates back to the 13th century. The use of ca. 10 different natural building stones (Triassic sandstone and limestone, Holocene fresh water carbonate), scattered roof tiles and bricks result in a highly heterogeneous character of the chapel’s ascending walls. In addition, various repairs over the last centuries, using inadequate materials, amplified damages and produced critical stability problems, in particular at the southern wall. Here, the suitability of the dimensional stones are evaluated for construction and replacement purposes. A semi-quantitative distribution of lithotypes was performed, and weathering forms were mapped in detail. On-site analyses (micro-drilling resistance, the Schmidt hammer rebound test, capillary water absorption) provide data on the deterioration state of the main lithologies. The petrophysical data show that stratigraphically comparable building stones exhibit different technical characteristics and weathering behavior. All data serve to characterize the state of weathering and provide the data set to plan for future restoration work. The amount needed for restoration work has been estimated to be approximately 435,000–550,000 EUR. Because the local church authorities evaluate the significance of a church based on the frequency of its use, a secular use would be able to save the Lütgenrode chapel, but then the church political leaders would have to act quickly.
Hypoxia: molecular pathophysiological mechanisms in human diseases
Authors: Della Rocca Ylenia , Fonticoli Luigia , Rajan Thangavelu Soundara , Trubiani Oriana , Caputi Sergio , Diomede Francesca , Pizzicannella Jacopo , Marconi Guya Diletta
Published: July 2022

Hypoxia, a low O2 tension, is a fundamental feature that occurs in physiological events as well as pathophysiological conditions, especially mentioned for its role in the mechanism of angiogenesis, glucose metabolism, and cell proliferation/survival. The hypoxic state through the activation of specific mechanisms is an aggravating circumstance commonly noticed in multiple sclerosis, cancer, heart disease, kidney disease, liver disease, lung disease, and in inflammatory bowel disease. On the other hand, hypoxia could play a key role in tissue regeneration and repair of damaged tissues, especially by acting on specific tissue stem cells, but their features may result as a disadvantage when it is concerned for neoplastic stem cells. Furthermore, hypoxia could also have a potential role in tissue engineering and regenerative medicine due to its capacity to improve the performance of biomaterials. The current review aims to highlight the hypoxic molecular mechanisms reported in different pathological conditions to provide an overview of hypoxia as a therapeutic agent in regenerative and molecular therapy.

Graphical abstract
Emergent Realities: Diffracting Barad within a quantum-realist ontology of matter and politics
Authors: Everth Thomas , Gurney Laura
Published: July 2022

One of the most influential contemporary authors of the new materialist turn in the social sciences is Karen Barad. Barad’s work in agential realism, based on her interpretations of quantum physics, has been widely cited within a growing body of new materialist publications. However, in translating Barad’s assertions into social domains, there has been increasing critical appraisal of the physics underlying her work and its relationship with non-quantum domains. In this paper, we contribute to this discussion by exploring aspects of agential realism through quantum decoherence and quantum Darwinism. We explore implications for Barad’s metaphysics and the relationship of the social with the rest of the material world.
On 2MP-, MP2- and C2MP-inverses for rectangular matrices
Authors: Hernández M. V. , Lattanzi M. B. , Thome N.
Published: July 2022

This paper introduces 2MP-inverses, MP2-inverses, and C2MP-inverses, for rectangular matrices following a different approach to that used in the recent literature. These new inverses generalize some classical inverses in the literature. Instead of considering a system of matrix equations as usually, in order to define 2MP-inverses and MP2-inverses, we consider a construction from oblique projectors represented by means of outer generalized inverses. We use an adequate equivalence relation, and then we pass to the quotient set in order to get the most simple canonical representative. An interesting advantage of our extension of CMP inverses from square to rectangular matrices is that we do not need any auxiliary weight matrix, but we are using the own matrix A for doing it. In addition, some properties and representations of 2MP-, MP2-, and C2MP-inverses are given.
Coevolutionary opinion dynamics with sparse interactions in open-ended societies
Authors: Bao Honglin , Neal Zachary P , Banzhaf Wolfgang
Published: July 2022

Opinion dynamics is a crucial topic in complex social systems. However, existing models rarely study limited information accessibility, sparse interactions, and the coevolution of opinion and an open-ended structure. In this paper, we propose the Sparse COevolutionary Open-Ended (SCOOE) model. We address the sparse interaction limitation through extrinsic collective interaction and intrinsic observation based on incomplete neighborhood information. We also consider the coevolution of opinion and open-ended structure by studying structure-opinion co-dynamics when dissidents are leaving and when newcomers with novel opinions are joining. From an opinion dynamics perspective, we find that the proposed mechanisms effectively form lean and fast decision strategies to reduce conflicts under uncertainty. The model is robust in boosting and enhancing a global consensus with only small odds of extreme results. The structure evolves toward a small-world network. We find that an emergent dialectic relationship exists between community segregation and community cohesion viewed from a structural dynamics perspective. We also study the influence of agent heterogeneity under different cognitive ability distributions.
Urban Non-urban Agglomeration Divide: Is There a Gap in Productivity and Wages?
Authors: Bartoloni Eleonora , Marino Andrea , Baussola Maurizio , Romaniello Davide
Published: July 2022

This paper investigates the productivity–wage relation using a novel and integrated employer-employee database covering the entire population of non-financial firms’ plants in one of the most developed regions in Europe, i.e., the Italian Lombardy region. We suggest that although a growing literature shows that locating in urban areas yields substantial productivity gains due to agglomeration economies, the interaction between productivity and wages is ultimately the key to ascertaining the true advantage of the high densely populated areas. By adopting an empirical specification that allows us to explore interaction effects between localization and the sector of activity at the establishment level, we find that agglomeration economies play a significant but conditional role in affecting productivity and wage differentials while also controlling for firm-specific factors (in particular, job-related characteristics) and selection effects. The estimated impacts are heterogeneous across sectors, depending on their technological features. The effect of locating in High-density urban areas on the productive-wage gap is significantly positive only in highly knowledge-intensive services sectors; for firms supplying less technologically sophisticated services and for manufacturing plants, the impact is either not significant or negative. Locating in Rural areas generally exerts a downward (or not significant) impact on the productivity-wage gap.
Effect of Evaporative Cooling on Photovoltaic Module Performance
Authors: Alktranee Mohammed , Bencs Peter
Published: July 2022

The photovoltaic module (PV) consists of many photovoltaic cells made of silicon that lose their properties with an increased temperature. Increasing photovoltaic cell temperature represents an intrinsic problem that causes a drop in the open-circuit voltage of the PV module, thus affecting its performance. The present work investigates using evaporating cooling as a passive cooling technique to absorb the generated heat from the PV module and lower its temperature by cotton wicks immersed in the water (CWIWs) attached to the backside photovoltaic module. The CWIWs decrease air dry temperature and increase humidity and then produce cool air to help cool PV modules. The results showed dropped PV module temperature by about 22% attributed to providing appropriate cooling produced by the moist condition of the cotton bristles immersed by water exposed to the wind. The output power generation and efficiency have increment by 16.3 W and 53%, respectively. The electrical exergy was equivalent to output power under the evaporating cooling, while entropy generation dropped about 14% with increased the PV module temperature.
Extensive Spinal Epidural Hematoma as the Cause of Postpartum Headache and Neck Pain After Epidural Anesthesia: a Case-Based Report
Authors: Bäck Anne Tuiskunen , Åkerstedt Josefin
Published: July 2022

Spinal epidural hematomas (SEH) are a rare hemorrhagic event occurring after trauma, epidural anesthesia, or operative inventions. However, in 40–50% of cases, they occur spontaneously. Spontaneous spinal epidural hematomas (SSEH) are rare in occurrence with an estimated incidence of 1 case per million annually. Pregnancy is an independent risk factor. Sudden neck or back pain, often in combination with a rapid onset of neurological symptoms, is the most common presentation of SEH (1). A 36-year-old Caucasian female with rheumatoid arthritis (RA) presented to the emergency department approximately 48 h after an uncomplicated vaginal delivery. She sought medical attention due to constant headaches and neck pain that started during active labor. An MRI of the spine revealed an extensive SEH spreading from C1 to L5. The patient was without neurological symptoms or deficits and was successfully treated conservatively without any sequelae. Even though the definitive cause of this case of SEH will remain unknown, several possible synergistic mechanisms have been identified. These include female gender, full-term pregnancy, physical activity with increased intraabdominal pressure (i.e., Valsalva maneuver), systemic administration of platelet aggregation inhibitor (PAI), and iatrogenic manipulation such as spinal epidural anesthesia. Even though autoimmune and inflammatory disorders have been described in the literature to be rare sources of hemorrhage in the spinal canal, it is unclear whether the patient’s RA should be regarded as an individual risk factor.

Key Facts

Spinal epidural hematomas are a rare hemorrhagic event characterized by an accumulation of blood between the vertebrae and the dura of the spinal canal, and can be a clinical challenge to diagnose due to the insidious presentation, with symptoms ranging from asymptomatic to non-specific head or neck pain, or neurological deficits.

The etiology of spontaneous spinal epidural hematomas remains largely unknown, although there are many predisposing factors, including vascular malformation, anticoagulation therapy, trauma, iatrogenic manipulations, and hypertension.

The differential diagnosis to spinal epidural hematomas are several, e.g., meningitis, migraine, subarachnoid or intracranial hemorrhage, pituitary apoplexy, venous sinus thrombosis, and thrombosis, and radiological examination is key to diagnose and map the distribution of the hemorrhage.
Method optimisation and application based on solid phase extraction of non steroidal anti-inflammatory drugs, antiretroviral drugs, and a lipid regulator from coastal areas of Durban, South Africa
Authors: Sigonya Sisonke , Onwubu Stanley Chibuzor , Mdluli Phumlani Selby , Mokhothu Thabang Hendrica
Published: July 2022

This study presents an optimized method that is applicable in monitoring the occurrence of pharmaceuticals in a wide range of aquatic environments. The optimised Solid Phase Extraction method is based on Bond Elut Plexa cartridges for the identification and quantification of three non-steroidal anti-inflammatory drugs, three antiretroviral drugs and a lipid regulator in the coastal area of Durban city, South Africa covering four seasons. The extracted compounds are qualitatively and quantitatively detected by a high-performance liquid phase chromatographic instrument coupled to a photodiode array detector. The recoveries range from 62 to 110% with a Relative Standard Deviation of 0.56−4.68%, respectively, for the determination of emtricitabine, tenofovir, naproxen, diclofenac, ibuprofen, efavirenz, and gemfibrozil. The analytical method is validated by spiking estuarine water samples with 5 µg L− 1 of a mixture containing the target pharmaceuticals and the matrix detection limit is established to be 0.62–1.78 µg L− 1 for the target compounds. The optimized method is applied to seasonal monitoring of pharmaceuticals at chosen study sites from winter and spring of 2019 and summer and autumn of 2020. The results indicate the concentration of the pharmaceuticals studied varies with the type of aquatic environment and season.
CAPTION: Caption Analysis with Proposed Terms, Image of Objects, and Natural Language Processing
Authors: Ferreira Leonardo A. , De Rizzo Meneghetti Douglas , Lopes Marcos , Santos Paulo E.
Published: July 2022

This paper proposes a novel algorithm, called CAPTION, for identifying and correcting errors in automatically generated image captions. The algorithm combines Deep Learning (DL) for object detection in images with Natural Language Processing techniques. CAPTION has been tested in the following three tasks: (1) classify a caption as correct or not; (2) detect wrong words in the caption, and (3) suggest text corrections. Results show that our method is superior with respect to others evaluated in the same data set in the error correction task. These other methods are generally based exclusively on DL models. This work shows that, although semantics still has not been used at its fullest in this type of task, a combination of DL with Natural Language Processing tools presents a better overall performance than using DL methods alone.
The potential impact of model horizontal resolution on the simulation of atmospheric cloud radiative effect in CMIP6 models
Authors: Lin Qiao-Jun , Yu Jia-Yuh
Published: July 2022

The simulations of atmospheric cloud-radiative effect (ACRE) from 54 Coupled Model Intercomparison Project phase 6 (CMIP6) models during the historical period of 2000/03–2014/12 are compared and evaluated against the satellite-based Clouds and the Earth’s Radiant Energy System (CERES) products. For ease of comparison, all CMIP6 models are divided into high-, medium-, and low-resolution groups to examine the potential impact of model horizontal resolution change on the simulations of ACRE distribution over the tropical oceans. The results show that ACRE is positive inside the ITCZs but negative in the subtropics and cold tongue areas, owing to the very different radiative forcing between deep and shallow clouds. Simulations of ACRE are sensitive to the model horizontal resolution used and the finer resolution models generally produce a better performance of ACRE simulations against the CERES observations. The reduced ACRE biases in finer resolution models are mainly contributed by the improved longwave ACRE (i.e., LWACRE) simulations, especially over the Pacific and Atlantic cold tongue areas where shallow stratocumulus clouds prevail.
Actual Fictions
Authors: Smeets Roel
Published: July 2022

This Element sheds a new light on the ubiquitous yet complex notion of mimesis. By systematically comparing the social dynamics of the Dutch population at a given time with the social dynamics of characters in Dutch literary fiction published in the same period, it aims to pinpoint the ways in and the extent with which literary fiction either mirrors or shapes the societal context from which it emerged. While close-reading-based scholarship on this topic has been limited to qualitative interpretations of allegedly exemplary works, the present study uses the data-driven tools of social network analysis to systematically determine the imitative elements of the social dynamics of characters within larger-scale, representative collections of books of literary fiction.
Wiretapped Cables and the Songs of Whales
Authors: Duncombe Jenessa
Published: July 2022

Researchers jerry-rigged fiber-optic cables in a fjord to eavesdrop on blue whales, with possible applications ranging from seafloor mapping to meteorology.
Ecological memory of prior nutrient exposure in the human gut microbiome
Authors: Letourneau Jeffrey , Holmes Zachary C , Dallow Eric P , Durand Heather K , Jiang Sharon , Carrion Verónica M , Gupta Savita K , Mincey Adam C , Muehlbauer Michael J , Bain James R , David Lawrence A
Published: July 2022

Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, whether microbial communities alter their response to repeated stimulus remains incompletely understood. Using the human gut microbiome as a model, we show that bacterial communities retain an “ecological memory” of past carbohydrate exposures. Memory of the prebiotic inulin was encoded within a day of supplementation among a cohort of human study participants. Using in vitro gut microbial models, we demonstrated that the strength of ecological memory scales with nutrient dose and persists for days. We found evidence that memory is seeded by transcriptional changes among primary degraders of inulin within hours of nutrient exposure, and that subsequent changes in the activity and abundance of these taxa are sufficient to enhance overall community nutrient metabolism. We also observed that ecological memory of one carbohydrate species impacts microbiome response to other carbohydrates, and that an individual’s habitual exposure to dietary fiber was associated with their gut microbiome’s efficiency at digesting inulin. Together, these findings suggest that the human gut microbiome’s metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. The dynamics of this ecological memory also highlight the potential for intra-individual microbiome variation to affect the design and interpretation of interventions involving the gut microbiome.
Acquisition and evolution of enhanced mutualism—an underappreciated mechanism for invasive success?
Authors: Sheng Min , Rosche Christoph , Al-Gharaibeh Mohammad , Bullington Lorinda S , Callaway Ragan M , Clark Taylor , Cleveland Cory C , Duan Wenyan , Flory S Luke , Khasa Damase P , Klironomos John N , McLeod Morgan , Okada Miki , Pal Robert W , Shah Manzoor A , Lekberg Ylva
Published: July 2022

Soil biota can determine plant invasiveness, yet biogeographical comparisons of microbial community composition and function across ranges are rare. We compared interactions between Conyza canadensis, a global plant invader, and arbuscular mycorrhizal (AM) fungi in 17 plant populations in each native and non-native range spanning similar climate and soil fertility gradients. We then grew seedlings in the greenhouse inoculated with AM fungi from the native range. In the field, Conyza plants were larger, more fecund, and associated with a richer community of more closely related AM fungal taxa in the non-native range. Fungal taxa that were more abundant in the non-native range also correlated positively with plant biomass, whereas taxa that were more abundant in the native range appeared parasitic. These patterns persisted when populations from both ranges were grown together in a greenhouse; non-native populations cultured a richer and more diverse AM fungal community and selected AM fungi that appeared to be more mutualistic. Our results provide experimental support for evolution toward enhanced mutualism in non-native ranges. Such novel relationships and the rapid evolution of mutualisms may contribute to the disproportionate abundance and impact of some non-native plant species.
Genomic architecture of FGFR2 fusions in cholangiocarcinoma and its implication for molecular testing
Authors: Neumann Olaf , Burn Timothy C. , Allgäuer Michael , Ball Markus , Kirchner Martina , Albrecht Thomas , Volckmar Anna-Lena , Beck Susanne , Endris Volker , Goldschmid Hannah , Lehmann Ulrich , Seker-Cin Huriye , Uhrig Sebastian , Roessler Stephanie , Budczies Jan , Fröhling Stefan , Longerich Thomas , Wagner Alex H. , Vogel Arndt , Schirmacher Peter , Stenzinger Albrecht , Kazdal Daniel
Published: July 2022

Background

Cholangiocarcinoma (CCA) is a primary malignancy of the biliary tract with a dismal prognosis. Recently, several actionable genetic aberrations were identified with significant enrichment in intrahepatic CCA, including FGFR2 gene fusions with a prevalence of 10–15%. Recent clinical data demonstrate that these fusions are druggable in a second-line setting in advanced/metastatic disease and the efficacy in earlier lines of therapy is being evaluated in ongoing clinical trials. This scenario warrants standardised molecular profiling of these tumours.

Methods

A detailed analysis of the original genetic data from the FIGHT-202 trial, on which the approval of Pemigatinib was based, was conducted.

Results

Comparing different detection approaches and displaying representative cases, we described the genetic landscape and architecture of FGFR2 fusions in iCCA and show biological and technical aspects to be considered for their detection. We elaborated parameters, including a suggestion for annotation, that should be stated in a molecular diagnostic FGFR2 report to allow a complete understanding of the analysis performed and the information provided.

Conclusion

This study provides a detailed presentation and dissection of the technical and biological aspects regarding FGFR2 fusion detection, which aims to support molecular pathologists, pathologists and clinicians in diagnostics, reporting of the results and decision-making.
RNA-based therapeutics: an overview and prospectus
Authors: Zhu Yiran , Zhu Liyuan , Wang Xian , Jin Hongchuan
Published: July 2022

The growing understanding of RNA functions and their crucial roles in diseases promotes the application of various RNAs to selectively function on hitherto “undruggable” proteins, transcripts and genes, thus potentially broadening the therapeutic targets. Several RNA-based medications have been approved for clinical use, while others are still under investigation or preclinical trials. Various techniques have been explored to promote RNA intracellular trafficking and metabolic stability, despite significant challenges in developing RNA-based therapeutics. In this review, the mechanisms of action, challenges, solutions, and clinical application of RNA-based therapeutics have been comprehensively summarized.
SALIS transcriptionally represses IGFBP3/Caspase-7-mediated apoptosis by associating with STAT5A to promote hepatocellular carcinoma
Authors: Liu Xingyuan , Jin Yi , Wan Xuan , Liang Xiaoting , Wang Ke , Liu Jieyu , Jiang Jiale , Meng Bingyao , Han Shuo , Zhou Liang , Cai Shaoxi , Zou Fei
Published: July 2022

Hepatocellular carcinoma (HCC) is the most common subtype of liver cancer and the second most fatal cancer in the world despite the great therapeutic advances in the past two decades, which reminds us of the gap in fully understanding the oncogenic mechanism of HCC. To explore the key factors contributing to the progression of HCC, we identified a LncRNA, termed SALIS (Suppression of Apoptosis by LINC01186 Interacting with STAT5A), functions in promoting the proliferation, colony formation, migration and invasion while suppressing apoptosis in HCC cells. Mechanistic study indicated SALIS physically associates with transcription factor STAT5A and binds to the promoter regions of IGFBP3 and Caspase-7 to transcriptionally repress their expression and further inhibit apoptosis. Our findings identified SALIS as an oncogene to promote HCC by physically binding with STAT5A to inhibit the expression of pro-apoptotic IGFBP3 and Caspase-7, which suggests novel therapeutic targets for HCC treatments.
Tripartite motif 25 ameliorates doxorubicin-induced cardiotoxicity by degrading p85α
Authors: Shen Yihui , Zhang Hui , Ni Yangyue , Wang Xuejun , Chen Yifan , Chen Jiahui , Wang Yan , Lin Jinyi , Xu Yuchen , Zhao Jian-Yuan , Cheng Leilei
Published: July 2022

Doxorubicin (DOX)-based chemotherapy is widely used to treat malignant tumors; however, the cardiotoxicity induced by DOX restricts its clinical usage. A therapeutic dose of DOX can activate ubiquitin-proteasome system. However, whether and how ubiquitin-proteasome system brings out DOX-induced cardiotoxicity remains to be investigated. Here we conducted a proteomics analysis of a DOX-induced cardiotoxicity model to screen the potentially ubiquitination-related molecules. Dysregulated TRIM25 was found to contribute to the cardiotoxicity. In vivo and in vitro cardiotoxicity experiments revealed that TRIM25 ameliorated DOX-induced cardiotoxicity. Electron microscopy and endoplasmic reticulum stress markers revealed that TRIM25 mitigated endoplasmic reticulum stress and apoptosis in DOX-induced cardiomyocytes. Mechanistically, the Co-immunoprecipitation assays and CHX pulse-chase experiment determined that TRIM25 affected p85α stability and promoted its ubiquitination and degradation. This leads to increase of nuclear translocation of XBP-1s, which mitigates endoplasmic reticulum stress. These findings reveal that TRIM25 may have a therapeutic role for DOX-induced cardiotoxicity.
Stress-testing the resilience of the Austrian healthcare system using agent-based simulation
Authors: Kaleta Michaela , Lasser Jana , Dervic Elma , Yang Liuhuaying , Sorger Johannes , Lo Sardo D. Ruggiero , Thurner Stefan , Kautzky-Willer Alexandra , Klimek Peter
Published: July 2022

Patients do not access physicians at random but rather via naturally emerging networks of patient flows between them. As mass quarantines, absences due to sickness, or other shocks thin out these networks, the system might be pushed to a tipping point where it loses its ability to deliver care. Here, we propose a data-driven framework to quantify regional resilience to such shocks via an agent-based model. For each region and medical specialty we construct patient-sharing networks and stress-test these by removing physicians. This allows us to measure regional resilience indicators describing how many physicians can be removed before patients will not be treated anymore. Our model could therefore enable health authorities to rapidly identify bottlenecks in access to care. Here, we show that regions and medical specialties differ substantially in their resilience and that these systemic differences can be related to indicators for individual physicians by quantifying their risk and benefit to the system.
Rep15 interacts with several Rab GTPases and has a distinct fold for a Rab effector
Authors: Rai Amrita , Singh Anurag K. , Bleimling Nathalie , Posern Guido , Vetter Ingrid R. , Goody Roger S.
Published: July 2022

In their GTP-bound (active) form, Rab proteins interact with effector proteins that control downstream signaling. One such Rab15 effector is Rep15, which is known to have a role in receptor recycling from the endocytic recycling compartment but otherwise remains poorly characterized. Here, we report the characterization of the Rep15:Rab15 interaction and identification of Rab3 paralogs and Rab34 as Rep15 interacting partners from a yeast two-hybrid assay. Biochemical validation of the interactions is presented and crystal structures of the Rep15:Rab3B and Rep15:Rab3C complexes provide additional mechanistic insight. We find that Rep15 adopts a globular structure that is distinct from other reported Rab15, Rab3 and Rab34 effectors. Structure-based mutagenesis experiments explain the Rep15:Rab interaction specificity. Rep15 depletion in U138MG glioblastoma cells impairs cell proliferation, cell migration and receptor recycling, underscoring the need for further clarification of the role of Rep15 in cancer.
Mechanochemistry-driven engineering of 0D/3D heterostructure for designing highly luminescent Cs–Pb–Br perovskites
Authors: Baek Kyeong-Yoon , Lee Woocheol , Lee Jonghoon , Kim Jaeyoung , Ahn Heebeom , Kim Jae Il , Kim Junwoo , Lim Hyungbin , Shin Jiwon , Ko Yoon-Joo , Lee Hyeon-Dong , Friend Richard H. , Lee Tae-Woo , Lee Jeongjae , Kang Keehoon , Lee Takhee
Published: July 2022

Embedding metal-halide perovskite particles within an insulating host matrix has proven to be an effective strategy for revealing the outstanding luminescence properties of perovskites as an emerging class of light emitters. Particularly, unexpected bright green emission observed in a nominally pure zero-dimensional cesium–lead–bromide perovskite (Cs4PbBr6) has triggered intensive research in better understanding the serendipitous incorporation of emissive guest species within the Cs4PbBr6 host. However, a limited controllability over such heterostructural configurations in conventional solution-based synthesis methods has limited the degree of freedom in designing synthesis routes for accessing different structural and compositional configurations of these host–guest species. In this study, we provide means of enhancing the luminescence properties in the nominal Cs4PbBr6 powder through a guided heterostructural configuration engineering enabled by solid-state mechanochemical synthesis. Realized by an in-depth study on time-dependent evaluation of optical and structural properties during the synthesis of Cs4PbBr6, our target-designed synthesis protocol to promote the endotaxial formation of Cs4PbBr6/CsPbBr3 heterostructures provides key insights for understanding and designing kinetics-guided syntheses of highly luminescent perovskite emitters for light-emitting applications.
A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response
Authors: Evans Jordan C. , McEneany Valentina Laclare , Coyne Michael J. , Caldwell Elizabeth P. , Sheahan Madeline L. , Von Salena S. , Coyne Emily M. , Tweten Rodney K. , Comstock Laurie E.
Published: July 2022

Phocaeicola vulgatus is one of the most abundant and ubiquitous bacterial species of the human gut microbiota, yet a comprehensive analysis of antibacterial toxin production by members of this species has not been reported. Here, we identify and characterize a previously undescribed antibacterial protein. This toxin, designated BcpT, is encoded on a small mobile plasmid that is largely confined to strains of the closely related species Phocaeicola vulgatus and Phocaeicola dorei. BcpT is unusual in that it requires cleavage at two distinct sites for activation, and we identify bacterial proteases that perform this activation. We further identify BcpT’s receptor as the Lipid A-core glycan, allowing BcpT to target species of other Bacteroidales families. Exposure of cells to BcpT induces a response involving an unusual sigma/anti-sigma factor pair that is likely triggered by cell envelope stress, resulting in the expression of genes that partially protect cells from multiple antimicrobial toxins.