bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a novel cell line‐derived xenograft model of primary herpesvirus 8‐unrelated effusion large B‐cell lymphoma and antitumor activity of birabresib in vitro and in vivo
Authors: Nishimori Tomohiro , Higuchi Tomonori , Hashida Yumiko , Ujihara Takako , Taniguchi Ayuko , Ogasawara Fumiya , Kitamura Naoya , Murakami Ichiro , Kojima Kensuke , Daibata Masanori
Published: November 2021

Background

Primary human herpesvirus 8 (HHV8)‐unrelated effusion large B‐cell lymphoma is a clinical disease entity distinct from HHV8‐positive primary effusion lymphoma (PEL). However, the lack of experimental HHV8‐unrelated effusion large B‐cell lymphoma models continues to hinder the pathophysiologic and therapeutic investigations of this disorder.

Methods

The lymphoma cells were obtained from the pleural effusion of a patient with primary HHV8‐unrelated effusion large B‐cell lymphoma and cultured in vitro.

Results

We established a novel HHV8‐unrelated effusion large B‐cell lymphoma cell line, designated Pell‐1, carrying a c‐MYC rearrangement with features distinct from those of HHV8‐positive PEL. Moreover, we developed an HHV8‐unrelated effusion large B‐cell lymphoma cell line‐derived xenograft model. Pell‐1 cells induced profuse lymphomatous ascites and subsequently formed intra‐abdominal tumors after intraperitoneal implantation into irradiated nonobese diabetic/severe combined immunodeficient mice. Thus, this xenograft mouse model mimicked the clinical phenomena observed in patients and recapitulated the sequential stages of aggressive HHV8‐unrelated effusion large B‐cell lymphoma. The bromodomain and extraterminal domain (BET) inhibitors JQ1 and birabresib (MK‐8628/OTX015) reduced the proliferation of Pell‐1 cells in vitro through the induction of cell cycle arrest and apoptosis. The antitumor effect of BET inhibition was also demonstrated in vivo, as birabresib significantly reduced ascites and suppressed tumor progression without apparent adverse effects in the xenografted mice.

Conclusion

These preclinical findings suggest the therapeutic potential of targeting c‐MYC through BET inhibition in HHV8‐unrelated effusion large B‐cell lymphoma.
Comparison of survival, acute toxicities, and dose–volume parameters between intensity‐modulated radiotherapy with or without internal target volume delineation method and three‐dimensional conformal radiotherapy in cervical cancer patients: A retrospective and propensity score‐matched analysis
Authors: Liang Yu‐Qin , Feng Sen‐Quan , Xie Wen‐Jia , Jiang Qiong‐Zhi , Yang Yan‐Fen , Luo Ren , Kidd Elizabeth A. , Zhai Tian‐Tian , Xie Liang‐Xi
Published: November 2021

Background

To evaluate whether the use of the internal target volume (ITV) delineation method improves the performance of intensity‐modulated radiotherapy (IMRT) and three‐dimensional conformal radiotherapy (3DCRT) in terms of survival, acute toxicities, and dose–volume parameters.

Methods

A total number of 477 cervical cancer patients who received concurrent chemoradiotherapy (CCRT) from January 2012 to December 2016 were retrospectively analyzed. They were divided into four groups: the non‐ITV (N‐ITV) + IMRT, ITV + IMRT, N‐ITV + 3DCRT, and ITV + 3DCRT groups, with 76, 41, 327, and 33 patients, respectively. Survival analysis was performed with the Kaplan–Meier and the log‐rank tests, and acute toxicity analysis was performed with the chi‐squared test and the binary logistic regression test. Using the propensity score matching (PSM) method, 92 patients were matched among the four groups, and their dose–volume parameters were assessed with the Kruskal–Wallis method.

Results

The median follow‐up time was 49 months (1–119) for overall survival (OS). The 5‐year OS rate was 66.4%. The ITV delineation method was an independent prognostic factor for OS (HR [95% CI]: 0.52 [0.27, 0.98], p = 0.044) and progression‐free survival (PFS) (HR [95% CI]: 0.59 [0.36, 0.99], p = 0.045). The ITV + IMRT group had the lowest incidence rate (22%) and the N‐ITV + IMRT group had the highest incidence rate of grade ≥3 hematological toxicity (HT) (46.1%) among the four groups. The pelvic bone marrow relative V10, V20, and V30 in the N‐ITV + IMRT group was higher than those in the ITV + IMRT and N‐ITV + 3DCRT groups (p < 0.05).

Conclusions

The use of ITV for IMRT treatment planning was associated with improved overall survival and progression‐free survival, with lower HT rate.
Netherton syndrome plus atopic dermatitis: Two new genetic mutations in the same patient
Authors: Moar Agata , Bruni Manfredo , Schena Donatella , Rigotti Erika , Colato Chiara , Novelli Antonio , Cesario Claudia , Girolomoni Giampiero
Published: November 2021

A child who comes to our attention for the appearance of erythematous, scaly lesions localized to the upper and lower limbs for 2 months. Histological features suggested ichthyosiform disease and concomitant mutations in the SPINK5 and FLG2 genes confirmed Netherton syndrome with severe atopic manifestations.
Is single‐point acupuncture effective in treating acute low back pain?
Authors: Tiwari Sagun , Sapkota Namrata
Published: November 2021

Acupuncture is often used for acute and chronic low back pain; however, its efficacy is controversial, primarily for acute low back pain (ALBP). An acupuncture point, GV‐26, could be used as an analgesic acupoint to treat acute low back pain. Our study suggests that single acupuncture could relieve ALBP within a short time without any adverse events. Acupuncture can be integrated with allopathic (western) medicine and used in the hospital's emergency department to treat acute painful conditions.
Successful implantation of S‐ICD using the intermuscular two‐incision technique in a patient with severe pectus excavatum
Authors: Guarracini Fabrizio , Marini Massimiliano , Strazzanti Mattia , Bonmassari Roberto , Guarracini Stefano , Di Mauro Michele , Droghetti Andrea
Published: November 2021

A patient with severe pectus excavatum, dilated ischemic heart disease, and indication for defibrillator implantation for primary prevention of sudden death underwent successful ultrasound‐guided serratus anterior plane block and parasternal block with intermuscular two‐incision technique implantation with no complications. At follow‐up, all the parameters resulted stable with excellent signal sensing.
Mixed Oxygen Ionic and Electronic Conducting Membrane Reactors for Pure Chemicals Production
Authors: Wang Ao , Liang Man , Xiang Qingyun , Xue Jian , Wang Haihui
Published: November 2021

Traditional gas separation technologies to produce pure oxygen, hydrogen and highly concentrated nitrogen, such as pressure swing adsorption and cryogenic separation, are cost and energy intensive. The mixed oxygen ionic and electronic conductor (MIEC) membrane can separate oxygen with 100 % selectivity, which can be applied as a platform reactor for pure chemicals production. In the MIEC membrane reactor, pure O2 can be directly produced. When the oxygen is all removed, highly concentrated N2 is generated. Moreover, if the feeding gas is water steam, hydrogen can be yielded through water decomposition. Significant progress has been made in the MIEC membrane reactor for pure chemicals production over the past few years. Therefore, this work summarizes the relative efforts on MIEC membranes for oxygen, nitrogen, and hydrogen purification. The principles of materials selection, membrane morphology optimizing, and reactions coupling are discussed in detail.
Analysis of commonly used scheduling models for multistage biopharmaceutical processes
Authors: Kumar Vaibhav , Shaik Munawar A. , Jain Arpit
Published: November 2021

Several works have been reported in the literature over the past two decades to schedule a multiproduct facility in the biopharmaceutical industry. The present work attempts to analyze a few commonly used scheduling models, based on different time representations, for midterm planning or long‐term scheduling of multistage, multiproduct biopharmaceutical facilities for multiperiod demand. Several model inconsistencies/limitations in the published literature and in the reported Gantt charts, such as (i) real‐time storage violation, (ii) early product delivery, (iii) inadequate mapping of upstream and downstream tasks, (iv) no initial setup time, and (v) incomplete sequencing/modelling of storage tasks, thus (iv) overestimating the reported objective values in their results, are identified. Accordingly, one of the unit‐specific‐event‐based literature models is improved in this work to address these limitations. An improved model is proposed with enhanced/new features such as modified material balances, proper sequencing of storage based on storage bypassing allowed for intermediates and bypassing not allowed for products, modified shelf‐life constraints, initial setup time constraints, and updated bounds on storage, giving better results compared to the published literature models.
Controllable Synthesis of Silicon‐Based Nanohybrids for Reliable Surface‐Enhanced Raman Scattering Sensing
Authors: Lu Xing , Wang Houyu , He Yao
Published: November 2021

Comprehensive Summary

Interface between metallic nanoparticles and dielectric silicon substrate can strongly confine electromagnetic field (EM‐field) through its localized surface plasmons, together contributing great surface‐enhanced Raman scattering (SERS) enhancement. Typically, silicon‐based nanohybrids (metallic nanoparticles in situ grown on silicon substrate) have been widely employed as SERS‐active substrates in sensing platforms for the detection of chemical and biological analytes. Silicon‐based nanohybrids with surface plasmons allow amplifying Raman signals that associate molecular binding events by several orders of magnitude. Together with interfacial architectures for the specific binding of target analyte on the silicon‐based nanohybrid surface, silicon‐based nanohybrid‐enhanced Raman scattering represents a promising method for increasing reliability and sensitivity. This review affords a presentation to the basics of SERS enhancement of silicon‐based nanohybrid, illustrates current advances in controllable synthesis of silicon‐based nanohybrid substrates, and outlines current implementations to sensors for reliable detection of ultralow amounts of analytes.

What is the most favorite and original chemistry developed in your research group?

The design and fabrication of silicon‐based platform for long‐term bioimaging and reliable biosensing analysis.

What is the most important personality for scientific research?

Cooperation and conscientiousness.

What are your hobbies? What's your favorite book(s)?

Music. History book.

Who influences you mostly in your life?

Family and supervisors.

What is your favorite journal(s)?

Nature serials, JACS, Angew. Chem., etc.

Could you please give us some advices on improving Chinese Journal of Chemistry?

Publishing original and significant discoveries.
Self‐assembly into Polymorphic 2D Nanosheets with Crystallization‐Induced Emission Enhancement
Authors: Zhang He , Jin Dong , Lin Dongqing , Huang Lei , Wang Jin , Wang Shasha , Xie Linghai
Published: November 2021

Comprehensive Summary

Organic micro/nanocrystals with polymorphic tailorability and perfect platform to modulate decode the complex relationship among molecular structures, supramolecular/noncovalent interactions, aggregates and exciton behaviors. Herein, we precisely tune the polymorphic two‐dimensional organic nanosheets (2DONs) of cyano‐spirocyclic aromatic hydrocarbon (2'‐CN‐SFX), where the crystal growth processes are dominated by precursor concentration. The low concentration (ca. 2 mmol/L) affords the rhombus‐like nanosheets with monoclinic P21/c space group, in which molecules adopt antiparallel and slipped stacking mode. In contrast, the high concentration (ca. 4 mmol/L) favors herringbone‐like molecular packing pattern and then generates shuttle‐like nanosheets with monoclinic C2/c space group. Both above polymorphic nanosheets exhibit unprecedented crystallization‐induced emission enhancement (CIEE) feature that increases the photoluminescence quantum yields (PLQYs) from 16% in solution, 21% in amorphous film to 37%—39% in crystalline states. This result will offer promising opportunities for nanophotonics and organic intelligent semiconductors.
Orthogonality of Redesigned tRNA Molecules with Three Stop Codons
Authors: Zhang Zhao‐Yang , Liao Dan‐Ni , Ma Yu‐Xin , Jia Bin , Yuan Ying‐Jin
Published: November 2021

Comprehensive Summary

The ability to expand genetic code in living cells has emerged as a powerful method with diverse applications. Here, we design replacement of the anticodons of E. coli tRNAs that recognize codons for 20 natural amino acids, with three anti‐stop codons, resulting in a total of 60 engineered tRNA constructs. We test these constructs one by one in E. coli, and found that six tRNAsCUA (tyrV, serX, hisR, trpT, glnV and leuX), two tRNAsUCA (trpT and leuX) and one tRNAUUA (tyrV) allowed efficient expression of Red Fluorescence Protein (RFP) with the presence of a corresponding stop codon in frame. Furthermore, we exploit the mutual orthogonality of tRNASerCUA, tRNATrpUCA and tRNATyrUUA with corresponding stop codons and demonstrated that the tRNASerCUA and the tRNATrpUCA can provide dynamic range and low crosstalk. Finally, we show the TAG and TGA can not only be used as an “AND gate” circuit to control the translation of target gene, but also be used to control the translation of a prodeoxyviolacein (PDV) pathway and a reporter in parallel. Overall, this work provides flexible tools for translational control and holds great potential to promote synthetic biology studies.
Mantle cell lymphoma: A clinical review of the changing treatment paradigms with the advent of novel therapies, and an insight into Indian data
Authors: Radhakrishnan Vivek Sulekha , Lokireddy Padmaja , Parihar Mayur , Prakash Prashanth Srirangapattana , Menon Hari
Published: November 2021

Background

Mantle cell lymphoma (MCL) is a rare type of mature B‐cell lymphoid malignancy with the pathologic hallmark of translocation t(11;14) (q13, q32), which leads to an overexpression of Cyclin D1 (CCND1). The disease is also characterized by the presence of a high number of recurrent genetic alterations, which include aberrations in several cellular pathways. MCL is a heterogeneous disease with a wide range of clinical presentations and a majority presenting with aggressive disease in advanced stages.

Recent findings

Management of MCL is bereft with challenges due to its resistant and relapsing pattern. Despite improvements in remission durations, the disease is currently incurable with standard therapy and has a median survival of about 3–5 years. The use of small molecules like the bruton tyrosine kinase (BTK) and BCL2 inhibitors, for treating relapsed MCL has been established leading to a diminishing role for conventional chemotherapy. Combinations of small molecule inhibitors with or without chemoimmunotherapy, are showing promising results. Cellular therapy in the form of CAR‐T cell therapy, has been approved recently.

Conclusions

Personalized cancer treatment and chemo‐free regimens are showing promise and results from well‐planned long‐term studies are evolving. In India, there is a paucity of epidemiological, clinical, and research data in this field.
Therapeutic engagement in robot‐assisted psychological interventions: A systematic review
Authors: Riches Simon , Azevedo Lisa , Vora Alkesh , Kaleva Ina , Taylor Lawson , Guan Peipei , Jeyarajaguru Priyanga , McIntosh Harley , Petrou Constantina , Pisani Sara , Hammond Neil
Published: November 2021

Purpose

Therapeutic engagement is a key component of psychological interventions. Robot‐assisted psychological interventions appear to have therapeutic benefits for service users that are challenging to engage. However, engagement with robots in robot‐assisted psychological interventions is not well understood. The aim of this systematic review is to evaluate the quality of therapeutic engagement in robot‐assisted psychological interventions (PROSPERO: 122437).

Methods

Scopus, Web of Science, PsycInfo and Medline were searched until 15 January 2021 for studies which quantitatively evaluated therapeutic engagement in robot‐assisted psychological interventions. The Effective Public Health Practice Project (EPHPP) quality assessment tool was used to assess methodological dimensions of studies.

Results

3647 studies were identified through database searching. Thirty studies (N = 1462), published between 2004 and 2020, and from 14 countries, were included. Robots were typically toy animals or humanoids and were used to provide support and improve wellbeing through social interaction. Studies primarily tested robots on older adults with dementia and children with autism and indicated positive therapeutic engagement. Twelve studies included a control group. EPHPP ratings were ‘strong’ (N = 1), ‘moderate’ (N = 10) and ‘weak’ (N = 19).

Conclusions

Therapeutic engagement between service users and robots is generally positive. Methodological limitations of studies, such as small sample sizes, and lack of control groups and longitudinal data, mean that the field is in early stages of its development and conclusions should be drawn with caution. There are important practical and ethical implications for policymakers to consider, such as responsible clinical practice and how service users may understand the therapeutic relationship with robots.
A OneStep Solution to Fix and Stain Cells for Correlative Live and Fixed Microscopy
Authors: Velle Katrina B. , Fermino do Rosário Carline , Wadsworth Patricia , Fritz‐Laylin Lillian K.
Published: November 2021

Correlating the location of subcellular structures with dynamic cellular behaviors is difficult when working with organisms that lack the molecular genetic tools needed for expressing fluorescent protein fusions. Here, we describe a protocol for fixing, permeabilizing, and staining cells in a single step while imaging on a microscope. In contrast to traditional, multi‐step fixing and staining protocols that take hours, the protocol outlined here achieves satisfactory staining within minutes. This approach takes advantage of well‐characterized small molecules that stain specific subcellular structures, including nuclei, mitochondria, and actin networks. Direct visualization of the entire process allows for rapid optimization of cell fixation and staining, as well as straightforward identification of fixation artifacts. Moreover, live imaging prior to fixation reveals the dynamic history of cellular features, making it particularly useful for model systems without the capacity for expressing fluorescent protein fusions. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Fixing, permeabilizing, and staining mammalian cells in one step on the microscope
Information wars as a threat to the information security of Ukraine
Authors: Sopilko Iryna , Svintsytskyi Andrii , Krasovska Yevheniia , Padalka Andrii , Lyseiuk Andrii
Published: November 2021

The study gives definitions of information war (information warfare) and related terms, such as cyberwar and others, indicates the purposes, objects, subject matter, and subjects of the concepts under consideration. The author also considers the features of strategic information warfare conducted by the Russian Federation against Ukraine, the stages in the development of information war, and the classification of its types and methods. The approaches of scientists who studied certain aspects of information warfare were analyzed, based on their work relevant conclusions were drawn and the conceptual basis of the paper was formed. Independently, the definition and characteristics of the concept of cyber warfare inextricably linked with information warfare are given. Methods for solving the problems arising during the information war are introduced, ways of ensuring the information security of the state are provided. Information war in this study is considered as methods and means of presenting information to form the point of view needed by the organizers of information propaganda and the corresponding public opinion in a certain group of people. The author made an in‐depth analysis of the regulatory and legal instruments in force for counterfeiting information warfare and protecting the Ukrainian people from it, pointed out the deficiencies of such documents, and gave recommendations for their further advancement. Recommendations are given to improve the current information awareness among Ukrainians, the directions of the state policy in this field are suggested and ways to ensure the stability of the national information security system of Ukraine are provided.
Links between organized visual search and reading ability in French primary school children
Authors: Guilbert Alma , Guiraud‐Vinatea Hélène
Published: November 2021

Visual search skills develop substantially during the primary school years, and in parallel with children's reading achievement. Reading requires an efficient visual search and exposure to reading from the left to the right could also influence the way we explore space. No study, however, made links between visual search strategies and reading ability. In this study, 70 primary school children performed a cancellation task (Bells test) and reading tests. Our results showed that reading was closely linked to visual search accuracy but also to visual search organization, even after controlling for age for some measures. Along with the development of reading abilities, children made fewer revisitation, moved more to the nearest unmarked targets than to the farthest ones and explored more in lines. It appears, therefore, essential to take more into account the visual search organization of children with reading impairments such as dyslexia.
Dense cold‐water coral garden of Paragorgia johnsoni suggests the importance of the Mid‐Atlantic Ridge for deep‐sea biodiversity
Authors: Morato Telmo , Dominguez‐Carrió Carlos , Mohn Christian , Ocaña Vicente Oscar , Ramos Manuela , Rodrigues Luís , Sampaio Íris , Taranto Gerald H. , Fauconnet Laurence , Tojeira Inês , Gonçalves Emanuel J. , Carreiro‐Silva Marina
Published: November 2021

Mid‐ocean ridges generate a myriad of physical oceanographic processes that favor the supply of food and nutrients to suspension‐ and filter‐feeding organisms, such as cold‐water corals and deep‐sea sponges. However, the pioneering work conducted along the Mid‐Atlantic Ridge failed to report the presence of large and dense living coral reefs, coral gardens, or sponge aggregations. Here, we describe the densest, near‐natural, and novel octocoral garden composed of large red and white colonies of Paragorgia johnsoni Gray, 1862 discovered at 545–595 m depth on the slopes of the Mid‐Atlantic Ridge, in the Azores region. This newly discovered octocoral garden is a good candidate for protection since it fits many of the FAO criteria that define what constitutes a Vulnerable Marine Ecosystem. The observations described here corroborate the existence of a close relationship between the octocoral structure and the ambient currents on ridge‐like topographies, providing new insights into the functioning of mid‐ocean ridges' ecosystems. The ubiquitous presence of biogenic and geological topographies associated with mid‐ocean ridges, which could act as climate refugia, suggests their global importance for deep‐sea biodiversity. A better understanding of the processes involved is, therefore, required. Our observations may inspire future deep‐sea research initiatives to narrow existing knowledge gaps of biophysical connections with benthic fauna at small spatial scales along mid‐ocean ridges.
A new model of forelimb ecomorphology for predicting the ancient habitats of fossil turtles
Authors: Dudgeon Thomas W. , Livius Marissa C. H. , Alfonso Noel , Tessier Stéphanie , Mallon Jordan C.
Published: November 2021

Various morphological proxies have been used to infer habitat preferences among fossil turtles and their early ancestors, but most are tightly linked to phylogeny, thereby minimizing their predictive power. One particularly widely used model incorporates linear measurements of the forelimb (humerus + ulna + manus), but in addition to the issue of phylogenetic correlation, it does not estimate the likelihood of habitat assignment. Here, we introduce a new model that uses intramanual measurements (digit III metacarpal + non‐ungual phalanges + ungual) to statistically estimate habitat likelihood and that has greater predictive strength than prior estimators. Application of the model supports the hypothesis that stem‐turtles were primarily terrestrial in nature and recovers the nanhsiungchelyid Basilemys (a fossil crown‐group turtle) as having lived primarily on land, despite some prior claims to the contrary.
Boreal tree species change as a climate mitigation strategy: impact on ecosystem C and N stocks and soil nutrient levels
Authors: Kjønaas O. Janne , Bárcena Teresa G. , Hylen Gro , Nordbakken Jørn‐Frode , Økland Tonje
Published: November 2021

To increase the annual uptake of CO2 as well as the long‐term storage of carbon (C) in forests, the Norwegian government consider large‐scale replacements of native, deciduous forests with faster‐growing species like Norway spruce. To assess the effects of tree species change on ecosystem C and nitrogen (N) stocks and soil chemistry, we used a paired plot approach including stands of native downy birch and planted 45‐ to 60‐yr‐old Norway spruce. The birch stands were used as reference for the assessment of differences following the tree species change. We found significantly higher C and N stocks in living tree biomass in the spruce stands, whereas no significant differences were found for dead wood. The cover of understory species groups, and the C and N stocks of the aboveground understory vegetation were significantly higher in the birch stands. The tree species change did not affect the soil organic carbon (SOC) stock down to 1 m soil depth; however, the significantly higher stock in the forest floor of the spruce stands suggested a re‐distribution of SOC within the profile. There was a significant positive correlation between the SOC stock down to 30 cm soil depth and the total ecosystem C stock for the birch stands, and a negative correlation for the spruce stands. Significant effects of tree species change were found for C and N concentrations, C/N, exchangeable acidity, base saturation, and exchangeable Ca, K, Mg, Na, S, and Fe in the organic horizon or the upper mineral soil layer. The total ecosystem C stock ranged between 197 and 277 Mg/ha for the birch stands, and 297 and 387 Mg/ha for the spruce stands. The ecosystem C accumulation varied between 32 and 142 Mg/ha over the past 45–60 yr, whereas the net ecosystem C capture was considerably lower and potentially negative. Our results suggest that the potential to meet the governments' targets to increase C sequestration depend on the C debt incurred from the removed birch stands, the rotation length, and potentially also the susceptibility of the different stand types to future risk factors related to climate change.
From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package
Authors: Qin Clara , Bartelme Ryan , Chung Y. Anny , Fairbanks Dawson , Lin Yang , Liptzin Daniel , Muscarella Chance , Naithani Kusum , Peay Kabir , Pellitier Peter , St. Rose Ayanna , Stanish Lee , Werbin Zoey , Zhu Kai
Published: November 2021

Soil microbial communities play critical roles in various ecosystem processes, but studies at a large spatial and temporal scale have been challenging due to the difficulty in finding the relevant samples in available data sets as well as the lack of standardization in sample collection and processing. The National Ecological Observatory Network (NEON) has been collecting soil microbial community data multiple times per year for 47 terrestrial sites in 20 eco‐climatic domains, producing one of the most extensive standardized sampling efforts for soil microbial biodiversity to date. Here, we introduce the neonMicrobe R package—a suite of downloading, preprocessing, data set assembly, and sensitivity analysis tools for NEON’s newly published 16S and ITS amplicon sequencing data products which characterize soil bacterial and fungal communities, respectively. neonMicrobe is designed to make these data more accessible to ecologists without assuming prior experience with bioinformatic pipelines. We describe quality control steps used to remove quality‐flagged samples, report on sensitivity analyses used to determine appropriate quality filtering parameters for the DADA2 workflow, and demonstrate the immediate usability of the output data by conducting standard analyses of soil microbial diversity. The sequence abundance tables produced by neonMicrobe can be linked to NEON’s other data products (e.g., soil physical and chemical properties, plant community composition) and soil subsamples archived in the NEON Biorepository. We provide recommendations for incorporating neonMicrobe into reproducible scientific workflows, discuss technical considerations for large‐scale amplicon sequence analysis, and outline future directions for NEON‐enabled microbial ecology. In particular, we believe that NEON marker gene sequence data will allow researchers to answer outstanding questions about the spatial and temporal dynamics of soil microbial communities while explicitly accounting for scale dependence. We expect that the data produced by NEON and the neonMicrobe R package will act as a valuable ecological baseline to inform and contextualize future experimental and modeling endeavors.
MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi
Authors: Nimz Ilana , Renshaw Mark A. , Baczenas John , Vanderlip Cynthia , Hyrenbach K. David , Iacchei Matthew
Published: November 2021

Morphological identification of digested prey remains from a generalist predator can be challenging, especially when attempting to match degraded remains to taxonomic keys. DNA techniques, whereby prey is sequenced and matched to large public nucleotide sequence databases, are increasingly being used to augment morphological identification. We used “metaBARFcoding” (DNA metabarcoding) to target a region of the cytochrome c oxidase subunit I (COI) mitochondrial gene to identify prey in highly digested regurgitations from Christmas shearwaters Puffinus nativitatis at Hōlanikū (Kure Atoll). Metabarcoding was used to bulk‐process 92 water samples from regurgitations collected from 2009 to 2017, providing an overview of the seabird's diet. We additionally Sanger‐sequenced 100 prey items from 50 randomly chosen regurgitations to verify that metabarcoding characterized key components of the diet. The metabarcoding technique identified 87 unique taxa from 29 families of fish and squid, spanning diverse taxa, including reef‐associated, pelagic–oceanic, and mesopelagic species. Rare prey (frequency of occurrence ≤5% of samples) constituted 66% of the species richness, demonstrating the highly diverse diet of this generalist predator. Overall, 81% of the families detected in the contemporary diet were previously documented in Christmas shearwater diets from the Northwestern Hawaiian Islands. Our results indicate that metabarcoding the COI region is useful in identifying a wide range of taxa from highly digested regurgitations, thus facilitating this approach to study seabird diets.
An integrative genomics approach identifies KDM4 as a modulator of trained immunity
Authors: Moorlag Simone J.C.F.M. , Matzaraki Vasiliki , van Puffelen Jelmer H. , van der Heijden Charlotte , Keating Sam , Groh Laszlo , Röring Rutger Jan , Bakker Olivier B. , Mourits Vera P. , Koeken Valerie A.C.M. , de Bree L. Charlotte J. , Smeekens Sanne P. , Oosting Marije , Gamboa Raúl Aguirre , Riksen Niels P. , Xavier Ramnik J. , Wijmenga Cisca , Kumar Vinod , van Crevel Reinout , Novakovic Boris , Joosten Leo A.B. , Li Yang , Netea Mihai G.
Published: November 2021

Innate immune cells are able to build memory characteristics via a process termed “trained immunity.” Host factors that influence the magnitude of the individual trained immunity response remain largely unknown. Using an integrative genomics approach, our study aimed to prioritize and understand the role of specific genes in trained immunity responses. In vitro‐induced trained immunity responses were assessed in two independent population‐based cohorts of healthy individuals, the 300 Bacillus Calmette‐Guérin (300BCG; n = 267) and 200 Functional Genomics (200FG; n = 110) cohorts from the Human Functional Genomics Project. Genetic loci that influence cytokine responses upon trained immunity were identified by conducting a meta‐analysis of QTLs identified in the 300BCG and 200FG cohorts. From the identified QTL loci, we functionally validated the role of PI3K‐Akt signaling pathway and two genes that belong to the family of Siglec receptors (Siglec‐5 and Siglec‐14). Furthermore, we identified the H3K9 histone demethylases of the KDM4 family as major regulators of trained immunity responses. These data pinpoint an important role of metabolic and epigenetic processes in the regulation of trained immunity responses, and these findings may open new avenues for vaccine design and therapeutic interventions.
Different pathways, same goals: A large‐scale qualitative study of autistic and non‐autistic patient‐generated definitions of recovery from an eating disorder
Authors: Sedgewick Felicity , Leppanen Jenni , Austin Amelia , Tchanturia Kate
Published: November 2021

Background

Definitions of recovery from an eating disorder (ED) have generally been formulated around clinical conceptualisations, rather than based on the views of patients. This paper therefore asked those with lived experience of ED for their own definitions of recovery.

Method

Data were collected as part of an online study looking at EDs, autism and relationships. About 173 participants identified as recovered from ED and gave free‐response definitions of recovery. Responses were subject to thematic analysis.

Results

Seven major themes were identified: Weight restoration, lack of ED behaviours, thoughts and behaviours, cognitions, emotional responses, getting on with life, and ongoing challenges.

Conclusions

Many definitions of recovery given by those who have lived experience of ED echoed those used by clinicians and researchers. There were also points of divergence around the ongoing challenges of recovery. Our findings highlight the need for continuing support post‐weight restoration to facilitate the successful long‐term recovery for those with ED.
Impact of Categorization and Scaling on Classification Agreement and Prediction Accuracy Statistics
Authors: Wang Wei , Dorans Neil J.
Published: November 2021

Agreement statistics and measures of prediction accuracy are often used to assess the quality of two measures of a construct. Agreement statistics are appropriate for measures that are supposed to be interchangeable, whereas prediction accuracy statistics are appropriate for situations where one variable is the target and the other variables are predictors. Using bivariate normality assumptions, we analytically examine the impact of categorization of a continuous variable and mean/sigma scaling on different measures of agreement and different measures of prediction accuracy. We vary the degree of relationship (squared correlation) between two continuous measures of a construct and the degree to which these measures are reduced to fewer and fewer categories (categorization). The main findings include that (a) categorization influences all the statistics investigated, (b) the correlation between the continuous variables affects the values of the statistics, and (c) scaling a prediction of a target variable to have the same mean and variability as the target increases agreement (according to Cohen's kappa and quadratic weighted kappa) but does so at the expense of prediction accuracy. The implications of these results for scoring of essays by humans or machines are also discussed.
Designing Efficient L2 Writing Assessment Tasks for Low‐Proficiency Learners of English
Authors: Sasayama Shoko , Garcia Gomez Pablo , Norris John M.
Published: November 2021

This report describes the development of efficient second language (L2) writing assessment tasks designed specifically for low‐proficiency learners of English to be included in the TOEFL® Essentials™ test. Based on the can‐do descriptors of the Common European Framework of Reference for Languages for the A1 through B1 levels of proficiency, four task types were identified to be prototypical candidate writing tasks for the target test‐taker population (i.e., adolescent and adult low‐proficiency English learners). Those four task types included: (a) Describe a Photo, (b) Write a Review, (c) Chat With a Friend, and (d) Write an E‐mail. These task types were also considered efficient in the framework of the test in that they had the potential to be accessible to low‐proficiency learners and to elicit sufficient spontaneous writing for assessment purposes within a short period of time. In the current study, eight assessment tasks, two for each task type, were developed and piloted with 169 A1–B1 learners of English from Japan and Colombia. The findings revealed that the Describe a Photo and Write an E‐mail tasks performed the best in eliciting substantial language use and emphasizing distinct performance attributes, both characteristics needed for efficiently measuring test takers' writing proficiency as well as discriminating among proficiency levels at the lower end of the spectrum. The report concludes by highlighting some observations on L2 writing assessment task design for low‐proficiency learners of English.
Biological activity and profiling of Salvia sclarea essential oil obtained by steam and hydrodistillation extraction methods via chemometrics tools
Authors: Aćimović Milica G. , Cvetković Mirjana T. , Stanković Jeremić Jovana M. , Pezo Lato L. , Varga Ana O. , Čabarkapa Ivana S. , Kiprovski Biljana
Published: November 2021

Salvia sclarea L. or clary sage is cultivated worldwide in temperate and sub‐tropical climates, as an ornamental and essential oil (EO) bearing plant. EO is obtained from fresh spikes in full flowering stage and is recognized as an important commercial product for food, beverage and cosmetic industries. This study investigated the EO composition of S. sclarea grown in Serbia (Southeast Europe) obtained by two different methods, steam (SD) and hydrodistillation (HD). GC‐MS analysis identified oxygenated monoterpenes as the main class of compounds for all EOs (between 81.8% and 88.2% depending on the distillation process). The most abundant oxygenated monoterpenes were linalyl acetate and linalool. In addition, in vitro antimicrobial (modified resazurin microtitre‐plate assay) and antioxidant activities (DPPH· assay) and total polyphenol content of obtained EOs were also evaluated. According to the assay used for the evaluation of the antibacterial activity, Gram‐negative bacteria were more sensitive to S. sclarea EO in comparison to Gram‐positive bacteria. EOs exhibited low antioxidant capacity, below 3% neutralized DPPH· radicals, reaching up to approximately 400 µg AAE mL‐1. This study also investigated a possibility for predicting retention indices (RIs) of compounds isolated from EOs. In total, 78 experimentally obtained RIs were applied to construct the prediction model. The quantitative structure‐chromatographic retention relationship (QSRR) model was used to anticipate the experimentally obtained RIs. Five molecular descriptors were selected by factor analysis and genetic algorithm to predict RIs. The obtained accuracy of the QSRR model reached r2 = .912, which showed that these models might be applied for predicting retention indices.
The Zygomatic Implant Perforated (ZIP) flap reconstructive technique for the management of low‐level maxillary malignancy – clinical & patient related outcomes on 35 consecutively treated patients
Authors: Butterworth Chris J. , Lowe Derek , Rogers Simon N.
Published: November 2021

Background

The zygomatic implant perforated (ZIP) flap technique provides immediate reconstruction and rapid dental rehabilitation for low‐level malignant tumors.

Methods

Patients who underwent ZIP flap reconstruction between December 2015 and February 2021 were followed prospectively.

Results

Thirty‐five consecutively treated patients were studied with 16 undergoing surgery alone and 19 undergoing surgery followed by radiotherapy. The median time to fit the prosthesis was 29 days with all patients requiring adjuvant radiotherapy receiving their fixed dental prosthesis prior to its commencement. Vascularized flap (100%), zygomatic implant (98.4%), and prosthesis (97%) survival were excellent and the ZIP flap protocol was highly rated by patient‐related outcome measures especially for the chewing domain.

Conclusions

The ZIP flap technique provides an excellent means of providing an autogenous oronasal seal and a foundation for immediate cortically anchored fixed dental rehabilitation.

Clinical Significance

This technique provides rapid and robust rehabilitation for patients presenting with low‐level maxillary malignancy despite the use of radiotherapy.
TGFβ‐induced FOXS1 controls epithelial–mesenchymal transition and predicts a poor prognosis in liver cancer
Authors: Bévant Kevin , Desoteux Matthis , Angenard Gaëlle , Pineau Raphaël , Caruso Stefano , Louis Corentin , Papoutsoglou Panagiotis , Sulpice Laurent , Gilot David , Zucman‐Rossi Jessica , Coulouarn Cédric
Published: November 2021

Transforming growth factor beta (TGF‐β) plays a key role in tumor progression, notably as a potent inducer of epithelial–mesenchymal transition (EMT). However, all of the molecular effectors driving TGFβ‐induced EMT are not fully characterized. Here, we report that forkhead box S1 (FOXS1) is a SMAD (mothers against decapentaplegic)–dependent TGFβ‐induced transcription factor, which regulates the expression of genes required for the initial steps of EMT (e.g., snail family transcription repressor 1) and to maintain a mesenchymal phenotype in hepatocellular carcinoma (HCC) cells. In human HCC, we report that FOXS1 is a biomarker of poorly differentiated and aggressive tumor subtypes. Importantly, FOXS1 expression level and activity are associated with a poor prognosis (e.g., reduced patient survival), not only in HCC but also in colon, stomach, and kidney cancers. Conclusion: FOXS1 constitutes a clinically relevant biomarker for tumors in which the pro‐metastatic arm of TGF‐β is active (i.e., patients who may benefit from targeted therapies using inhibitors of the TGF‐β pathway).
Intrinsic functional connectivity in the default mode network predicts mnemonic discrimination: A connectome‐based modeling approach
Authors: Wahlheim Christopher N. , Christensen Alexander P. , Reagh Zachariah M. , Cassidy Brittany S.
Published: November 2021

The ability to distinguish existing memories from similar perceptual experiences is a core feature of episodic memory. This ability is often examined using the mnemonic similarity task in which people discriminate memories of studied objects from perceptually similar lures. Studies of the neural basis of such mnemonic discrimination have mostly focused on hippocampal function and connectivity. However, default mode network (DMN) connectivity may also support such discrimination, given that the DMN includes the hippocampus, and its connectivity supports many aspects of episodic memory. Here, we used connectome‐based predictive modeling to identify associations between intrinsic DMN connectivity and mnemonic discrimination. We leveraged a wide range of abilities across healthy younger and older adults to facilitate this predictive approach. Resting‐state functional connectivity in the DMN predicted mnemonic discrimination outside the MRI scanner, especially among prefrontal and temporal regions and including several hippocampal regions. This predictive relationship was stronger for younger than older adults, primarily for temporal–prefrontal connectivity. The novel associations established here are consistent with mounting evidence that broader cortical networks including the hippocampus support mnemonic discrimination. They also suggest that age‐related network disruptions undermine the extent that the DMN supports this ability. This study provides the first indication of how intrinsic functional properties of the DMN support mnemonic discrimination.
The Covid‐19 pandemic reinforces the need for sustainable health planning
Authors: Garcia Ana Cristina , Beja André , Cupertino de Barros Fernando Passos , Delgado António Pedro , Ferrinho Paulo
Published: November 2021

The 2030 Agenda for Sustainable Development highlighted the growing attention to the adequacy of health planning models to sustainable development. A re‐reading of the results of a round table debate on “sustainable planning”, which took place at the 5th National Congress of Tropical Medicine (Portugal, 2019) under a participant observation strategy, framed by the findings of a “synthesis of better evidence” literature review and cross–referenced with the reflections of different authors and experts about the momentum created by the COVID–19 pandemic, underlined the challenges to sustainable health planning that have emerged and are projected beyond the current pandemic context. Variable perceptions of the term “sustainable health development”, leading to the potential loss of their relevance in guiding the elaboration of policies and strategic plans, and the potential higher effectiveness of the participatory approaches of health planning in achieving sustainable health were highlighted in the debate and literature, in general and in public health emergency contexts. Those results gained new relevance during the current COVID–19 pandemic, bringing back to the forefront a reflection of the inadequate planning framework that has usually been used to understand and respond to global health challenges, despite the already existing experience, evidence and support instruments.
Association of CYBA C242T and superoxide dismutase 2 A16V genetic variants with preeclampsia
Authors: Hu Kaifeng , Liu Xinghui , Bai Huai , Zhou Mi , Jiang Chenyu , Fan Ping
Published: November 2021

Objective

To investigate the relationship between NADPH oxidase p22phox subunit (CYBA; C242T) and superoxide dismutase 2 (SOD2; A16V) polymorphisms and the risk of preeclampsia (PE) in Chinese women.

Methods

This case‐control study included 325 patients with PE and 1294 controls. The genotypes were determined by polymerase chain reaction‐restriction fragments length polymorphism method. Clinical, metabolic, and oxidative stress parameters were analyzed.

Results

Participants with T allele of the CYBA C242T polymorphism had a decreased risk of PE (OR = 0.62, 95% CI: 0.42–0.92, P = 0.016) and those with the A allele of the SOD2 A16V polymorphism had increased risk of PE (OR = 1.44, 95% CI: 1.09–1.89, P = 0.010). The coexistence of the SOD2 AA + AV genotypes and the CYBA CC genotype further increased the risk of PE (OR = 2.32, 95% CI: 1.31–4.10, P = 0.003) when the CT + TT/VV combined genotype was the reference category.

Conclusion

The T allele of the CYBA C242T polymorphism is related to a decreased risk of PE, while the A allele of the SOD2 A16V polymorphism and its combination with the CYBA CC genotype are associated with an increased risk of PE in Chinese women.