bluuebunny/crossref_metadata_2025 huggingface dataset:
Longitudinal Molecular Profiling of Circulating Tumor Cells in Metastatic Renal Cell Carcinoma
Authors: Bootsma Matthew , McKay Rana R. , Emamekhoo Hamid , Bade Rory M. , Schehr Jennifer L. , Mannino Matthew C. , Singh Anupama , Wolfe Serena K. , Schultz Zachery D. , Sperger Jamie , Xie Wanling , Signoretti Sabina , Kyriakopoulos Christos E. , Kosoff David , Abel Edwin J. , Helzer Kyle T. , Rydzewski Nicholas , Bakhtiar Hamza , Shi Yue , Blitzer Grace , Bassetti Michael , Floberg John , Yu Menggang , Sethakorn Nan , Sharifi Marina , Harari Paul M. , Choueiri Toni K. , Lang Joshua M. , Zhao Shuang G.
Published: May 2022

PURPOSE

Liquid biopsies in metastatic renal cell carcinoma (mRCC) provide a unique approach to understand the molecular basis of treatment response and resistance. This is particularly important in the context of immunotherapies, which target key immune-tumor interactions. Unlike metastatic tissue biopsies, serial real-time profiling of mRCC is feasible with our noninvasive circulating tumor cell (CTC) approach.

METHODS

We collected 457 longitudinal liquid biopsies from 104 patients with mRCC enrolled in one of two studies, either a prospective cohort or a phase II multicenter adaptive immunotherapy trial. Using a novel CTC capture and automated microscopy platform, we profiled CTC enumeration and expression of HLA I and programmed cell death-ligand 1 (PD-L1). Given their diametric immunological roles, we focused on the HLA I to PD-L1 ratio (HP ratio).

RESULTS

Patients with radiographic responses showed significantly lower CTC abundances throughout treatment. Furthermore, patients whose CTC enumeration trajectory was in the highest quartile (> 0.12 CTCs/mL annually) had shorter overall survival (median 17.0 months v 21.1 months, P < .001). Throughout treatment, the HP ratio decreased in patients receiving immunotherapy but not in patients receiving tyrosine kinase inhibitors. Patients with an HP ratio trajectory in the highest quartile (≥ 0.0012 annually) displayed significantly shorter overall survival (median 18.4 months v 21.2 months, P = .003).

CONCLUSION

In the first large longitudinal CTC study in mRCC to date to our knowledge, we identified the prognostic importance of CTC enumeration and the change over time of both CTC enumeration and the HP ratio. These insights into changes in both tumor burden and the molecular profile of tumor cells in response to different treatments provide potential biomarkers to predict and monitor response to immunotherapy in mRCC.
Somatic RET Indels in Sporadic Medullary Thyroid Cancer: Prevalence and Response to Selpercatinib
Authors: Elisei Rossella , Ciampi Raffaele , Matrone Antonio , Prete Alessandro , Gambale Carla , Ramone Teresa , Simeakis George , Materazzi Gabriele , Torregrossa Liborio , Ugolini Clara , Romei Cristina
Published: May 2022

Context

Although the majority of RET alterations are single nucleotide variants (SNV), small deletions and/or insertions have been reported at variable prevalence. No information about the efficacy of RET-specific inhibitors in patients harboring RET indels has been provided.

Objective

We present an update on the prevalence of RET indels in medullary thyroid cancer (MTC) and describe the efficacy of selpercatinib in patients with advanced MTC with RET indels.

Methods

The MTC tissues of 287 patients were analyzed using an Ion S5 targeted sequencing. The functional role of the reported indels have been evaluated by MutationTaster. Clinical and pathological data of MTC patients harboring a RET indel were collected and analyzed. Two patients with a RET indel were treated with selpercatinib.

Results

Among 178 RET-positive cases, 147 (82.6%) harbored a SNV and 31 (17.4%) a RET in-frame indel. Nine indels were not previously reported and were found to be disease causing by MutationTaster. Patients harboring an indel were found to have an aggressive disease and 2 of them were treated with selpercatinib, experiencing a good response to the treatment.

Conclusion

These data show that RET indels are not infrequent and correlate with an aggressive disease. Two RET indel–positive patients showed a partial response to the treatment with a highly selective RET inhibitor; thus, these RET indels can be considered actionable mutations. In order to not miss these alterations, the analysis of the full gene is recommended.
Lifespan and ROS levels in different Drosophila melanogaster strains after 24 h hypoxia exposure
Authors: Malacrida Sandro , De Lazzari Federica , Mrakic-Sposta Simona , Vezzoli Alessandra , Zordan Mauro A. , Bisaglia Marco , Menti Giulio Maria , Meda Nicola , Frighetto Giovanni , Bosco Gerardo , Dal Cappello Tomas , Strapazzon Giacomo , Reggiani Carlo , Gussoni Maristella , Megighian Aram
Published: May 2022

During recent decades, model organisms such as Drosophila melanogaster have made it possible to study the effects of different environmental oxygen conditions on lifespan and oxidative stress. However, many studies have often yielded controversial results usually assigned to variations in Drosophila genetic background and differences in study design. In this study, we compared longevity and ROS levels in young, unmated males of three laboratory wild-type lines (Canton-S, Oregon-R and Berlin-K) and one mutant line (Sod1n1) as a positive control of redox imbalance, under both normoxic and hypoxic (2% oxygen for 24 h) conditions. Lifespan was used to detect the effects of hypoxic treatment and differences were analysed by means of Kaplan–Meier survival curves and log-rank tests. Electron paramagnetic resonance spectroscopy was used to measure ROS levels and analysis of variance was used to estimate the effects of hypoxic treatment and to assess ROS differences between strains. We observed that the genetic background is a relevant factor involved in D. melanogaster longevity and ROS levels. Indeed, as expected, in normoxia Sod1n1 are the shortest-lived, while the wild-type strains, despite a longer lifespan, show some differences, with the Canton-S line displaying the lowest mortality rate. After hypoxic stress these variances are amplified, with Berlin-K flies showing the highest mortality rate and most evident reduction of lifespan. Moreover, our analysis highlighted differential effects of hypoxia on redox balance/unbalance. Canton-S flies had the lowest increase of ROS level compared to all the other strains, confirming it to be the less sensitive to hypoxic stress. Sod1n1 flies displayed the highest ROS levels in normoxia and after hypoxia. These results should be used to further standardize future Drosophila research models designed to investigate genes and pathways that may be involved in lifespan and/or ROS, as well as comparative studies on specific mutant strains.
SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo
Authors: Malaguti Mattias , Portero Migueles Rosa , Annoh Jennifer , Sadurska Daina , Blin Guillaume , Lowell Sally
Published: May 2022

Cell-cell interactions govern differentiation and cell competition in pluripotent cells during early development, but the investigation of such processes is hindered by a lack of efficient analysis tools. Here, we introduce SyNPL: clonal pluripotent stem cell lines that employ optimised Synthetic Notch (SynNotch) technology to report cell-cell interactions between engineered ‘sender’ and ‘receiver’ cells in cultured pluripotent cells and chimaeric mouse embryos. A modular design makes it straightforward to adapt the system for programming differentiation decisions non-cell-autonomously in receiver cells in response to direct contact with sender cells. We demonstrate the utility of this system by enforcing neuronal differentiation at the boundary between two cell populations. In summary, we provide a new adaptation of SynNotch technology that could be used to identify cell interactions and to profile changes in gene or protein expression that result from direct cell-cell contact with defined cell populations in culture and in early embryos, and that can be customised to generate synthetic patterning of cell fate decisions.
Translation initiation factor eIF4G1 modulates assembly of the polypeptide exit tunnel region in yeast ribosome biogenesis
Authors: Tseng Yun-Ting , Sung Yu-Cheng , Liu Ching-Yu , Lo Kai-Yin
Published: May 2022

eIF4G is an important eukaryotic translation initiation factor. In this study, eIF4G1, one of the eIF4G isoforms, was shown to directly participate in biogenesis of the large (60S) ribosomal subunit in Saccharomyces cerevisiae cells. Mutation of eIF4G1 decreased the amount 60S ribosomal subunits significantly. The C-terminal fragment of eIF4G1 could complement the function in 60S biogenesis. Analyses of its purified complex with mass spectrometry indicated that eIF4G1 associated with the pre-60S form directly. Strong genetic and direct protein–protein interactions were observed between eIF4G1 and Ssf1 protein. Upon deletion of eIF4G1, Ssf1, Rrp15, Rrp14 and Mak16 were abnormally retained on the pre-60S complex. This purturbed the loading of Arx1 and eL31 at the polypeptide exit tunnel (PET) site and the transition to a Nog2 complex. Our data indicate that eIF4G1 is important in facilitating PET maturation and 27S processing correctly.

This article has an associated First Person interview with the first author of the paper.
Metabolic Alterations Differentiating Cardiovascular Maladaptation from Athletic Training in American-Style Football Athletes
Authors: TSO JASON V. , LIU CHANG , TURNER CASEY G. , UPPAL KARAN , PRABAKARAN GANESH , EJAZ KIRAN , BAGGISH AARON L. , JONES DEAN P. , QUYYUMI ARSHED A. , KIM JONATHAN H.
Published: May 2022

Purpose

Metabolomics identifies molecular products produced in response to numerous stimuli, including both adaptive (includes exercise training) and disease processes. We analyzed a longitudinal cohort of American-style football (ASF) athletes, who reliably acquire maladaptive cardiovascular (CV) phenotypes during competitive training, with high-resolution metabolomics to determine whether metabolomics can discriminate exercise-induced CV adaptations from early CV pathology.

Methods

Matched discovery (n = 42) and validation (n = 40) multicenter cohorts of collegiate freshman ASF athletes were studied with longitudinal echocardiography, applanation tonometry, and high-resolution metabolomics. Liquid chromatography–mass spectrometry identified metabolites that changed (P < 0.05, false discovery rate <0.2) over the season. Metabolites demonstrating similar changes in both cohorts were further analyzed in linear and mixed-effects models to identify those associated with left ventricular mass, tissue-Doppler myocardial E′ velocity (diastolic function), and arterial function (pulse wave velocity).

Results

In both cohorts, 20 common metabolites changed similarly across the season. Metabolites reflective of favorable CV health included an increase in arginine and decreases in hypoxanthine and saturated fatty acids (heptadecanoate, arachidic acid, stearate, and hydroxydecanoate). In contrast, metabolic perturbations of increased lysine and pipecolate, reflective of adverse CV health, were also observed. Adjusting for player position, race, height, and changes in systolic blood pressure, weight, and pulse wave velocity, increased lysine (β = 0.018, P = 0.02) and pipecolate (β = 0.018, P = 0.02) were associated with increased left ventricular mass index. In addition, increased lysine (β = −0.049, P = 0.01) and pipecolate (β = −0.052, P = 0.008) were also associated with lower E′ (reduced diastolic function).

Conclusions

ASF athletes seem to develop metabolomic changes reflective of both favorable CV health and early CV maladaptive phenotypes. Whether metabolomics can discriminate early pathologic CV transformations among athletes is a warranted future research direction.
Pathogenic Enterobacteriaceae require multiple culture temperatures for detection in Cannabis sativa L.
Authors: McKernan Kevin , Helbert Yvonne , Kane Liam T , Zhang Lei , Houde Nathan , Bennett Anne , Silva Juliana , Ebling Heather , McLaughlin Stephen
Published: May 2022

Background: Cannabis safety testing requires adequate detection of a broad class of bacteria known as Enterobacteria, from the family of Enterobacteriaceae. These organisms are responsible for many food-borne illnesses including gastroenteritis, and are common targets in the food testing industry. While all these organisms contain 16S DNA, not all of them grow on commercial culture-based platforms at a single culture temperature.

Methods: We assessed four Enterobacteria (Aeromonas hydrophila, Pantoea agglomerans, Yersinia enterocolitica, Rahnella aquatilis) that vary in their preferred culture temperature, human pathogenicity and prevalence in cannabis. We cultured them on two different plating media and compared these results to two different qPCR assays.

Results: All four bacteria grew on one plating medium at 30°C. 75% of them failed to grow at 36°C. Using a different plating medium, 75% grew at 30°C and zero grew at 36°C. Two different commercialy available quantitative PCR assays detected 100% of the organisms.

Conclusions: Several Enterobacteria are highly medium- and temperature-sensitive, and can easily evade culture-based detection. Some of these bacteria are known to infect cannabis and may pose a clinical risk to cannabis trimmers or consumers. Quantitative PCR detected all of these species. Quantitative PCR is often criticized for failing to discern live versus dead DNA, but the definition of “live” is dependent on the culture medium and temperature used.
Establishment of diagnostic reference level and radiation dose variation in head & neck and pelvis treatment planning in radiation therapy computed tomography
Authors: Rao Ms. Shreekripa , Kadavigere Dr. Rajagopal , Sharan Dr. Krishna , Sukumar Dr. Suresh , GC Mr. Srinidhi , Dsouza Mrs. Rechal Nisha , S Mr. Suman
Published: May 2022

Background: This observational study aims to establish a discrepancy in the radiation dose distributed for head & neck and pelvis localization in Computed Tomography (CT) imaging in radiation therapy. The objective and need of the current study are to establish Diagnostic Reference Level (DRL) for head & neck and pelvic CT protocols in Radiation Therapy planning and compare them with other regional, national and international DRL. The established DRL will be used to find further optimized DRL for Radiation Therapy Computed Tomography (RTCT).

Methods: A total of 120 patients with Head & Neck cancers and 90 patients with pelvic cancers to be treated with radiotherapy prescribed for the RTCT with ages above 18 years old and above were included in the current study. The advanced Philips 16 slice big bore CT acquired all the CT simulation images.

Results: Third quartile standards of Dose Length Product and effective dose for Head & Neck, and pelvis were 790.65mGy.cm, 2.45179 mSv, and 999.7 mGy.cm, 15.48mSv respectively. The third quartile CTDIvol value for the same order of procedure is 17.6 mGy. Tube voltage of 120kVp and 300mAs and used for radiotherapy planning.

Conclusion: The first regional Radiation therapy Computed tomography simulation Diagnostic reference levels have been projected and deliver a platform for dose evaluation and optimization due to the limited number of papers on radiation therapy, computed tomography, and diagnostic reference levels. Comparison with previously available RT CT diagnostic reference levels indicated some radiation dose variation, so exposure parameters should be revised and improved.
Mindful Caring: A pilot study of an online mindfulness workshop for medical students to improve self-compassion
Authors: Tan Guan Hao Chester , Hong Daniel Zhihao , Lim Isis Claire Zhen Yu , Toh Ying Pin , Loh Victor Weng Keong , Lien Virginia
Published: May 2022

Background: This study examines the effectiveness of a pilot Mindful Caring workshop in improving self-compassion, mindfulness, and empathy, while reducing stress.

Methods: Year 3 and 4 medical students from the National University of Singapore underwent 16 hours of online workshops over 4 days with didactic and experiential learning activities on self-compassion and mindfulness. Primary outcomes of self-compassion were measured with the Self-Compassion Scale (SCS). Secondary outcomes include mindfulness measured with the Five Facet Mindfulness Questionnaire-15 (FFMQ-15), empathy and stress levels. Qualitative comments were also sought in the feedback. 

Results: Out of 21 participants, 90.5% (n =19) completed both pre- and post-intervention questionnaires. Participants experienced significant mean improvements in self-compassion (p<0.05) and mindfulness (p<0.05), while improvements in empathy and stress levels did not reach statistical significance. 

Conclusions: A short online Mindful Caring workshop could be an avenue to improve self-compassion and mindfulness, which may have a downstream effect on burnout.
SCoVMod – a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics
Authors: Banks Christopher J. , Colman Ewan , Doherty Thomas , Tearne Oliver , Arnold Mark , Atkins Katherine E. , Balaz Daniel , Beaunée Gaël , Bessell Paul R. , Enright Jessica , Kleczkowski Adam , Rossi Gianluigi , Ruget Anne-Sophie , Kao Rowland R.
Published: May 2022

Background: Mobility restrictions prevent the spread of infections to disease-free areas, and early in the coronavirus disease 2019 (COVID-19) pandemic, most countries imposed severe restrictions on mobility as soon as it was clear that containment of local outbreaks was insufficient to control spread. These restrictions have adverse impacts on the economy and other aspects of human health, and it is important to quantify their impact for evaluating their future value.

Methods: Here we develop Scotland Coronavirus transmission Model (SCoVMod), a model for COVID-19 in Scotland, which presents unusual challenges because of its diverse geography and population conditions. Our fitted model captures spatio-temporal patterns of mortality in the first phase of the epidemic to a fine geographical scale.

Results: We find that lockdown restrictions reduced transmission rates down to an estimated 12\% of its pre-lockdown rate. We show that, while the timing of COVID-19 restrictions influences the role of the transmission rate on the number of COVID-related deaths, early reduction in long distance movements does not. However, poor health associated with deprivation has a considerable association with mortality; the Council Area (CA) with the greatest health-related deprivation was found to have a mortality rate 2.45 times greater than the CA with the lowest health-related deprivation considering all deaths occurring outside of carehomes.

Conclusions: We find that in even an early epidemic with poor case ascertainment, a useful spatially explicit model can be fit with meaningful parameters based on the spatio-temporal distribution of death counts. Our simple approach is useful to strategically examine trade-offs between travel related restrictions and physical distancing, and the effect of deprivation-related factors on outcomes.
Context effects on object recognition in real-world environments: A study protocol
Authors: Nicholls Victoria I. , Alsbury-Nealy Benjamin , Krugliak Alexandra , Clarke Alex
Published: May 2022

Background: The environments that we live in impact on our ability to recognise objects, with recognition being facilitated when objects appear in expected locations (congruent) compared to unexpected locations (incongruent). However, these findings are based on experiments where the object is isolated from its environment. Moreover, it is not clear which components of the recognition process are impacted by the environment. In this experiment, we seek to examine the impact real world environments have on object recognition. Specifically, we will use mobile electroencephalography (mEEG) and augmented reality (AR) to investigate how the visual and semantic processing aspects of object recognition are changed by the environment.

Methods: We will use AR to place congruent and incongruent virtual objects around indoor and outdoor environments. During the experiment a total of 34 participants will walk around the environments and find these objects while we record their eye movements and neural signals. We will perform two primary analyses. First, we will analyse the event-related potential (ERP) data using paired samples t-tests in the N300/400 time windows in an attempt to replicate congruency effects on the N300/400. Second, we will use representational similarity analysis (RSA) and computational models of vision and semantics to determine how visual and semantic processes are changed by congruency.

Conclusions: Based on previous literature, we hypothesise that scene-object congruence would facilitate object recognition. For ERPs, we predict a congruency effect in the N300/N400, and for RSA we predict that higher level visual and semantic information will be represented earlier for congruent scenes than incongruent scenes. By collecting mEEG data while participants are exploring a real-world environment, we will be able to determine the impact of a natural context on object recognition, and the different processing stages of object recognition.
Information Nudges and Self-Control
Authors: Mariotti Thomas , Schweizer Nikolaus , Szech Nora , von Wangenheim Jonas
Published: May 2022

We study the optimal design of information nudges directed to present-biased consumers who make consumption decisions over time without exact prior knowledge of their long-term consequences. For any distribution of risks, there exists a consumer-optimal information nudge that is of cutoff type, recommending abstinence if the risk is high enough. Depending on the distribution of risks, more or fewer consumers have to be sacrificed, as they cannot be credibly warned even though they would like to be. Under a stronger present bias, the target group receiving a credible warning to abstain must be tightened, but this need not increase the probability of harmful consumption. If some consumers have a stronger present bias than others, traffic-light nudges turn out to be optimal and, when subgroups of consumers differ sufficiently, the optimal traffic-light nudge is also subgroup optimal. We finally compare the consumer-optimal nudge with those that a health authority or a lobbyist would favor.

This paper was accepted by Manel Baucells, behavioral economics and decision analysis.

Funding: This research benefited from the financial support of the Agence Nationale de la Recherche [Programme d’Investissements d’Avenir Grant ANR-17-EURE-0010], the German Research Foundation [Grants Collaborative Research Center Transregio 190 and 224 Project B03], and the research foundation Toulouse School of Economics-Partnership.

Supplemental Material: The online appendix is available at https://doi.org/10.1287/mnsc.2022.4428 .
High-Throughput Sequencing Provides Insight into Soil Fungal Community Structure and Diversity in Plant Protected Areas of Songkhla Zoo in Southern Thailand
Authors:   King Mongkut’s University of Technology Thonburi, Ratchaburi Campus, Ratchaburi 70150, Thailand, Phoka Nongnat , Pornsuriya Chaninun ,   Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand, Sunpapao Anurag ,   Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
Published: May 2022

The rapid expansion of the agricultural fi eld has had negative impacts on soil ecological functions. Soil fungi play an important role in nutrient cycling and the maintenance of soil functions in terrestrial ecosystems. However, our understanding of soil fungal communities and the interaction among microbial taxa in plant protected areas is still limited. This study applied high-throughput sequencing in an investigation of fungal communities and their diversity within the plant protected areas of Songkhla zoo in Southern Thailand. The sampling sites fell into three zones: zone I (dry evergreen forest, mixed deciduous forest and agricultural fi eld); zone II (evergreen forest and mixed deciduous forest); and zone III (evergreen forest, mixed deciduous forest and rubber tree crop). Soil samples were collected from each zone and subjected to physicochemical tests. Total DNA was extracted from soil samples, and we analyzed the nuclear ribosomal internal transcribed spacer 1 (ITS1) region of the rDNA gene of the fungi by Illumina Miseq sequencing to assess the fungal communities. The soil parameters revealed that the total calcium (Ca), manganese (Mg) and potassium (K) in zone III were signifi cantly higher than in the other zones. A total of 637, 702 and 745 OTUs were observed from zone I, zone II and zone III samples, respectively, with 143 OTUs common across all sampling sites. The fungal communities were signifi cantly different between the sampling sites. Zone III had the highest levels of community richness and diversity, followed by zone II and zone I. The dominant genera in zones I, II and III were Beauveria, Staphylotrichum and Trichoderma, respectively. Furthermore, the high concentration of K, Ca and Mg affected the fungal communities and diversity in the plant protected areas in Songkhla zoo. Our fi ndings provide insights into the importance of soil fungi, and this study identifi ed key differences in the fungal communities in the plant protected areas in Songkhla zoo.
Diff erent Levels of Nitrogen Fertilizer in Nursery Stage Positively Aff ect the Activity of Defense-related Enzymes and Resistance of Tobacco Plant to Phytophthora nicotianae
Authors:   College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, Yunnan, China, Song Ruifang , Ahmed Waqar ,   College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, Yunnan, China,   State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, Yunnan, China, Tan Yujiao ,   College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, Yunnan, China,   College of Tobacco Science, Yunnan Agricultural University, Kunming, 650201, Yunnan, China, Zhao Zhengxiong ,   College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
Published: May 2022

Black shank caused by Phytophthora nicotianae is a serious threat to the production of better-quality fl ue-cured tobacco. Protein’s are executors of plant functions and most disease resistance mechanisms in plants are related to differential expression of proteins. In our previous study, 17 different proteins induced by P. nicotianae were screened out through proteomics analysis. In this study, we evaluated the effect of three different levels of nitrogen fertilizer (High, medium, and low) at the seedling stage on the expression of these proteins, physiological response of fl ue-cured tobacco, and occurrence of black shank disease. Results of this study showed that before and after inoculation of P. nicotianae, the activity of defense-related enzymes except for MDA contents in tobacco plants grown under low- nitrogen level was higher than tobacco plants grown under the high-nitrogen level at seedling stage. Through analysis of 17 different proteins, we found the expression of 12 proteins (three proteins involved in photosynthesis, six proteins involved in oxidative phosphorylation, one protein involved in tricarboxylic acid cycle, one heat shock protein, and one 14-3-3 protein) were up-regulated in tobacco seedlings raised under low nitrogen level. However, the expression of fi ve pathogenesis-related proteins was not detected. This study highlights the effect of effi cient use of nitrogen fertilizer during the nursery growing stage for producing healthy tobacco seedlings. It is concluded that a proper supply of nitrogen fertilizer at the seedling stage ensures the quality production of tobacco seedlings and reduces the incidence of black shank disease.
A New Tropical Species Of Lycoperdon Subgenus Morganella (Agaricales, Basidiomycota) From Yunnan Province, China
Authors:   Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China, Ye Lei ,   CIFOR-ICRAF China Program, World Agroforestry Centre, East and Central Asia, 132 Lanhei Road, Kunming 650201, China,   The Research Institute of Alpine Economic Plant, Yunnan Academy of Agricultural Sciences, Lijiang 674100, China
Published: May 2022

Two specimens of Lycoperdon were collected in 2012 and 2013 during surveys conducted in evergreen broadleaf forests of Xishuangbanna, Yunnan Province, China. Macro- and micro- morphological characteristics, together with analyses of combined ITS and LSU sequence data, showed that fi ve specimens represent a single new species and is thus named as Lycoperdon mengsongense. The new species is distinguished from the known taxa in Lycoperdon by its greyish white to dark grey exoperidium covered by minute and blackish grey granules, smooth to wrinkled endoperidium, non- chambered subgleba and echinate basidiospores. Comprehensive morphological descriptions, color photographs of macro- and micro- characteristics and a phylogenetic tree to show the placement of the new species are provided. In addition, the new species is compared with closely related taxa in Lycoperdon subgenus Morganella.
New species of Cercosporoid on Mango in Thailand
Authors:   Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand, Tamakaew Nisachon , Karunarathna Anuruddha ,   Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand, Pakdeeniti Parichad ,   Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand, Withee Patchareeya ,   Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand, Senwanna Chanokned ,   Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand, Haituk Sukanya ,   Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand, Cheewangkoon Ratchadawan ,   Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand,   Innovative Agriculture Research Centre, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand.
Published: May 2022

Fungi in Cercospora and Pseudocercospora are commonly known as cercosporoid fungi. In the current study, a cercosporoid fungus was isolated from Mangifera indica from Chiang Mai, Thailand. The isolate was identifi ed as Pseudocercospora mangiferae sp. nov. based on morphology and ITS, act, tef1-α and rpb2 multigene phylogeny. Further, this is the fi rst report of a Pseudocercospora species on M. indica in Thailand.
Lepiota lilacea (Agaricales, Basidiomycota), a New Record from Pakistan
Authors:   Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, 54590, Lahore, Pakistan, Naseer Arooj , Jabeen Sana ,   Department of Botany, Division of Science and Technology, University of Education, Township, Lahore, Pakistan, Khanum Samia ,   Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, 54590, Lahore, Pakistan, Waseem Bushra ,   Department of Botany, Division of Science and Technology, University of Education, Township, Lahore, Pakistan, Khalid Abdul Nasir ,   Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, 54590, Lahore, Pakistan
Published: May 2022

Macrofungi were survayed and collected in Pakistan during a period of 2014–2019. Basidiomata of Lepiota lilacea were collected from different forests of Swat and Kurruam districts, Khyber Pahtukhwa, Pakistan. These were analyzed by sequencing the rDNA internal transcribed spacer region. The morphology of the taxon is also described. Based on morphology and molecular phylogenetic analysis of ITS region, these basidiomata were found to represent L. lilacea and clustered within Lepiota section lilacae. Lepiota lilacea is an addition to the mycofl ora of Pakistan and this is the fi rst report of this species.
Comparative Analysis of the Mitochondrial DNA of Wild Varieties and Domesticated Pleurotus citrinopileatus
Authors:   Agricultural College, Jilin Agriculture Science and Technology University, Jilin 132101, Jilin, China, Zhou Yi , Wang Tiantian ,   Agricultural College, Yanbian University, Yanji 133000, Yanbian, China, Xu Jize ,   Agricultural College, Jilin Agriculture Science and Technology University, Jilin 132101, Jilin, China,   Agricultural College, Yanbian University, Yanji 133000, Yanbian, China,   Jilin University, Jilin 130015, China
Published: May 2022

In this study, the mitochondrial DNA of wild and domesticated Pleurotus citrinopileatus varieties were sequenced, assembled, and compared. The three mitochondrial DNA of 4681-0, 4681-1, and 4681-2 comprised circular DNA molecules, with the size of 60,331 bp, 60,661 bp and 60,661 bp, respectively. All mitochondrial DNA of the three contained 2 ribosomal RNA genes (rRNAs) and 24 transfer RNA genes (tRNAs). Both 4681-1 and 4681-2 had 17 standard protein-encoding genes, which was higher than 4681-0. Both 4681-0 and 4681-2 had 7 open reading frames, which was less than 4681-1. Among mitochondrial DNA of three varieties, we found gene and intron gain/loss events. By performing a comparative analysis of mitochondrial DNA of three varieties, we identifi ed gene rearrangements between 4681-0, 4681-1 and 4681-2. Predictions of the single nucleotide polymorphisms (SNPs) and RNA editing sites of mitochondrial DNA of three varieties, revealed a feasibility of molecular labeling and gene editing at the mRNA level of P. citrinopileatus. We proposed that mitochondrial DNA, which plays an important role in biological oxidation, is changed to adapt different environments during the domestication of wild species of P. citrinopileatus. We promit an evolutionary strategie of domestication of P. citrinopileatus, aiming to provide some molecular-level theoretical foundations for factory cultivation and genetic breeding of P. citrinopileatus.
Single Crystalline Zinc Oxide Nanorods Grown by R-F Sputtering Technique Onto P-Si Substrate for Sensing Applications
Authors: A. I. Aljameel A. I. Aljameel
Published: May 2022

A high-quality, single-crystal ZnO nanorod thin film was successfully deposited onto p-type monocrystalline silicon (P-Si) substrates using an RF sputtering technique. An XRD analysis of ZnO nanorods was carried out to investigate crystallinity and aspect ratio of the deposited thin film. Adjusting deposition conditions makes it possible to grow single-crystalline ZnO nanorods with preferred orientations (002) on the substrate. More than the substrate type, crystal size is determined by single-crystal growth conditions. These sample had the exact. With the exception of a small variance at Raman shifts 414 cm-1, which correspond to E2. Raman spectra measurements with a slight variation at Raman shifts 414 cm-1, corresponding to E2 (high). In response to the compressive stress, the peak shifts upwards (blue dress). Data from FE-SEM shows vertical growth of hexagonal prism. Finally, the hall effect measurement and UV-vis spectroscopy were carried out the electrical and optical properties of the sample respectively.
Data Mining and Machine Learning Technique in Contingency Analysis of Power System with UPFC
Authors: Angadi Ravi V. , Daram Suresh Babu , Venkataramu P. S , Manohar V Joshi
Published: May 2022

This paper explains how to predict the severity of the system by connecting with and without a unified power flow controller under different load and n-1 conditions by calculating the LVSI and by the application of data mining and machine learning techniques. A large amount of data will occur during the process of contingency analysis and it is necessary that how to get this to the system value to assess the severity of the system. With the help of data mining and machine learning techniques, analysis of data generated from the simulations for different load conditions are carried out and is used to estimate the severity of the line. In this, the IEEE 30 Bus System is used by calculating the line voltage stability index and the simulation work is carried out by using MATLAB and WEKA software.
On the Controllability of Artificial Intelligence: An Analysis of Limitations
Authors: Yampolskiy Roman V.
Published: May 2022

The invention of artificial general intelligence is predicted to cause a shift in the trajectory of human civilization. In order to reap the benefits and avoid the pitfalls of such a powerful technology it is important to be able to control it. However, the possibility of controlling artificial general intelligence and its more advanced version, superintelligence, has not been formally established. In this paper, we present arguments as well as supporting evidence from multiple domains indicating that advanced AI cannot be fully controlled. The consequences of uncontrollability of AI are discussed with respect to the future of humanity and research on AI, and AI safety and security.
The influence of frailty on outcomes for older adults admitted to hospital with benign biliary disease: a single-centre, observational cohort study
Authors: Thomas M , Baltatzis M , Price A , Fox J , Pearce L , Vilches-Moraga A
Published: May 2022

Introduction

The prevalence and complications of biliary disease increase with age. Frailty has been associated with adverse outcomes in the hospital setting. We describe the prevalence of frailty in older patients hospitalised with benign biliary disease and its association with duration of hospital stay, and 90-day and 1-year mortality.

Methods

We performed a retrospective cohort study of patients aged 75 years and over admitted with acute biliary disease between 17 September 2014 and 20 March 2017. Clinical Frailty Scale (CFS) score was recorded on admission.

Results

We included 200 patients with a median age of 82 (75–99) years, 60% were female; 154 (77%) were independent for personal activities of daily living (ADLs) and 99 (49.5%) for instrumental ADLs. Cholecystitis was the most common diagnosis (43%) followed by cholangitis (36%) and pancreatitis (21%). Ninety-nine patients were non frail (NF; CFS 1–4) and 101 were frail (F; CFS 5–9). Some 104 patients received medical treatment only. Surgery was more common in NF patients (11% vs F 2%), percutaneous drainage more frequently performed in F patients (15% vs NF 5%) and endoscopic cholangiopancreatography was similar in both groups (F 32% vs NF 31%). Frailty was associated with worse clinical outcomes in F vs NF: functional deconditioning (34% vs 11%), increased care level (19% vs 3%), length of stay (12 vs 7 days), 90-day mortality (8% vs 3%) and 1-year mortality (48% vs 24%).

Conclusions

Half of patients in our cohort were frail and spent longer in hospital, were less likely to undergo surgery and were less likely to remain alive at 1 year after discharge.
The effect of local anaesthetic biopsy in head and neck cancer on cancer pathway waiting times
Authors: Lim AE , Zahra B , Moen C , Montgomery J
Published: May 2022

Introduction

The 31-day target in urgent suspicion of cancer (USOC) referrals fast-tracks patients through the cancer pathway. Local anaesthetic (LA) biopsy can be performed during an outpatient clinic and may improve pathway times. The aim of this study was to compare LA biopsy in head and neck USOC referrals with the traditional general anaesthetic (GA) pathway.

Methods

This was a retrospective cohort study of USOC referrals to the NHS Greater Glasgow and Clyde head and neck multidisciplinary team between 1 June 2018 and 28 December 2020, and compared pathway times in LA and GA biopsies.

Results

The mean number of days from clinic to biopsy was 4.4 in the LA group and 28.0 in the GA group. This was significantly faster in the LA biopsy group (p < 0.05). The overall pathway time in the LA and GA biopsy groups was 35.7 and 61.5 days, respectively, and was significantly faster in LA biopsy group (p < 0.05).

Conclusions

The LA cohort had significantly faster pathway times compared with GA biopsy. LA biopsy requires careful patient selection, but is an effective alternative to GA biopsy in the appropriate patient group.
Muslim volunteers as social services providers during the COVID-19 pandemic in Israel
Authors: Magadlah Haneen , Cnaan Ram
Published: May 2022

In the early stages of the COVID-19 pandemic, the Israeli government paid little attention to its impact on the Palestinian population. Allocations of state aid under-funded Palestinian communities, and all state communications and public announcements were delivered in Hebrew, effectively excluding native Arabic speakers from vital safety information. In response, Muslim volunteers and organisations filled the service and information gaps created by government neglect. In this article, we describe how Muslim volunteers organised and responded in order to support the Muslim community in Israel. Based on in-depth interviews with 19 volunteers in the early days of the pandemic, we show that their motivation was both religious and political, and firmly grounded in Muslim theology. We describe new services provided by volunteers and show that they were uniquely suited to meet Muslim community needs in the moment.
Trajectories of intimate partner violence (IPV) in a primary care cohort of women with depressive symptoms
Authors: Hegarty Kelsey , Densley Konstancja , Gilchrist Gail , Elliott Peter , Gunn Jane
Published: May 2022

Aims:

To assess trajectories of women’s experience of intimate partner violence (IPV) over time, and baseline risk factors and associated four-year outcomes for different trajectories.

Design:

A cohort study of 548 women with depressive symptoms, attending primary care appointments, were surveyed annually for four years. Secondary analysis was undertaken using growth mixture modelling to generate IPV trajectories. Analyses of associations of these generated classes of IPV with hypothesised baseline and four-year measures were undertaken.

Results:

At baseline, 42% (231) women experienced IPV in past 12 months. Five-class IPV trajectory model showed five groups over time: consistently ‘high IPV’ (5%, n=28), ‘some IPV’ (14%, n=77), ‘minimal IPV’ (9%, n=52), ‘decreasing IPV’ (11%, n=62), and ‘no IPV’ (60%, n=329). Baseline differences showed women in ‘high’ and ‘some’ group had more childhood abuse, low income and poor mental health compared to ‘minimal’ or ‘no IPV’ groups. At four years, ‘decreasing IPV’ group was aligned with ‘minimal/no IPV’ groups on mental health, quality of life and social support measures.

Conclusion:

Women exhibited different trajectories of IPV over time with high burden of mental health problems, except for when IPV decreases. Clinical identification of IPV and tailoring of responses to decrease exposure to IPV is warranted to reduce disease burden.
Examining ‘dirty work’ using an analysis of place and territorial stigma: low-income communities and the home credit sector
Authors: Marks Abigail , Terry Esme
Published: May 2022

Based on data from over 70 interviews with people working in the home credit industry, this article makes a unique contribution to knowledge about work in sub-prime financial services. The article demonstrates how extant positions constructing home credit agents as ‘dirty workers’ are to some extent misleading, omitting analysis of the place(s) in which such work is enacted. Home credit has been established in disadvantaged, stigmatised communities for decades and is central to the history and geography of many working-class territories. Drawing on theory surrounding place and territorial stigma, this article considers the complicated relationship between the conflicting feelings of taint and value held by home credit workers, thus contributing to a more nuanced and contextually aware understanding of ‘dirty work’. Moreover, by exploring the value of home credit agents to their borrowers, it is possible to gain insights as to how to better structure financial support in low-income communities.
Design parameters for Airy beams in light-sheet microscopy
Authors: Taege Yanis , Borre Anja Lykke , Veettikazhy Madhu , Schulz Sophia Laura , Marti Dominik , Andersen Peter Eskil , Messerschmidt Bernhard , Ataman Çağlar
Published: May 2022

We derive analytical expressions for the length, thickness, and
curvature of an Airy light sheet in terms of basic parameters of the
cubic phase and the paraxially defined focusing optics that form the
beam. The length and thickness are defined analogously to the Rayleigh
range and beam waist of a Gaussian beam, hence providing a direct and
quantitative comparison between the two beam types. The analytical
results are confirmed via numerical Fresnel propagation simulations
and discussed within the context of light-sheet microscopy, providing
a comprehensive guide for the design of the illumination unit.
Polarization property analysis of single lenses
Authors: Kukushkin Dmitrii E. , Zhukova Tatiana I. , Bakholdin Alexey V.
Published: May 2022

We have studied the basic polarization properties of variously shaped lenses for the on-axis beam in the exit pupil and present the data obtained. The Mueller calculus and three-dimensional polarization calculus methods were applied for polarization ray tracing. The calculation methods were compared on different samples. We have demonstrated that taking into account the shape of lenses when designing lens optical systems contributes to the minimization of the diattenuation magnitude.
Tailored approach to study Legionella infection using a lattice light sheet microscope (LLSM)
Authors: Yi Xiyu , Miao Haichao , Lo Jacky Kai-yin , Elsheikh Maher M. , Lee Tek-Hyung , Jiang Chenfanfu , Zhang Yuliang , Segelke Brent W. , Overton K. Wesley , Bremer Peer-Timo , Laurence Ted A.
Published: May 2022

Legionella is a genus of ubiquitous environmental pathogens found in freshwater systems, moist soil, and composted materials. More than four decades of Legionella research has provided important insights into Legionella pathogenesis. Although standard commercial microscopes have led to significant advances in understanding Legionella pathogenesis, great potential exists in the deployment of more advanced imaging techniques to provide additional insights. The lattice light sheet microscope (LLSM) is a recently developed microscope for 4D live cell imaging with high resolution and minimum photo-damage. We built a LLSM with an improved version for the optical layout with two path-stretching mirror sets and a novel reconfigurable galvanometer scanner (RGS) module to improve the reproducibility and reliability of the alignment and maintenance of the LLSM. We commissioned this LLSM to study Legionella pneumophila infection with a tailored workflow designed over instrumentation, experiments, and data processing methods. Our results indicate that Legionella pneumophila infection is correlated with a series of morphological signatures such as smoothness, migration pattern and polarity both statistically and dynamically. Our work demonstrates the benefits of using LLSM for studying long-term questions in bacterial infection. Our free-for-use modifications and workflow designs on the use of LLSM system contributes to the adoption and promotion of the state-of-the-art LLSM technology for both academic and commercial applications.