bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of the influence of wire metals on dissimilar welds
Authors: Benlamnouar M.F. , Bensaid N. , Badji R. , Saadi T. , IDDIR M. , Zidani M. , SOUALILI M.A.
Published: April 2022

The aim of this study is to investigate the effect wire metal on microstructure and mechanical properties of dissimilar welds between HSLA-X70 high strength steel alloy and 304L austenitic stainless steel produced by automatic tungsten arc welding (TIG). The weld joints were prepared using E304L, E316L, E2209L, and E7010 wire metal. The mechanical characteristics obtained from hardness, tensile and impact testing, were correlated to the optical and SEM microscopy, to establish a relationship between wire metal composition and the microstructures in different weld regions. It is concluded that E2209 wire metal lead to improve in the resilience characteristics and tenacity with a slight reduction in the ultimate tensile strength and hardness.
Al3+ and Cr3+ co-substituted NiZnCo nano ferrites: synthesis and structural properties
Authors: Vishnu Priya G. , Murali N. , Madhuri Sailaja J. , Ragavendra Vemuri , Parajuli D. , Lakshmi Narayana P.V.
Published: April 2022

The Al3+ and Cr3+ substituted in Ni0.4Zn0.35Co0.25Fe2-x-yAlxCryO4 (x = y = 0.0, 0.05, 0.1, 0.15 and 0.2) ferrite nanoparticles were prepared with sol-gel method. X-ray diffraction (XRD), Field Effect Scanning Microscopy (FESEM), and Fourier Transform Inferred Spectroscopy (FT-IR) were used for their characterization. They have a single-phase spinel structure. The lattice constant decreases with increasing concentrations. Agglomerated small particles with stoichiometric proportions were obtained from FESEM. The region around 600 cm-1 and 400 cm-1 has two absorption bands related to two interstitial sites by FTIR agree with the spinel lattice.
Giant dielectric behavior in NdCrO3 perovskite nanoparticles
Authors: Shanker Jada , Ananthaiah J , Pavan Kumar N , Venkataramana Kasarapu , Anand pandarinath M , Ujwal U P , Raju P. , Meher Abhinav E , Suresh babu D
Published: April 2022

NdCrO3 perovskite compound synthesized via sol-gel process. Impedance spectroscopic data have been studied in the wide frequency range (0.1Hz-10MHz), at various temperatures (RT-500°C). Structural analysis have done by X-ray diffractometer, it indicates single-phase orthorhombic structure. Particle size is found to be 32nm. Microstructure seems to be uniform distribution of grains throughout the surface. This material showed the giant dielectric behaviour (ε1
> 104). Impedance studies of NdCrO3 noticed that it is negative temperature coefficient of resistance type semiconductor. The dc conductivity and relaxation plots were followed by Arrhenius law. Frequency reliant ac conductivity plots followed Jonscher’s power law. These results suggesting that NdCrO3 is suitable for gaint capacitors applications.
Effect of high contents of nickel and silicon on the microstructure and properties of Cu–Ni–Si alloys
Authors: Tao Shiping , Lu Zhenlin , Xie Hui , Zhang Jinlong , Wei Xin
Published: April 2022

Cu-Ni-Si alloys have been widely used in electronics and electrical industries.The preparation method of alloy was not limited to smelting, powder metallurgy method has also attracted the attention of many researchers. In this study, Cu-Ni-Si alloys were prepared using hot-pressed sintering and elemental copper powders, in which nickel and silicon powders were used as raw materials. The results show that, when the Cu-Ni-Si alloys were prepared using hot-pressed sintering, there were no Ni-Si intermetallic compounds except the δ-Ni2Si phase in the microstructure of alloys. After the ageing treatment, when the mass ratios of Ni/Si were 2:1 and 3:1, the precipitation of δ-Ni2Si phase was significantly less. However, when the mass ratios of Ni/Si were 4:1 and 5:1, the precipitation of δ-Ni2Si phase particles increased significantly. The results from electrical conductivity and Vickers hardness show that, after the ageing treatment, both the electrical conductivity and Vickers hardness of the alloys greatly improved.
Plasma sanitization of cherry belle radish seeds for Space agricultural applications
Authors: Gott Ryan P , Engeling K. W , Johnson Christina M , Boles Haley O , Brown Victoria C , Hummerick Mary , Massa Gioia D , Meier Annie J
Published: April 2022

As human innovation continuously expands the knowledge base for life beyond Earth, the need for self-sufficient spacecraft is essential. With that, space crop production facilities are ever expanding for research and development. A current area of key interest is seed sanitation before transport from ground to the International Space Station (ISS). Sanitation practices are performed to mitigate any potential biohazard and to ensure the viability of the seed. Conventional methods involve fumigation of seeds or chemical processes but are not effective with all seed types. Therefore, plasma technology was implemented in this research to explore low-temperature plasmas as an alternative means for seed sanitation without the need for chemicals. This project investigated the viability of plasma as a means for sanitation by incorporating three different plasma types within the study. For the treatment of Cherry Belle radish seeds, the optimal system was a radio frequency (RF) sub-atmospheric plasma chamber. Treatments of 100 W for 10 min or longer with the Diener system consistently reduced microbial loads by 90% or more. While 20-min treatments caused reductions in germination rate, a treatment of 15 min with the Diener system at 100 W consistently resulted in germination rates above 80% after 1 month of seed storage. For the 5 and 10 min treatments at a pressure of 187 mTorr and power of 100 W, growth was also accelerated. Additionally, plasma provided 90% reduction of Escherichia coli and Bacillus pumilis and a 99% reduction of Fusarium ozysporum on inoculated seeds. Overall, the plasma systems show promising potential but require further exploration.
Optical wafer defect inspection at the 10 nm technology node and beyond
Authors: Zhu Jinlong , Liu Jiamin , Xu Tianlai , Yuan Shuai , Zhang Zexu , Jiang Hao , Gu Honggang , Zhou Renjie , Liu Shiyuan
Published: April 2022

The growing demand for electronic devices, smart devices, and the Internet of Things constitutes the primary driving force for marching down the path of decreased critical dimension and increased circuit intricacy of integrated circuits. However, as sub-10 nm high-volume manufacturing is becoming the mainstream, there is greater awareness that defects introduced by original equipment manufacturer components impact yield and manufacturing costs. The identification, positioning, and classification of these defects, including random particles and systematic defects, are becoming more and more challenging at the 10 nm node and beyond. Very recently, the combination of conventional optical defect inspection with emerging techniques such as nanophotonics, optical vortices, computational imaging, quantitative phase imaging, and deep learning is giving the field a new possibility. Hence, it is extremely necessary to make a thorough review for disclosing new perspectives and exciting trends, on the foundation of former great reviews in the field of defect inspection methods. In this article, we give a comprehensive review of the emerging topics in the past decade with a focus on three specific areas: (a) the defect detectability evaluation, (b) the diverse optical inspection systems, and (c) the post-processing algorithms. We hope, this work can be of importance to both new entrants in the field and people who are seeking to use it in interdisciplinary work.
Analysis of finite element methods for surface vector-Laplace eigenproblems
Authors: Reusken Arnold
Published: April 2022

In this paper we study finite element discretizations of a surface vector-Laplace eigenproblem. We consider two known classes of finite element methods, namely one based on a vector analogon of the Dziuk-Elliott surface finite element method and one based on the so-called trace finite element technique. A key ingredient in both classes of methods is a penalization method that is used to enforce tangentiality of the vector field in a weak sense. This penalization and the perturbations that arise from numerical approximation of the surface lead to essential nonconformities in the discretization of the variational formulation of the vector-Laplace eigenproblem. We present a general abstract framework applicable to such nonconforming discretizations of eigenproblems. Error bounds both for eigenvalue and eigenvector approximations are derived that depend on certain consistency and approximability parameters. Sharpness of these bounds is discussed. Results of a numerical experiment illustrate certain convergence properties of such finite element discretizations of the surface vector-Laplace eigenproblem.
A range characterization of the single-quadrant ADRT
Authors: Li Weilin , Ren Kui , Rim Donsub
Published: April 2022

This work characterizes the range of the single-quadrant approximate discrete Radon transform (ADRT) of square images. The characterization follows from a set of linear constraints on the codomain. We show that for data satisfying these constraints, the exact and fast inversion formula by Rim [Appl. Math. Lett. 102 (2020), 106159] yields a square image in a stable manner. The range characterization is obtained by first showing that the ADRT is a bijection between images supported on infinite half-strips, then identifying the linear subspaces that stay finitely supported under the inversion formula.
Overcoming biases in causal inference of molecular interactions
Authors: Kumar Sajal , Song Mingzhou
Published: April 2022

Motivation

Computer inference of biological mechanisms is increasingly approachable due to dynamically rich data sources such as single-cell genomics. Inferred molecular interactions can prioritize hypotheses for wet-lab experiments to expedite biological discovery. However, complex data often come with unwanted biological or technical variations, exposing biases over marginal distribution and sample size in current methods to favor spurious causal relationships.

Results

Considering function direction and strength as evidence for causality, we present an adapted functional chi-squared test (AdpFunChisq) that rewards functional patterns over non-functional or independent patterns. On synthetic and three biology datasets, we demonstrate the advantages of AdpFunChisq over 10 methods on overcoming biases that give rise to wide fluctuations in the performance of alternative approaches. On single-cell multiomics data of multiple phenotype acute leukemia, we found that the T-cell surface glycoprotein CD3 delta chain may causally mediate specific genes in the viral carcinogenesis pathway. Using the causality-by-functionality principle, AdpFunChisq offers a viable option for robust causal inference in dynamical systems.

Availability and implementation

The AdpFunChisq test is implemented in the R package ‘FunChisq’ (2.5.2 or above) at https://cran.r-project.org/package=FunChisq. All other source code along with pre-processed data is available at Code Ocean https://doi.org/10.24433/CO.2907738.v1

Supplementary information

Supplementary materials are available at Bioinformatics online.
Scoring protein sequence alignments using deep learning
Authors: Shrestha Bikash , Adhikari Badri
Published: April 2022

Motivation

A high-quality sequence alignment (SA) is the most important input feature for accurate protein structure prediction. For a protein sequence, there are many methods to generate a SA. However, when given a choice of more than one SA for a protein sequence, there are no methods to predict which SA may lead to more accurate models without actually building the models. In this work, we describe a method to predict the quality of a protein’s SA.

Results

We created our own dataset by generating a variety of SAs for a set of 1351 representative proteins and investigated various deep learning architectures to predict the local distance difference test (lDDT) scores of distance maps predicted with SAs as the input. These lDDT scores serve as indicators of the quality of the SAs.

Using two independent test datasets consisting of CASP13 and CASP14 targets, we show that our method is effective for scoring and ranking SAs when a pool of SAs is available for a protein sequence. With an example, we further discuss that SA selection using our method can lead to improved structure prediction.

Availability and implementation

Code and the data underlying this article are available at https://github.com/ba-lab/Alignment-Score/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Short-term prediction of atrial fibrillation from ambulatory monitoring ECG using a deep neural network
Authors: Singh Jagmeet P , Fontanarava Julien , de Massé Grégoire , Carbonati Tanner , Li Jia , Henry Christine , Fiorina Laurent
Published: April 2022

Aims

Atrial fibrillation (AF) is associated with significant morbidity but remains underdiagnosed. A 24 h ambulatory electrocardiogram (ECG) is largely used as a tool to document AF but yield remains limited. We hypothesize that a deep learning model can identify patients at risk of AF in the 2 weeks following a 24 h ambulatory ECG with no documented AF.

Methods and results

We identified a training set of Holter recordings of 7–15 days duration, in which no AF could be found in the first 24 h. We trained a neural network to predict the presence or absence of AF in the 15 following days, using only the first 24 h of the recording. We evaluated the neural network on a testing set and an external data set not used during algorithm development. In the testing data set, out of 9993 Holters with no AF on the first day, we found 361 (4%) recordings with AF within the 15 subsequent days of monitoring [5808, 218 (4%), respectively in the external data set]. The neural network could discriminate future AF with an area under the receiver operating curve, a sensitivity, and specificity of 79.4%, 76%, and 69%, respectively (75.8%, 78%, and 58% in the external data set), and outperformed ECG features previously shown to be predictive of AF.

Conclusion

We show here the very first study of short-term AF prediction using 24 h Holter monitoring. This could help identify patients who would benefit the most from longer recordings and proactively initiate treatment and AF mitigation strategies in high-risk patients.
The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production
Authors: Firrman Jenni , Liu LinShu , Mahalak Karley , Tanes Ceylan , Bittinger Kyle , Tu Vincent , Bobokalonov Jamshed , Mattei Lisa , Zhang Huanjia , Van den Abbeele Pieter
Published: April 2022

Environmental pH is a critical parameter for maintenance of the gut microbiota. Here, the impact of pH on the gut microbiota luminal and mucosal community structure and short chain fatty acid (SCFA) production was evaluated in vitro, and data compiled to reveal a donor-independent response to an increase or decrease in environmental pH. The results found that raising environmental pH significantly increased luminal community richness and decreased mucosal community evenness. This corresponded with an increased abundance of Ruminococcaceae Ruminococcus and Erysipelotrichaceae Erysipelatoclostridium, and a decreased abundance of Coriobacteriaceae Collinsella and Enterobacteriaceae Shigella for both the luminal and mucosal communities. Total SCFA levels were significantly higher, primarily due to an increase in acetic and 2-methylbutanoic acids. Lowering pH decreased luminal community evenness and decreased mucosal community evenness and richness. This corresponded with an increased abundance of Lachnospiraceae Enterocloster, Veillonellaceae Megasphaera, Veillonellaceae Sporomusa, Erysipelotrichaceae Eubacterium, and Alcaligenaceae Sutterella, and decreased abundance of Odoribacteraceae Butyricimonas, Fusobacteriaceae Fusobacterium, Veillonellaceae Phascolarctobacterium, and multiple Enterobacteriaceae species for both the luminal and mucosal communities. Total SCFA levels were significantly lower, with an observed drop in acetic and propionic acids, and increased butyric and valeric acids. Taken together, these results indicate that alterations to environmental pH can modulate the gut microbiota community structure and function, and some changes may occur in a donor-independent manner.
Giant viruses of theMegavirinaesubfamily possess biosynthetic pathways to produce rare bacterial-like sugars in a clade-specific manner
Authors: Notaro Anna , Poirot Olivier , Garcin Elsa D , Nin Sebastien , Molinaro Antonio , Tonetti Michela , De Castro Cristina , Abergel Chantal
Published: April 2022

The recent discovery that giant viruses encode proteins related to sugar synthesis and processing paved the way for the study of their glycosylation machinery. We focused on the proposed Megavirinae subfamily, for which glycan-related genes were proposed to code for proteins involved in glycosylation of the layer of fibrils surrounding their icosahedral capsids. We compared sugar compositions and corresponding biosynthetic pathways among clade members using a combination of chemical and bioinformatics approaches. We first demonstrated that Megavirinae glycosylation differs in many aspects from what was previously reported for viruses, as they have complex glycosylation gene clusters made of six and up to 33 genes to synthetize their fibril glycans (biosynthetic pathways for nucleotide-sugars and glycosyltransferases). Second, they synthesize rare amino-sugars, usually restricted to bacteria and absent from their eukaryotic host. Finally, we showed that Megavirinae glycosylation is clade-specific and that Moumouvirus australiensis, a B-clade outsider, shares key features with Cotonvirus japonicus (clade E) and Tupanviruses (clade D). The existence of a glycosylation toolbox in this family could represent an advantageous strategy to survive in an environment where members of the same family are competing for the same amoeba host. This study expands the field of viral glycobiology and raises questions on how Megavirinae evolved such versatile glycosylation machinery.
The Graying of Divorce: A Half Century of Change
Authors: Brown Susan L , Lin I-Fen
Published: April 2022

Objectives

We traced the historical arc of the rise in gray divorce (i.e., divorce that occurs among adults aged 50 and older) in the United States since 1970, elucidating unique patterns for middle-aged (aged 50–64) versus older (aged 65 and older) adults.

Methods

Data from the 1970, 1980, and 1990 U.S. Vital Statistics Reports and the 2010 and 2019 American Community Survey (ACS) were used to chart the trends in gray divorce over the past half century. Drawing on the 2019 ACS, we estimated gray divorce rates across sociodemographic subgroups for today’s middle-aged and older adults. We pooled the 2010 (N = 757,835) and 2019 (N = 892,714) ACS data to assess whether divorce risks are shifting for middle-aged versus older adults.

Results

The gray divorce rate was low and grew only modestly between 1970 and 1990 before doubling by 2010. Since 2010, the rate has decreased slightly (but the decrease is not statistically significant). The gray divorce rate has stagnated among middle-aged adults but continues to climb among older adults.

Discussion

Our study illustrates the graying of divorce over the past half century. Nowadays, 36% of U.S. adults getting divorced are aged 50 or older. The only age group with an increasing divorce rate is adults aged 65 and older, raising new questions about how they will navigate old age.
Why APIs? Anticipated value, barriers, and opportunities for standards-based application programming interfaces in healthcare: perspectives of US thought leaders
Authors: Gordon William J , Rudin Robert S
Published: April 2022

Objective

Improving health data interoperability through application programming interfaces (APIs) is a focus of US policy initiatives and could have tremendous impact on many aspects of care delivery, such as innovation, operational efficiency, and patient-centered care. To better understand the landscape of API use cases, we interviewed US thought leaders involved in developing and implementing standard-based APIs.

Materials and Methods

We conducted semi-structured virtual interviews with US subject matter experts (SMEs) on APIs. SMEs were asked to describe API use cases along with value and barriers for each use case. Written summaries were checked by the SME and analyzed by the study team to identify findings and themes.

Results

We interviewed 12 SMEs representing diverse sectors of the US healthcare system, including academia, industry, public health agencies, electronic health record vendors, government, and standards organizations. Use cases for standards-based APIs fell into six categories: patient-facing, clinician-facing, population health and value-based care, public health, administrative, and social services. The value across use cases was viewed as unrealized to date, and barriers to the use of APIs varied by use case.

Conclusions

SMEs identified a diverse set of API use cases where standard-based APIs had the potential to generate value. As policy efforts seek to increase API adoption, our work provides an early look at the landscape of API use cases, value propositions, and barriers. Additional effort is needed to better understand the barriers and how to overcome them to create value, such as through demonstration projects and rigorous evaluations for specific use cases.
Findings from the first colorectal cancer screening among 103 542 individuals in Vietnam with systematic review of colorectal cancer screening programs in Asia-Pacific region
Authors: Tran Chi Thi-Du , Nguyen Mai Vu-Tuyet , Tran Mo Thi , Tuong Thuy Thi-Van , Tran Quang Hong , Le Linh Cu , Pham Huong Thi-Thu , Bui Nam Chi , Vu Hien Huy , Nguyen Tu Thi-Cam , Ta Phuong Que , Ha Hien Thi-Thu , Trinh Dung Tuan , Bui Hanh Thi-My , Trinh Dien Quang , Van Nguyen Khanh , Le Song Huu , Van Vu Khien , Van Tran Thuan , Tran Huong Thi-Thanh , Shrubsole Martha J , Ye Fei , Cai Qiuyin , Zheng Wei , Boffetta Paolo , Shu Xiao-Ou , Luu Hung N
Published: April 2022

Background

Colorectal cancer is a leading cancer incidence and cause of death worldwide and in Vietnam. Although screening is considered an effective measure to prevent and control colorectal cancer, there is no such effort in Vietnam.

Methods

Between 01 January 2018 and 31 October 2019, a population-based colorectal cancer screening program was conducted in Hanoi, Vietnam. A health advocacy campaign and follow-up phone calls were used to enroll residents aged ≥40 years old to complete an immunochemical-fecal occult blood testing. Positive immunochemical-fecal occult blood testing was followed by a colonoscopy. We also conducted a systematic review of the colorectal cancer screening programs in the Asia-Pacific region that used similar approach by searching Ovid Medline and PubMed databases.

Results

During study period, 103 542 individuals among 672 742 eligible residents attended the screening of whom 81.5% participants finished immunochemical-fecal occult blood testing test and the positive rate was 6.1%. The coverage rate for immunochemical-fecal occult blood testing test was 11.9%. Among 2278 individuals who underwent colonoscopy, 3.5% were histologically diagnosed with cancer, 17.8% with advanced adenomas, and 23.1% with non-advanced adenomas. Males had significantly higher detection rate of advanced adenomas, cancer or ≥ two polyps/tumor than females (P < 0.0001). The systematic review showed that in two-step modality (i.e. immunochemical-fecal occult blood testing/fecal immunochemical test and colonoscopy), the test positive was from 4.1 to 10.6%. Once colonoscopy was performed subsequently, the rate of cancer among positive participants was from 1.7 to 16.4% and that of advanced adenomas was from 7.1 to 23.1%.

Conclusion

We showed that the two-step modality is a promising strategy for colorectal cancer screening in Vietnam that might apply to similar settings with limited resources
Combining canopy reflectance spectrometry and genome-wide prediction to increase response to selection for powdery mildew resistance in cultivated strawberry
Authors: Tapia Ronald , Abd-Elrahman Amr , Osorio Luis , Whitaker Vance M , Lee Seonghee
Published: April 2022

High-throughput phenotyping is an emerging approach in plant science, but thus far only a few applications have been made in horticultural crop breeding. Remote sensing of leaf or canopy spectral reflectance can help breeders rapidly measure traits, increase selection accuracy, and thereby improve response to selection. In the present study, we evaluated the integration of spectral analysis of canopy reflectance and genomic information for the prediction of strawberry (Fragaria × ananassa) powdery mildew disease. Two multi-parental breeding populations of strawberry comprising a total of 340 and 464 pedigree-connected seedlings were evaluated in two separate seasons. A single-trait Bayesian prediction method using 1001 spectral wavebands in the ultraviolet–visible–near infrared region (350–1350 nm wavelength) combined with 8552 single nucleotide polymorphism markers showed up to 2-fold increase in predictive ability over models using markers alone. The integration of high-throughput phenotyping was further validated independently across years/trials with improved response to selection of up to 90%. We also conducted Bayesian multi-trait analysis using the estimated vegetative indices as secondary traits. Three vegetative indices (Datt3, REP_Li, and Vogelmann2) had high genetic correlations (rA) with powdery mildew visual ratings with average rA values of 0.76, 0.71, and 0.71, respectively. Increasing training population sizes by incorporating individuals with only vegetative index information yielded substantial increases in predictive ability. These results strongly indicate the use of vegetative indices as secondary traits for indirect selection. Overall, combining spectrometry and genome-wide prediction improved selection accuracy and response to selection for powdery mildew resistance, demonstrating the power of an integrated phenomics–genomics approach in strawberry breeding.
Reduced auxin signalling through the cyclophilin geneDIAGEOTROPICAimpacts tomato fruit development and metabolism during ripening
Authors: Batista-Silva Willian , Carvalho de Oliveira Alice , Martins Auxiliadora Oliveira , Siqueira João Antonio , Rodrigues-Salvador Acácio , Omena-Garcia Rebeca P , Medeiros David Barbosa , Peres Lázaro Eustáquio Pereira , Ribeiro Dimas Mendes , Zsögön Agustín , Fernie Alisdair R , Nunes-Nesi Adriano , Araújo Wagner L
Published: April 2022

Auxin is an important hormone playing crucial roles during fruit growth and ripening; however, the metabolic impact of changes in auxin signalling during tomato (Solanum lycopersicum L.) ripening remains unclear. Here, we investigated the significance of changes in auxin signalling during different stages of fruit development by analysing changes in tomato fruit quality and primary metabolism using mutants with either lower or higher auxin sensitivity [diageotropica (dgt) and entire mutants, respectively]. Altered auxin sensitivity modifies metabolism, through direct impacts on fruit respiration and fruit growth. We verified that the dgt mutant plants exhibit reductions in fruit set, total fruit dry weight, fruit size, number of seeds per fruit, and fresh weight loss during post-harvest. Sugar accumulation was associated with delayed fruit ripening in dgt, probably connected with reduced ethylene levels and respiration, coupled with a lower rate of starch degradation. In contrast, despite exhibiting parthenocarpy, increased auxin perception (entire) did not alter fruit ripening, leading to only minor changes in primary metabolism. By performing a comprehensive analysis, our results connect auxin signalling and metabolic changes during tomato fruit development, indicating that reduced auxin signalling led to extensive changes in sugar concentration and starch metabolism during tomato fruit ripening.
Challenging Ancient DNA Results About Putative HLA Protection or Susceptibility to Yersinia pestis
Authors: Di Da , Simon Thomas Jeanne , Currat Mathias , Nunes José Manuel , Sanchez-Mazas Alicia
Published: April 2022

In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059–4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA.
Efficacy of laser interstitial thermal therapy (LITT) for newly diagnosed and recurrent IDH wild-type glioblastoma
Authors: de Groot John F , Kim Albert H , Prabhu Sujit , Rao Ganesh , Laxton Adrian W , Fecci Peter E , O’Brien Barbara J , Sloan Andrew , Chiang Veronica , Tatter Stephen B , Mohammadi Alireza M , Placantonakis Dimitris G , Strowd Roy E , Chen Clark , Hadjipanayis Constantinos , Khasraw Mustafa , Sun David , Piccioni David , Sinicrope Kaylyn D , Campian Jian L , Kurz Sylvia C , Williams Brian , Smith Kris , Tovar-Spinoza Zulma , Leuthardt Eric C
Published: April 2022

Background

Treatment options for unresectable new and recurrent glioblastoma remain limited. Laser ablation has demonstrated safety as a surgical approach to treating primary brain tumors. The LAANTERN prospective multicenter registry (NCT02392078) data were analyzed to determine clinical outcomes for patients with new and recurrent IDH wild-type glioblastoma.

Methods

Demographics, intraprocedural data, adverse events, KPS, health economics, and survival data were prospectively collected and then analyzed on IDH wild-type newly diagnosed and recurrent glioblastoma patients who were treated with laser ablation at 14 US centers between January 2016 and May 2019. Data were monitored for accuracy. Statistical analysis included individual variable summaries, multivariable differences in survival, and median survival numbers.

Results

A total of 29 new and 60 recurrent IDH wild-type WHO grade 4 glioblastoma patients were treated. Positive MGMT promoter methylation status was present in 5/29 of new and 23/60 of recurrent patients. Median physician-estimated extent of ablation was 91%-99%. Median overall survival (OS) was 9.73 months (95% confidence interval: 5.16, 15.91) for newly diagnosed patients and median post-procedure survival was 8.97 months (6.94, 12.36) for recurrent patients. Median OS for newly diagnosed patients receiving post-LITT chemo/radiation was 16.14 months (6.11, not reached). Factors associated with improved survival were MGMT promoter methylation, adjuvant chemotherapy within 12 weeks, and tumor volume <3 cc.

Conclusions

Laser ablation is a viable option for patients with new and recurrent glioblastoma. Median OS for IDH wild-type newly diagnosed glioblastoma is comparable to outcomes observed in other tumor resection studies when those patients undergo radiation and chemotherapy following LITT.
Silencing the conserved small nuclear ribonucleoprotein SmD1 target gene alters susceptibility to root-knot nematodes in plants
Authors: Mejias Joffrey , Chen Yongpan , Bazin Jérémie , Truong Nhat-My , Mulet Karine , Noureddine Yara , Jaubert-Possamai Stéphanie , Ranty-Roby Sarah , Soulé Salomé , Abad Pierre , Crespi Martin D , Favery Bruno , Quentin Michaël
Published: April 2022

Root-knot nematodes (RKNs) are among the most damaging pests of agricultural crops. Meloidogyne is an extremely polyphagous genus of nematodes that can infect thousands of plant species. A few genes for resistance (R-genes) to RKN suitable for use in crop breeding have been identified, but virulent strains and species of RKN have emerged that render these R-genes ineffective. Secretion of RKN effectors targeting plant functions mediates the reprogramming of root cells into specialized feeding cells, the giant cells, essential for RKN development and reproduction. Conserved targets among plant species define the more relevant strategies for controlling nematode infection. The EFFECTOR18 (EFF18) protein from M. incognita interacts with the spliceosomal small nuclear ribonucleoprotein D1 (SmD1) in Arabidopsis (Arabidopsis thaliana), disrupting its function in alternative splicing regulation and modulating the giant cell transcriptome. We show here that EFF18 is a conserved RKN-specific effector that targets this conserved spliceosomal SmD1 protein in Solanaceae. This interaction modulates alternative splicing events produced by tomato (Solanum lycopersicum) in response to M. incognita infection. The alteration of SmD1 expression by virus-induced gene silencing in Solanaceae affects giant cell formation and nematode development. Thus, our work defines a promising conserved SmD1 target gene to develop broad resistance for the control of Meloidogyne spp. in plants.
The Choice of Peers for Relative Performance Evaluation in Executive Compensation
Authors: Bizjak John , Kalpathy Swaminathan , Li Zhichuan Frank , Young Brian
Published: April 2022

Relative performance evaluation (RPE) awards have become an important component of executive compensation. We examine whether RPE awards, particularly the peer group, are structured in a manner consistent with economic theory. For RPE awards using a custom peer group, we find that the custom group is significantly more effective than four plausible alternative peer groups at filtering out common shocks, lowering the cost of compensation, and increasing managerial incentives. For RPE awards using a market index, we find some evidence that firms could have selected a custom set of peers with better filtering properties at a lower cost with similar incentives. For example, firms could have saved around $118,000 in present value terms, on average, for an RPE award had they chosen a custom group comprising their product market peers instead of a market index.
A model bridging waterlogging, stomatal behavior and water use in trees in drained peatland
Authors: Liu Che , Wang Qian , Mäkelä Annikki , Hökkä Hannu , Peltoniemi Mikko , Hölttä Teemu
Published: April 2022

Waterlogging causes hypoxic or anoxic conditions in soils, which lead to decreases in root and stomatal hydraulic conductance. Although these effects have been observed in a variety of plant species, they have not been quantified continuously over a range of water table depths (WTD) or soil water contents (SWC). To provide a quantitative theoretical framework for tackling this issue, we hypothesized similar mathematical descriptions of waterlogging and drought effects on whole-tree hydraulics and constructed a hierarchical model by connecting optimal stomata and soil-to-leaf hydraulic conductance models. In the model, the soil-to-root conductance is non-monotonic with WTD to reflect both the limitations by water under low SWC and by hypoxic effects associated with inhibited oxygen diffusion under high SWC. The model was parameterized using priors from literature and data collected over four growing seasons from Scots pine (Pinus sylvestris L.) trees grown in a drained peatland in Finland. Two reference models (RMs) were compared with the new model, RM1 with no belowground hydraulics and RM2 with no waterlogging effects. The new model was more accurate than the RMs in predicting transpiration rate (fitted slope of measured against modeled transpiration rate = 0.991 vs 0.979 (RM1) and 0.984 (RM2), R2 = 0.801 vs 0.665 (RM1) and 0.776 (RM2)). Particularly, RM2’s overestimation of transpiration rate under shallow water table conditions (fitted slope = 0.908, R2 = 0.697) was considerably reduced by the new model (fitted slope = 0.956, R2 = 0.711). The limits and potential improvements of the model are discussed.
Induction of Defense Responses and Protection of Almond Plants Against Xylella fastidiosa by Endotherapy with a Bifunctional Peptide
Authors: Moll Luís , Baró Aina , Montesinos Laura , Badosa Esther , Bonaterra Anna , Montesinos Emilio
Published: April 2022

Xylella fastidiosa is a plant pathogenic bacterium that has been introduced in the European Union (EU), causing significant yield losses in economically important Mediterranean crops. Almond leaf scorch (ALS) is currently one of the most relevant diseases observed in Spain, and no cure has been found to be effective for this disease. In previous reports, the peptide BP178 has shown a strong bactericidal activity in vitro against X. fastidiosa and to other plant pathogens, and to trigger defense responses in tomato plants. In the present work, BP178 was applied by endotherapy to almond plants of cultivar Avijor using preventive and curative strategies. The capacity of BP178 to reduce the population levels of X. fastidiosa and to decrease disease symptoms and its persistence over time were demonstrated under greenhouse conditions. The most effective treatment consisted of a combination of preventive and curative applications, and the peptide was detected in the stem up to 60 days posttreatment. Priming plants with BP178 induced defense responses mainly through the salicylic acid pathway, but also overexpressed some genes of the jasmonic acid and ethylene pathways. It is concluded that the bifunctional peptide is a promising candidate to be further developed to manage ALS caused by X. fastidiosa.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Developing BSN Students’ Quality Improvement Skills Through Addressing Real-World Problems
Authors: Turner Christine , Mikelaites Catherine
Published: April 2022

To create a preferred future for nursing, our prelicensure program teaches students to think critically, communicate effectively, and be leaders and change agents in health care. As seniors, students apply the Institute for Healthcare Improvement Model for Improvement to search the literature for research evidence about a problem, collect and analyze data, and perform a root cause analysis to develop solutions and plans for implementation. At the semester’s end, formal presentations are provided to academic and practice partners.
Linking the Humanities With Clinical Reasoning: Proposing an Integrative Conceptual Model for a Graduate Medical Education Humanities Curriculum
Authors: Prince G. , Osipov R. , Mazzella A.J. , Chelminski P.R.
Published: April 2022

Discussion surrounding the role of the humanities as an important analytic epistemology within medical education is generally less robust than literature supporting its value in building empathy and promoting personal reflection and wellness. As such, the humanities have not been considered to be as relevant when teaching medical reasoning or technical skills. Yet, might the humanities offer value in emboldening the analytic thinking of medical learners?

This article proposes an integrative conceptual model that links the thought process defining medicine—clinical reasoning—with humanistic analysis in an effort to advance the argument that the humanities offer a complementary and innovative platform that can be used within traditional medical education. The article then discusses preliminary findings from a pilot curriculum based on this model, implemented during internal medicine morning report at the University of North Carolina at Chapel Hill School of Medicine.

Preliminary qualitative analysis of transcripts from the pilot curriculum demonstrates that a thought process analogous to that of clinical reasoning can be identified within guided group analyses of humanities works. Participants simultaneously used thought processes that were analytic and intuitive. The emergence of ambiguity/intuition as a theme in the pilot curriculum suggests the humanities could be a powerful tool for exploring and embracing ambiguity in clinical practice.

Through the development of an integrative conceptual model, this article helps to demonstrate more explicitly the theoretical link between the reasoning pathways of the humanities and clinical medicine. Though a refined curriculum and more rigorous analysis are needed before arguing for the incorporation of the humanities into traditional graduate medical education on a larger scale, the preliminary findings here support the feasibility and promise of a curriculum based on the proposed integrative conceptual model.
No Taxation Without Representation: Addressing the “Deaf Tax” in Academic Medicine
Authors: Aldalur Aileen , Hall Wyatte C. , DeAndrea-Lazarus Ian A.
Published: April 2022

Minority faculty and trainees experience unique factors that can hinder their success in academic medicine—collectively referred to as “minority tax.” The authors argue that a similar “deaf tax” of unique barriers, experiences, and responsibilities disproportionately burdens deaf trainees and faculty. The cumulative effects of these deaf tax experiences represent a significant disadvantage for deaf professionals in academic medicine. Through a combination of relevant literature and the authors’ personal experiences as deaf professionals, several causative domains of deaf tax are outlined, including the fight for reasonable accommodations, prejudice and discrimination, training and diversity barriers, and a lack of deaf mentorship. In addition, a number of practical steps are offered for institutional leaders to consider implementing to improve equity and inclusion in academic medicine, including facilitating language equity and communication access, implementing deaf awareness training, fostering effective deaf mentorship, and promoting deaf professionals into leadership positions. Addressing these issues would help remove the obstacles that create the high deaf tax burden and lower the near-insurmountable barrier of entry, advancement, and retention in academic medicine for deaf professionals.
Role of Individual, Family, and Community Resilience in Moderating Effects of Adverse Childhood Experiences on Mental Health Among Children
Authors: Okwori Glory
Published: April 2022

Objective:

Mental health outcomes such as attention-deficit/hyperactivity disorder (ADHD), behavior disorders, anxiety, depression, and adverse childhood experiences (ACEs) are common disorders among children in the United States. Little is known on how potential resilient factors may moderate the relationship between exposure to ACEs and mental health outcomes. This study examines associations between ACEs and resilience on mental health outcomes using the 2018 National Survey of Children's Health (N = 26,572).

Method:

Logistic regression and interactions examined the association between ACEs, resilience, and mental health outcomes. ACE exposure and low resiliency were associated with an increased likelihood of mental health outcomes.

Results:

There were significant interactions between exposure to ACEs and family resilience as well as significant interactions between ACE exposure and community resilience. On stratification, the presence of individual resilience and having all resilience measures decreased the odds of ADHD, behavioral disorders, anxiety, and depression and the presence of community resilience decreased the odds of depression among individuals who had experienced 4 or more ACEs.

Conclusion:

These results illustrate the need to promote resilience measures for tackling mental health problems and reducing the negative effect of trauma in children.
RETINAL INFILTRATION IN A CASE OF CHRONIC MYELOID LEUKEMIA
Authors: Yee Claudine , Scruggs Brittni A. , Flaxel Christina J.
Published: April 2022

Purpose:

To describe a case of chronic myeloid leukemia with retinal leukemic infiltration identified by optical coherence tomography (OCT) and OCT angiography.

Methods:

Case report.

Results:

A 64-year-old man presented with bilateral painless blurred vision and three weeks of fatigue, unintentional weight loss, and complete hearing loss. Dilated fundus examination of both eyes showed peripheral intraretinal hemorrhages with white centers, vascular tortuosity, and peripheral nonperfusion. No macular lesions were identified by slit-lamp examination, fundus photography, fundus autofluorescence, or fluorescein angiography. Optical coherence tomography through the macula revealed multiple hyperreflective lesions throughout the inner retinal layers. Some of these lesions showed intrinsic flow by OCT angiography, but many lesions did not. The bone marrow biopsy confirmed chronic myeloid leukemia, and these intraretinal lesions were deemed to be leukemic infiltrates. The patient regained vision after systemic chemotherapy with resolution of the retinal infiltrates over time.

Conclusion:

Primary leukemic retinal involvement can be challenging to diagnose, especially when the macula appears normal clinically. Optical coherence tomography and OCT angiography are useful imaging modalities for the detection of retinal leukemic infiltration. Completing a thorough review of systems and initiating an urgent, systemic work-up are warranted in cases of retinal infiltration.
TREATMENT OF HYPOTONY WITH AN INTRAVITREAL GAS BUBBLE
Authors: Kokame Gregg T. , Card Kevin , Yim Michael C.
Published: April 2022

Purpose:

To describe a case of successful resolution of severe hypotony and choroidal detachments following nonfiltering glaucoma surgery with an intravitreal injection of C3F8 gas after a poor response to topical steroids and cycloplegia.

Methods:

Retrospective chart review of a case report.

Results:

89 year-old male presented with a central retinal vein occlusion, hyphema, vitreous hemorrhage and neovascular glaucoma. After initial intravitreal injection of aflibercept he was treated with pars plana vitrectomy with panretinal photocoagulation and endocyclophotocoagulation to the ciliary body, but he continued to have elevated intraocular pressure. Subsequent external cyclophotocoagulation was performed but severe hypotony with inflammation, choroidal detachments, and corneal edema developed one week later without response to cycloplegic and steroid medications. A therapeutic injection of perfluorpropane (C3F8) gas led to resolution of the hypotony and choroid detachment and long-term maintenance of intraocular pressure.

Discussion/Conclusion:

An intravitreal gas bubble can be a very useful outpatient procedure to immediately reverse hypotony, resolve choroidal detachment, and decrease associated inflammation. When hypotony does not respond to medical therapy with cycloplegic drops and steroid medications, then an intravitreal gas bubble can rapidly resolve these complications and result in stabilization of intraocular pressure long-term.