bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft Genome Sequence of the Plant Growth Promoter and Biocontrol Agent Bacillus velezensis Strain BIB0110
Authors: Carvalho Isabela de , Apaza-Castillo Gladys Angélica , Paz Isabel Cristina Padula , Guimarães Alexandre Martins , Quecine Maria Carolina , Bonatelli Maria L.
Published: May 2023

Here, we report the draft genome sequence of
Bacillus velezensis
strain BIB0110, a broad-range biocontrol agent isolated from cultivated eucalyptus in Brazil. The genome has a size of 4.19 Mbp, with a GC content of 45.87%, and it was assembled into 32 scaffolds.
Complete Genome Sequences of the Species Type Strains Sinorhizobium garamanticum LMG 24692 and Sinorhizobium numidicum LMG 27395 and CIP 109850
Authors: Kaur Sabhjeet , Espinosa-Sáiz Daniel , Velázquez Encarna , Menéndez Esther , diCenzo George C.
Published: May 2023

The genus
Sinorhizobium
comprises rhizobia that fix nitrogen in symbiosis with legumes. To support taxonomic studies of this genus and of rhizobia more broadly, we report complete genome sequences and annotations for the species type strains
Sinorhizobium garamanticum
LMG 24692 and
Sinorhizobium numidicum
LMG 27395 and CIP 109850.
No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community
Authors: Ritchie Gordon , Leung Victor , Himsworth Chelsea G. , Byers Kaylee A. , Lee Lisa K. F. , Chorlton Samuel D. , Stefanovic Aleksandra , Romney Marc G. , Matic Nancy , Lowe Christopher F.
Published: May 2023

This article describes a novel molecular method to show relatedness between bacterial infections, which may not be able to grow in the laboratory due to treatment with antibiotics or for bacteria requiring unique conditions to grow well. Uniquely, we applied this technique to
Shigella
isolates from human cases associated with a local cluster in an underserved community, as well as rat samples from the same community.
Clinical influence of exercise therapy on sarcopenia in patients with chronic pancreatitis: a study protocol for a randomised controlled trial
Authors: Yoh Kazunori , Nishikawa Hiroki , Enomoto Hirayuki , Iwata Yoshinori , Ishii Akio , Yuri Yukihisa , Ishii Noriko , Miyamoto Yuho , Hasegawa Kunihiro , Nakano Chikage , Takata Ryo , Nishimura Takashi , Aizawa Nobuhiro , Sakai Yoshiyuki , Ikeda Naoto , Takashima Tomoyuki , Iijima Hiroko , Nishiguchi Shuhei
Published: May 2023

Introduction and purpose

Chronic pancreatitis (CP) involves progressive inflammatory changes to the pancreas and can lead to permanent structural damage and impairment of both endocrine and exocrine functions. Current reports highlight a rise in the incidence and prevalence of CP. However, there is limited data currently available concerning patients with CP undergoing exercise therapy (ET). We aim to prospectively examine the influence of ET on sarcopenia in patients with CP.

Methods and analysis

A detailed evaluation of the nutritional condition and the daily physical activities of each participant will be conducted prior to entering the study. Our patients will be randomly allocated to either: (1) the ET group or (2) the control group. In the ET group, our patients with CP will receive nutritional guidance once a month. The patients with CP will also be instructed to perform exercises with >3 metabolic equivalents (mets; energy consumption in physical activities/resting metabolic rate) for 60 min/day and to perform exercises >23 mets/week. The primary end point will be an improvement in sarcopenia, defined as an increase in muscle mass and muscle strength, at 3 months postrandomisation. A comparison of the amelioration of sarcopenia in the two groups will be undertaken.

Ethics and dissemination

The Institutional Review Board at Hyogo College of Medicine approved this study protocol (approval no. 2766). Final data will be publicly announced. A report releasing the study results will be submitted for publication to an appropriate journal.

Trial registration number

UMIN000029263; Pre-results. No patient is registered at the submission of our manuscript.
HiatoGast 1: an exploring, semiblinded trial establishing a new endoscopical categorisation of axial hiatal hernias
Authors: Eckhardt Daniel , Engel Matthias A , Golcher Henriette , Krautz Christian , Grützmann Robert , Elshafei Moustafa
Published: May 2023

Introduction

Axial hiatal hernias are a common incidental finding in endoscopical examinations, but reflux symptoms do not necessarily correspond to the presence of hiatal hernias. Diagnosing a reflux disease is difficult due to a leak of existing distinct criteria, especially in order to evaluate a surgical indication. Also a preoperative measurement of the hernia is necessary to choose between surgical options.

Methods and analysis

We planned a semiblinded trial including a questionnaire and an oesophagogastroduodenoscopy afterwards. While the endoscopy is done, the hiatus oesophagi should be measured in inversion technique under maximum insufflation including length, width and herniated volume. A sample of 210 participants until December 2020 is determined to evaluate the primary endpoint: we look forward to evaluate the anatomical parameters of reflux and non-reflux participants.

Ethics and Dissemination

The study has been approved by the local ethics committee on 12th February 2019, the data will bei published after closure of inclusion.

Trial registration number

German Clinical Trials Register (DRKS00016863).
Evaluation of hospital readmission rates as a quality metric in adult cardiac surgery
Authors: Ebrahimian Shayan , Bakhtiyar Syed Shahyan , Verma Arjun , Williamson Catherine , Sakowitz Sara , Ali Konmal , Chervu Nikhil L , Sanaiha Yas , Benharash Peyman
Published: May 2023

Objective

To assess the reliability of 30-day non-elective readmissions as a quality metric for adult cardiac surgery.

Background

Unplanned readmissions is a quality metric for adult cardiac surgery. However, its reliability in benchmarking hospitals remains under-explored.

Methods

Adults undergoing elective isolated coronary artery bypass grafting (CABG), surgical aortic valve replacement/repair (SAVR) or mitral valve replacement/repair (MVR) were tabulated from 2019 Nationwide Readmissions Database. Multi-level regressions were developed to model the likelihood of 30-day unplanned readmissions and major adverse events (MAE). Random intercepts were estimated, and associations between hospital-specific risk-adjusted rates of readmissions and were assessed using the Pearson correlation coefficient (r).

Results

Of an estimated 86 024 patients meeting study criteria across 298 hospitals, 62.6% underwent CABG, 22.5% SAVR and 14.9% MVR. Unadjusted readmission rates following CABG, SAVR and MVR were 8.4%, 9.3% and 11.8%, respectively. Unadjusted MAE rates following CABG, SAVR and MVR were 35.1%, 32.3% and 37.0%, respectively. Following adjustment, interhospital differences accounted for 4.1% of explained variance in readmissions for CABG, 7.6% for SAVR and 10.0% for MVR. There was no association between readmission rates for CABG and SAVR (r=0.10, p=0.09) or SAVR and MVR (r=0.09, p=0.1). A weak association was noted between readmission rates for CABG and MVR (r=0.20, p<0.001). There was no significant association between readmission and MAE for CABG (r=0.06, p=0.2), SAVR (r=0.04, p=0.4) and MVR (r=−0.03, p=0.6).

Conclusion

Our findings suggest that readmissions following adult cardiac surgery may not be an ideal quality measure as hospital factors do not appear to influence this outcome.
Cell surface marker-based capture of neoantigen-reactive CD8+T-cell receptors from metastatic tumor digests
Authors: Chatani Praveen D , Lowery Frank J , Parikh Neilesh B , Hitscherich Kyle J , Yossef Rami , Hill Victoria , Gartner Jared J , Paria Biman , Florentin Maria , Ray Satyajit , Bera Alakesh , Parkhust Maria , Robbins Paul , Krishna Sri , Rosenberg Steven A
Published: May 2023

Background

Cellular immunotherapies using autologous tumor-infiltrating lymphocytes (TIL) can induce durable regression of epithelial cancers in selected patients with treatment-refractory metastatic disease. As the genetic engineering of T cells with tumor-reactive T-cell receptors (TCRs) comes to the forefront of clinical investigation, the rapid, scalable, and cost-effective detection of patient-specific neoantigen-reactive TIL remains a top priority.

Methods

We analyzed the single-cell transcriptomic states of 31 neoantigen-specific T-cell clonotypes to identify cell surface dysfunction markers that best identified the metastatic transcriptional states enriched with antitumor TIL. We developed an efficient method to capture neoantigen-reactive TCRs directly from resected human tumors based on cell surface co-expression of CD39, programmed cell death protein-1, and TIGIT dysfunction markers (CD8+TILTP).

Results

TILTPTCR isolation achieved a high degree of correlation with single-cell transcriptomic signatures that identify neoantigen-reactive TCRs, making it a cost-effective strategy using widely available resources. Reconstruction of additional TILTPTCRs from tumors identified known and novel antitumor TCRs, showing that at least 39.5% of TILTPTCRs are neoantigen-reactive or tumor-reactive. Despite their substantial enrichment for neoantigen-reactive TCR clonotypes, clonal dynamics of 24 unique antitumor TILTPclonotypes from four patients indicated that most in vitro expanded TILTPpopulations failed to demonstrate neoantigen reactivity, either by loss of neoantigen-reactive clones during TIL expansion, or through functional impairment during cognate neoantigen recognition.

Conclusions

While direct usage of in vitro-expanded CD8+TILTPas a source for cellular therapy might be precluded by profound TIL dysfunction, isolating TILTPrepresents a streamlined effective approach to rapidly identify neoantigen-reactive TCRs to design engineered cellular immunotherapies against cancer.
Individual responses to the implementation of mandatory fitness testing within a fire department
Authors: Martin Joel , Toczko Michael , Lockie Robert G
Published: May 2023

Objectives

To examine the effects of implementing a consequential fitness assessment (pull-ups, curl-ups, push-ups, 3 min step test) in a fire department on an individual level.

Methods

We used a repeated-measures design to analyse fitness assessment data from 2019 to 2020 in Northern Virginia. A total of 631 professional firefighters completed the fitness assessment in both years. Repeated measures analysis of variances (ANOVAs) and multiple regression modelling were used to examine the effects of the fitness assessment and factors associated with changes in fitness, respectively.

Results

Overall all aspects of fitness improved over the first year of implementation with a majority of firefighters improved on all components of the fitness assessment except for pull-ups (16.1% improved). Greater levels of baseline fitness and being female were negatively associated with changes in all fitness measures. Older firefighters had smaller changes in pull-up, curl-up and push-up performance.

Conclusions

During the first year of fitness assessment implementation, the fire department generally improved. The findings suggest that fire departments which enforce mandatory fitness assessments must establish policies for dealing with inadequate performance and offer resources to aid individual firefighters.
Real-world study of intranasal ketamine for use in patients with refractory chronic migraine: a retrospective analysis
Authors: Yuan Hsiangkuo , Natekar Aniket , Park Jade , Lauritsen Clinton G , Viscusi Eugene R , Marmura Michael J
Published: May 2023

Introduction

Subanesthetic ketamine infusion has been used for managing refractory headache in inpatient or outpatient infusion settings. Intranasal ketamine may be an alternative option for outpatient care.

Methods

A retrospective study was conducted at a single tertiary headache center to assess the clinical effectiveness and tolerability of intranasal ketamine in patients with refractory chronic migraine. Candidates who received intranasal ketamine between January 2019 and February 2020 were screened through an electronic medical record query. Manual chart reviews and structured telephone interviews were conducted on obtaining informed consent.

Results

Of 242 subjects screened, 169 (79.9% women) of median (IQR) age 44 (22) years were interviewed. They reported a median (IQR) of 30 (9) monthly headache days and tried 4 (1) classes of preventive medications. Overall, they used 6 (6) sprays per day, with a median (IQR) of spray use of 10 (11) days per month. Intranasal ketamine was reported as ‘very effective’ in 49.1% and the quality of life was considered ‘much better’ in 35.5%. At the time of the interview, 65.1% remained current intranasal ketamine users and 74.0% reported at least one adverse event.

Conclusion

In this descriptive study, intranasal ketamine served as an acute treatment for refractory chronic migraine by reducing headache intensity and improving quality of life with relatively tolerable adverse events. Most patients found intranasal ketamine effective and continued to use it despite these adverse events. Given the potential for overuse, it should be reserved for those clearly in need of more effective rescue treatment with appropriate safety precautions. Well-designed prospective placebo-controlled trials are necessary to demonstrate the efficacy and safety of intranasal ketamine in patients with migraine.
Clinical, radiological and pathological features of anti-MDA5 antibody-associated interstitial lung disease
Authors: Chen Xixia , Jiang Wei , Jin Qiwen , Peng Qinglin , Zhang Lu , Lin Sang , Lu Xin , Liu Min , Wang Yuli , Song Aiping , Feng Ruie , Wang Guochun
Published: May 2023

Introduction

To investigate the clinical, radiographic and pathological features of interstitial lung disease (ILD) in patients with anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis (anti-MDA5+DM).

Methods

We retrospectively analysed the medical records of patients with anti-MDA5+DM who had undergone radiological examination, and lung histopathology was performed on 17 of them.

Results

This study examined 329 patients with anti-MDA5+DM, of whom 308 (93.6%) were diagnosed with ILD and 177 (53.8%) exhibited rapidly progressive ILD (RPILD). The most common radiographic patterns were organising pneumonia (OP) (43.2%), non-specific interstitial pneumonia (NSIP) (26.4%) and NSIP+OP (18.5%). Histological analysis showed NSIP (41.2%) and NSIP+OP (47.1%) to be the predominant patterns. However, in the 17 patients who underwent lung histopathology, the coincidence rate between radiological and histopathological diagnoses was only 11.8%. Compared with patients without RPILD, those with RPILD showed a higher prevalence of NSIP+OP (26.6% vs 10.7%, p=0.001) and a lower prevalence of NSIP pattern (21.5% vs 37.4%, p=0.002) on high-resolution CT. Furthermore, patients with radiographic patterns of NSIP+OP or diffuse alveolar damage (DAD) had more risk factors for poor prognosis, with 12-month mortality rates of 45.9% and 100%, respectively.

Conclusions

RPILD was commonly observed in patients with anti-MDA5+DM. OP was identified as the predominant radiographic pattern, which corresponded to a histopathological pattern of NSIP or NSIP+OP. Notably, patients exhibiting radiographic patterns of NSIP+OP or DAD were shown to have a poor prognosis.
Variation in the supercooling points of laboratory-reared Canadian Dermacentor variabilis (Acari: Ixodidae)
Authors: Yunik Matthew E.M. , Dergousoff Shaun J. , Chilton Neil B.
Published: May 2023

The geographical range of the American dog tick, Dermacentor variabilis (Say, 1821) in Canada is expanding northwards into areas where ticks experience colder temperatures during winter. Understanding the ability of D. variabilis to cope with freezing temperatures is important for determining what limits the distributional range of this species. In this study, the supercooling point (SCP = the sub-zero temperature at which freezing occurs) was measured for 318 laboratory-reared D. variabilis individuals (109 nymphs and 209 adults). These ticks were reared from questing adult ticks collected from an area adjacent to Blackstrap Provincial Park in Saskatchewan, Canada. The results showed that there was no relationship between the SCP and body weight of adult ticks, and no difference in the SCP of female and male ticks. However, the mean SCP of nymphs (−23.6 °C) was significantly lower than that of adults (−21.6 °C). The biological significance of this finding needs to be explored further given that D. variabilis larvae and adults are the primary overwintering stages at northern latitudes.
Dynamical galactic effects induced by solitonic vortex structure in bosonic dark matter
Authors: Korshynska K. , Bidasyuk Y. M. , Gorbar E. V. , Jia Junji , Yakimenko A. I.
Published: May 2023

The nature of dark matter (DM) remains one of the unsolved mysteries of modern physics. An intriguing possibility is to assume that DM consists of ultralight bosonic particles in the Bose–Einstein condensate (BEC) state. We study stationary DM structures by using the system of the Gross–Pitaevskii and Poisson equations, including the effective temperature effect with parameters chosen to describe the Milky Way galaxy. We have investigated DM structure with BEC core and isothermal envelope. We compare the spherically symmetric and vortex core states, which allows us to analyze the impact of the core vorticity on the halo density, velocity distribution, and, therefore, its gravitational field. Gravitational field calculation is done in the gravitoelectromagnetism approach to include the impact of the core rotation, which induces a gravimagnetic field. As a result, the halo with a vortex core is characterized by smaller orbital velocity in the galactic disk region in comparison with the non-rotating halo. It is found that the core vorticity produces gravimagnetic perturbation of celestial body dynamics, which can modify the circular trajectories.
A compact accelerator driven neutron source at the Applied Nuclear Physics Laboratory, Lund University
Authors: Frost R. J. W. , Elfman M. , Fissum K. , Kristiansson P. , Mauritzson N. , Pallon J. , Pédehontaa-Hiaa G. , Perrey H. , Stenström K. E. , Sjöland A.
Published: May 2023

The Applied Nuclear Physics Group at Lund University has constructed a CANS (Compact Accelerator-driven Neutron Source). The CANS is based around a 3 MV, single-ended, Pelletron accelerator, which is used to impinge a 2.8 MeV deuterium beam into a beryllium target. The anticipated neutron production will be on the order of 1010 n/s in 4π sr, with future upgrades expected to increase neutron production to 1011 n/s. Neutron energy will be up to 9 MeV with peak emission at ∼5 MeV. Shielding and moderation will be provided by a large water tank surrounding the target, with exit ports to allow moderated neutrons to be directed to experiments. The thermal-neutron flux at the exit of the extraction ports is anticipated to be up to 106 n/cm2/s. The CANS will be used to forward the activities of the group in the area of neutron-activation analysis, in addition to a broader range of neutron related applications.
Numerical analysis of ferromagnetic Carreau fluid flow comprising viscos dissipation aspects
Authors: Hobiny A. , Tabrez M. , Khan W. A. , Hussain I.
Published: May 2023

Process of transportation of heat in ferrofluids has innumerable applications in the fields of electronics and automobile industry. By tracing the materials, the ferrofluid got popularity among researchers and engineers, also most ferrofluids are non-Newtonian in nature so here the non-Newtonian fluid is under consideration. In this study, the influences of viscous dissipation and magnetic parameter in the flow of ferromagnetic Carraeu fluid for a stretching surface are examined. Suitable similarity transformations in the system that consists of nonlinear form of Partial Differential Equations (PDEs) are transformed into a system of nonlinear form of ODEs, then the resulting Ordinary Differential Equations (ODEs) are resolved by use of a mathematical technique known as bvp4c. Effects of ferromagnetic interaction factor, Curie temperature, viscous dissipation and material parameter are examined for temperature profile as well as velocity fields. Moreover, the variations in velocity and thermal gradients are analyzed and described with the help of graphs. An upsurge in the values of magnetic interaction parameter and Weissenberg number causes a decline in the velocity field while the thermal gradient shows opposite behavior. It is detected that the temperature of Carreau fluid intensifies for larger [Formula: see text] and [Formula: see text].
Prompt-based for Low-Resource Tibetan Text Classification
Authors: An Bo
Published: May 2023

Text classification is a critical and foundational task in Tibetan natural language processing, it plays a crucial role in various applications, such as sentiment analysis and information extraction. However, the limited availability of annotated data poses a significant challenge to Tibetan natural language processing. This paper proposes a prompt learning-based method for low-resource Tibetan text classification to overcome this challenge. This method utilizes pre-trained language models to learn text representation and generation capabilities on a large-scale unsupervised Tibetan corpus, enabling few-shot Tibetan text classification. Experimental results demonstrate that the proposed method significantly improves the performance of Tibetan text classification in low-resource scenarios. This work provides a new research idea and method for low-resource language processing, such as Tibetan natural language processing. Hopefully, it will inspire subsequent work on low-resource language processing.
Medical Aid in Dying: New Frontiers in Medicine, Law, and Culture
Authors: Buchbinder Mara , Cain Cindy
Published: May 2023

Medical aid in dying (MAID) has been a productive target for social scientific inquiry at the intersections of law and medicine over the past two decades. Insofar as MAID crystallizes and reflects personal and cultural understandings of key concepts such as individualism, dependency, dignity, and care, it is a rich site for social scientific theorizing. This article reviews and assesses the contributions of social scientific perspectives to research on MAID. We propose that social scientific research on MAID offers four distinctive contributions: its descriptive (rather than normative) orientation, its focus on cultural meanings, its insights into processes of knowledge production, and its comparative lens. The article's major sections describe ( a) attitudes toward MAID, ( b) MAID-related social movements, ( c) legalization approaches, and ( d) lived experiences of MAID in permissive jurisdictions. We conclude by reflecting on how MAID scholarship can inform social inquiry into other areas in which law and medicine converge.
Regulating Government AI and the Challenge of Sociotechnical Design
Authors: Engstrom David Freeman , Haim Amit
Published: May 2023

Artificial intelligence (AI) is transforming how governments work, from distribution of public benefits, to identifying enforcement targets, to meting out sanctions. But given AI's twin capacity to cause and cure error, bias, and inequity, there is little consensus about how to regulate its use. This review advances debate by lifting up research at the intersection of computer science, organizational behavior, and law. First, pushing past the usual catalogs of algorithmic harms and benefits, we argue that what makes government AI most concerning is its steady advance into discretion-laden policy spaces where we have long tolerated less-than-full legal accountability. The challenge is how, but also whether, to fortify existing public law paradigms without hamstringing government or stymieing useful innovation. Second, we argue that sound regulation must connect emerging knowledge about internal agency practices in designing and implementing AI systems to longer-standing lessons about the limits of external legal constraints in inducing organizations to adopt desired practices. Meaningful accountability requires a more robust understanding of organizational behavior and law as AI permeates bureaucratic routines.
Comparing the Effectiveness of S-Ketamine Combined with Sufentanil versus Sufentanil Alone for Postoperative Pain Management in Elderly Patients Undergoing Laparoscopic Radical Resection of Gastrointestinal Cancer: A Randomized Controlled Trial
Authors: Wang Ji , Du Yu , Tan Yue-Shuang , Liu Yu , Wen Ai-Ping
Published: May 2023

Background. The optimal analgesic dose of S-ketamine after laparoscopic gastrointestinal malignancy surgery remains unclear. This study aimed to evaluate the effect of S-ketamine combined with sufentanil in patient-controlled intravenous analgesia (PCIA) on postoperative pain relief in elderly patients undergoing laparoscopic surgery for gastrointestinal tumors. Methods. Elderly patients undergoing laparoscopic radical resection of gastrointestinal cancer were randomly assigned to one of three postoperative analgesia groups: F group received 2 ug/kg sufentanil in PCIA, LSF group received 0.5 mg/kg S-ketamine and 1.5 ug/kg sufentanil, and SF group received 1 mg/kg S-ketamine and 1 ug/kg sufentanil. The PCIA also contained 0.15 mg/kg of butorphanol and 0.02 mg/kg of ramosetron. Study drugs were administered via PCIA for 48 hours postoperatively. The primary outcome was the accumulated parecoxib sodium requirements within 48 hours after surgery. Results. A total of 105 patients were randomized, and 95 completed the trial (F group: n = 32, LSF group: n = 32, and SF group: n = 31). The cumulative consumption of parecoxib sodium within 48 hours postoperatively was lower in the SF group compared to that in the F group (median difference: −40 mg; 95% confidence interval: −40 to 0;

P
=
0.0028

). The number of PCIA compressions within 48 hours after surgery was smaller in the SF group compared to that in the F group. NRS pain scores at 6 h and 12 h postoperatively were reduced in the SF group compared to that in the F group, both at rest and during movement. Compared to the F group, the incidence of postoperative mild depression was lower, the time to first flatus and time to first defecation were shorter, and the incidence of postoperative vomiting was lower in the SF group. The mechanical pain threshold, hyperalgesia area, and sedation scores were similar between the SF and F groups. No differences were observed in the abovementioned parameters between the LSF group and the F group. Conclusion. This trial demonstrated that 1.0 mg/kg S-ketamine combined with 1 ug/kg sufentanil in PCA decreased cumulative parecoxib sodium consumption within 48 hours after laparoscopic radical resection of gastrointestinal cancer in elderly patients.
Convergence Analysis of Two Parallel Methods for Common Variational Inclusion Problems Involving Demicontractive Mappings
Authors: Mouktonglang Thanasak , Poochinapan Kanyuta , Varnakovida Pariwate , Suparatulatorn Raweerote , Moonchai Sompop
Published: May 2023

The main objective of this article is to propose two novel parallel methods for solving common variational inclusion and common fixed point problems in a real Hilbert space. Strong convergence theorems of both methods are established by allowing for some mild conditions. Moreover, numerical studies of the signal recovery problem consisting of various blurred filters demonstrate the computational behavior of the proposed methods and other existing methods.
Focusing on scRNA-seq-Derived T Cell-Associated Genes to Identify Prognostic Signature and Immune Microenvironment Status in Low-Grade Glioma
Authors: Wen Jiayu , Huang Qiaoyi , Yao Jiuxiu , Wei Wei , Li Zehui , Zhang Huiqin , Chang Surui , Pei Hui , Cao Yu , Li Hao
Published: May 2023

Background. The clinical outcomes of low-grade glioma (LGG) are associated with T cell infiltration, but the specific contribution of heterogeneous T cell types remains unclear. Method. To study the different functions of T cells in LGG, we mapped the single-cell RNA sequencing results of 10 LGG samples to obtain T cell marker genes. In addition, bulk RNA data of 975 LGG samples were collected for model construction. Algorithms such as TIMER, CIBERSORT, QUANTISEQ, MCPCOUTER, XCELL, and EPIC were used to depict the tumor microenvironment landscape. Subsequently, three immunotherapy cohorts, PRJEB23709, GSE78820, and IMvigor210, were used to explore the efficacy of immunotherapy. Results. The Human Primary Cell Atlas was used as a reference dataset to identify each cell cluster; a total of 15 cell clusters were defined and cells in cluster 12 were defined as T cells. According to the distribution of T cell subsets (CD4+ T cell, CD8+ T cell, Naïve T cell, and Treg cell), we selected the differentially expressed genes. Among the CD4+ T cell subsets, we screened 3 T cell-related genes, and the rest were 28, 4, and 13, respectively. Subsequently, according to the T cell marker genes, we screened six genes for constructing the model, namely, RTN1, HERPUD1, MX1, SEC61G, HOPX, and CHI3L1. The ROC curve showed that the predictive ability of the prognostic model for 1, 3, and 5 years was 0.881, 0.817, and 0.749 in the TCGA cohort, respectively. In addition, we found that risk scores were positively correlated with immune infiltration and immune checkpoints. To this end, we obtained three immunotherapy cohorts to verify their predictive ability of immunotherapy effects and found that high-risk patients had better clinical effects of immunotherapy. Conclusion. This single-cell RNA sequencing combined with bulk RNA sequencing may elucidate the composition of the tumor microenvironment and pave the way for the treatment of low-grade gliomas.
Effects of Dietary Protein and Lipid Levels on Growth, Metabolism, Antioxidative Capacity, and Fillet Quality of Adult Triploid Rainbow Trout Farmed in Net Cage
Authors: Cao Songjing , Guan Lingling , Li Changzhong , Sun Guoliang , Tian Haining , Sun Ruijian , Tu Jun , Meng Yuqiong , Ma Rui
Published: May 2023

The research is aimed at investigating the effects of dietary protein and lipid levels on adult triploid rainbow trout growth performance, feed utilization, digestive and metabolic enzyme activities, antioxidative capacity, and fillet quality. Nine diets containing three dietary protein levels (DP) (300, 350, and 400 g kg-1) and three dietary lipid levels (DL) (200, 250, and 300 g kg-1) were prepared using a

3
×
3

factorial design. In freshwater cages, 13,500 adult female triploid rainbow trout (

3.2
±
0.1

 kg) were cultured for 77 days. Triplicate cages (500 fish per cage) were used as repetitions of each experimental diet. The findings revealed that as DP increased to 400 g kg-1 and DL raised to 300 g kg-1, the weight gain ratio (WGR) elevated significantly (

P
<
0.05

). However, when

DP
≥
350

 g kg-1, WGR was similar in the DL250 and DL300 groups. As DP raised to 350 g kg-1, the feed conversion ratio (FCR) notably decreased (

P
<
0.05

). In the DP350DL300 group, lipids had a protein-sparing impact. High DP diet (400 g kg-1) generally improved fish health status by increasing antioxidant capacity in the liver and intestine. A high DL diet (300 g kg-1) showed no harmful effect on hepatic health based on plasma levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) and antioxidant capacity in the liver. For fillet quality, a high DP diet could increase fillet yield, improve fillet hardness, springiness, and water-holding capacity values, and inhibit the production of off-flavors caused by n-6 fatty acids. A high DL diet could increase odor intensity, and EPA, DHA, and n-3 fatty acid concentrations decrease the thrombogenicity index value. The maximum fillet redness value was discovered in the DP400DL300 group. Overall, for adult triploid rainbow trout (≥3 kg), the minimum recommended DP and DL according to growth performance were 400 and 250 g kg-1, respectively; DP and DL based on feed utilization were 350 and 200 g kg-1, respectively; DP and DL based on fillet quality were 400 and 300 g kg-1, respectively.
Intelligent Path Planning for AGV-UAV Transportation in 6G Smart Warehouse
Authors: Guo Weiya , Li Shoulin
Published: May 2023

Recently, deep reinforcement learning (DRL) has attracted increasing interest in the field of intelligent navigation and path planning in smart warehousing. The latest imitation augmented DRL (IADRL) model has achieved good performance for the cooperative transportation tasks of automatic guided vehicles (AGVs) and unmanned aerial vehicles (UAVs). However, this model cannot always transport target cargoes with the optimized policy due to premature convergence. Therefore, we propose an intelligent path planning model for AGV-UAV transportation in this paper. The proposed model utilizes the proximal policy optimization with covariance matrix adaptation (PPO-CMA) in the imitation learning and DRL networks, which enables the AGV-UAV coalition to plan the optimal transportation route at a lower cost. Experiments conducted in simulation warehousing scenarios demonstrated the proposed model and improved the accumulated training reward by more than 10%, outperforming the existing state-of-the-art models in terms of effectiveness and efficiency.
The Requirement and Protective Effects of Dietary Protein against Chronic Ammonia Exposure in Juvenile Genetically Improved Farmed Tilapia (Oreochromis niloticus)
Authors: Lu Xing , Ji Zhe-Hui , Wang Mei-Zi , Tian Juan , Dong Li-Xue , Guo Zhong-Bao , Luo Yong-Ju , Wen Hua , Jiang Ming
Published: May 2023

Ammonia is a key risk factor in intensive aquaculture systems. This experiment is aimed at investigating the influence of dietary protein levels on genetically improved farmed tilapia (GIFT, Oreochromis niloticus) under chronic ammonia stress. GIFT juveniles of

4.00
±
0.55

 g were exposed to high ammonia level at 0.88 mg/L and fed with six diets comprising graded protein levels at 22.64%, 27.26%, 31.04%, 35.63%, 38.47%, and 42.66% for 8 weeks. The fish in negative control was fed the diet with 31.04% protein in normal water (0.02 mg ammonia/L water). Our results showed that high ammonia exposure (0.88 mg/L) caused significant decrease in fish growth performance, hematological parameters, liver antioxidant enzymes (catalase and glutathione peroxidase), and gill Na+- and K+-dependent adenosine triphosphatase (Na+/K+-ATP) activity. When fish were under high ammonia exposure, the weight gain rate, special growth rate, feed efficiency, and survival rate elevated significantly with dietary protein supplementation increase to 35.63%, whereas protein efficiency ratio, hepatosomatic index, and viscerosomatic index showed a decreased tendency. Dietary protein administration significantly enhanced crude protein but reduced crude lipid contents in the whole fish. Fish fed diets with 35.63%-42.66% protein had higher red blood cell counts and hematocrit percentage than fish fed 22.64% protein diet. The values of serum biochemical indices (lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase), hepatic antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase), and gill Na+/K+-ATP activity were all elevated with the increment of dietary protein. Moreover, histological analysis indicated that dietary protein administration could prevent the ammonia-induced damages in fish gill, kidney, and liver tissues. Based on weight gain rate as a response criterion, the optimal dietary protein requirement for GIFT juveniles under chronic ammonia stress was 37.9%.
Clinical and Functional Characterization of Novel AGL Variants in Two Families with Glycogen Storage Disease Type III
Authors: Yu Tingting , Fu Hao , Yang Aoyu , Liang Yan
Published: May 2023

Purpose. Glycogen storage disease type III (GSDIII) is a uncommon autosomal recessive inherited metabolic disorder, which is caused by variants in the AGL gene. The purpose of this study was to elucidate the clinical and functional features of two novel variants in two families with GSDIIIa. Methods. We collected the clinical and laboratory data of the two patients. Genetic testing was performed using GSDs gene panel sequencing, and the identified variants were classified according to the American College of Medical Genetics (ACMG) criteria. The pathogenicity of the novel variants was furthermore assessed through bioinformatics analysis and cellular functional validation experiments. Results. The two patients were hospitalized with abnormal liver function or hepatomegaly, which was characterized by remarkably elevated liver enzyme and muscle enzyme levels, as well as hepatomegaly, and were eventually diagnosed with GSDIIIa. Genetic analysis detected two novel variants of AGL gene in the two patients: c.1484A > G (p.Y495C), c.1981G > T (p.D661Y). Bioinformatics analysis indicated that the two novel missense mutations most likely altered the protein’s conformation and therefore made the enzyme it encodes less active. Based on the ACMG criteria, both variants were considered likely pathogenic, in accordance with the functional analysis results, which demonstrated that the mutated protein was still localized in the cytoplasm and that the glycogen content of cells transfected with the mutated AGL was increased compared to cells transfected with the wild-type one. Conclusion. These findings indicated that the two newly identified variants in the AGL gene (c.1484A > G; c.1981G > T) were undoubtedly pathogenic mutations, inducing a slight reduction in glycogen debranching enzyme activity and a mild increase in intracellular glycogen content. Two patients who visited us with abnormal liver function, or hepatomegaly, improved dramatically after treatment with oral uncooked cornstarch, but the effects on skeletal muscle and myocardium required further observation.
An Improved Adaptive Simulated Annealing Particle Swarm Optimization Algorithm for ARAIM Availability
Authors: Wang Ershen , Shi Xiaozhu , Deng Xidan , Gao Jing , Zhang Wei , Wang Huan , Xu Song
Published: May 2023

Civil aviation transportation equipment is more convenient and faster than other transportation tools and is an essential part of intelligent transportation. It is significant to study the reliability of positioning information and enhance traffic safety. Advanced receiver autonomous integrity monitoring (ARAIM) can provide vertical guidance during the different navigation stages in civil aviation fields. The traditional multiple hypothesis solution separation (MHSS) algorithm distributes the probability of hazardous misleading information (PHMI) and probability of false alarm (PFA) uniformly over all visible satellites resulting in reduced global availability of ARAIM. Aiming at this problem, we proposed an adaptive simulated annealing particle swarm optimization (ASAPSO) algorithm to redistribute integrity and continuity risks and establish a protection level optimization model. Based on the real BeiDou navigation satellite system/global positioning system (BDS/GPS) data, the experimental results show that the optimized algorithm can reduce the vertical protection level (VPL), and the ARAIM global availability of BDS/GPS is improved by 1.73%∼2.73%. The optimized algorithm can improve the availability of integrity monitoring at different stages of the navigation system and provide a basis for ensuring the reliability of the positioning results.
Supplementary Table S2 from Associations of Race and Ethnicity with Hepatocellular Carcinoma, Decompensation, and Mortality in US Veterans with Cirrhosis
Authors: VoPham Trang , Cravero Anne , Feld Lauren D. , Green Pamela , Feng Ziding , Berry Kristin , Kim Nicole J. , Vutien Philip , Mendoza Jason A. , Ioannou George N.
Published: May 2023

Supplementary Table S2. ICD-9 codes for type 2 diabetes mellitus, alcohol use disorders, hemochromatosis, primary biliary cirrhosis, primary sclerosing cholangitis, autoimmune hepatitis, human immunodeficiency virus, and low socioeconomic status
A Review of the Application of Spatial Survival Methods in Cancer Research: Trends, Modeling, and Visualization Techniques
Authors: Bizuayehu Habtamu Mellie , Cameron Jessica K. , Dasgupta Paramita , Baade Peter D.
Published: May 2023

Spatial modeling of cancer survival is an important tool for identifying geographic disparities and providing an evidence base for resource allocation. Many different approaches have attempted to understand how survival varies geographically. This is the first scoping review to describe different methods and visualization techniques and to assess temporal trends in publications. The review was carried out using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline using PubMed and Web of Science databases. Two authors independently screened articles. Articles were eligible for review if they measured cancer survival outcomes in small geographical areas by using spatial regression and/or mapping. Thirty-two articles were included, and the number increased over time. Most articles have been conducted in high-income countries using cancer registry databases. Eight different methods of modeling spatial survival were identified, and there were seven different ways of visualizing the results. Increasing the use of spatial modeling through enhanced data availability and knowledge sharing could help inform and motivate efforts to improve cancer outcomes and reduce excess deaths due to geographical inequalities. Efforts to improve the coverage and completeness of population-based cancer registries should continue to be a priority, in addition to encouraging the open sharing of relevant statistical programming syntax and international collaborations.
Supplementary Table 6 from ZEB1 is Regulated by K811 Acetylation to Promote Stability, NuRD Complex Interactions, EMT, and NSCLC Metastasis
Authors: Perez-Oquendo Mabel , Manshouri Roxsan , Tian Yanhua , Fradette Jared J. , Rodriguez B. Leticia , Kundu Samrat T. , Gibbons Don L.
Published: May 2023

Protein expression values of the immunoprecipitated samples
Supplementary Table 4 from ZEB1 is Regulated by K811 Acetylation to Promote Stability, NuRD Complex Interactions, EMT, and NSCLC Metastasis
Authors: Perez-Oquendo Mabel , Manshouri Roxsan , Tian Yanhua , Fradette Jared J. , Rodriguez B. Leticia , Kundu Samrat T. , Gibbons Don L.
Published: May 2023

qPCR Primer Sequences
Supplementary Figure S4 from Overlaid Transcriptional and Proteome Analyses Identify Mitotic Kinesins as Important Targets of Arylsulfonamide-Mediated RBM39 Degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Jürg , Abdel-Wahab Omar , Gillingham Dennis
Published: May 2023

Supplementary Figure S4
Supplementary Table 1 from ZEB1 is Regulated by K811 Acetylation to Promote Stability, NuRD Complex Interactions, EMT, and NSCLC Metastasis
Authors: Perez-Oquendo Mabel , Manshouri Roxsan , Tian Yanhua , Fradette Jared J. , Rodriguez B. Leticia , Kundu Samrat T. , Gibbons Don L.
Published: May 2023

Tandem-mass spectrometry (MS/MS) analysis on ZEB1 uncovered five novel post-translational modification.
Supplementary Data from Preclinical Evidence of an Allogeneic Dual CD20xCD22 CAR to Target a Broad Spectrum of Patients with B-cell Malignancies
Authors: Aranda-Orgilles Beatriz , Chion-Sotinel Isabelle , Skinner Jordan , Grudman Steven , Mumford Ben , Dixon Chantel , Postigo Fernandez Jorge , Erler Piril , Duchateau Phillipe , Gouble Agnes , Galetto Roman , Poirot Laurent
Published: May 2023

Supplementary Tables 1-4, supplementary Figures 1-10 and legends
Data from Preclinical Evidence of an Allogeneic Dual CD20xCD22 CAR to Target a Broad Spectrum of Patients with B-cell Malignancies
Authors: Aranda-Orgilles Beatriz , Chion-Sotinel Isabelle , Skinner Jordan , Grudman Steven , Mumford Ben , Dixon Chantel , Postigo Fernandez Jorge , Erler Piril , Duchateau Phillipe , Gouble Agnes , Galetto Roman , Poirot Laurent
Published: May 2023

Abstract
Despite the remarkable success of autologous chimeric antigen receptor (CAR) T cells, some patients relapse due to tumor antigen escape and low or uneven antigen expression, among other mechanisms. Therapeutic options after relapse are limited, emphasizing the need to optimize current approaches. In addition, there is a need to develop allogeneic “off-the-shelf” therapies from healthy donors that are readily available at the time of treatment decision and can overcome limitations of current autologous approaches. To address both challenges simultaneously, we generated a CD20xCD22 dual allogeneic CAR T cell. Herein, we demonstrate that allogeneic CD20x22 CAR T cells display robust, sustained and dose-dependent activity in vitro and in vivo, while efficiently targeting primary B-cell non–Hodgkin lymphoma (B-NHL) samples with heterogeneous levels of CD22 and CD20. Altogether, we provide preclinical proof-of-concept data for an allogeneic dual CAR T cell to overcome current mechanisms of resistance to CAR T-cell therapies in B-NHL, while providing a potential alternative to CD19 targeting.
Figure S1 from Targeting CHAF1B Enhances IFN Activity against Myeloproliferative Neoplasm Cells
Authors: Saleiro Diana , Kosciuczuk Ewa M. , Fischietti Mariafausta , Perez Ricardo E. , Yang G. Sohae , Eckerdt Frank , Beauchamp Elspeth M. , Hou Ye , Wang Qixuan , Weinberg Rona Singer , Fish Eleanor N. , Yue Feng , Hoffman Ronald , Platanias Leonidas C.
Published: May 2023

Biological processes in which putative ULK1-protein complexes are involved in the cytosol.
Supplementary Table S9 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

The discrimination performance in the two cohorts
Supplementary Figure S4 from Maternal embryonic leucine zipper kinase is associated with metastasis in triple-negative breast cancer
Authors: Xie Xuemei , Chauhan Gaurav B , Edupuganti Ramakrishna , Kogawa Takahiro , Park Jihyun , Tacam Moises J , Tan Alex W , Mughees Mohd , Vidhu Fnu , Liu Diane D , Taliaferro Juliana M. , Pitner Mary K , Browning Luke Samuel , Lee Ju-Hyeon , Shen Yu , Wang Jian , Ueno Naoto T. , Krishnamurthy Savitri , Hortobagyi Gabriel N. , Tripathy Debu , Van Laere Steven , Bartholomeusz Geoffrey , Dalby Kevin N. , Bartholomeusz Chandra
Published: May 2023

Supplementary Figure S4. Graphical representation of the physical protein-protein interaction network involved in modulating MELK activity in MDA-MB-231 cells.
Supplementary Table S7 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Multivariate analyses in stage II CRC patients
Supplementary Table S6 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Patient clinicopathologic characteristics in ACT and surgery only groups
Supplementary Table S3 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Uni- and multivariate analyses of DFS
Table S2 from Targeting fatty acid reprogramming suppresses CARM1-expressing ovarian cancer
Authors: Lombardi Simona , Goldman Aaron R , Tang Hsin-Yao , Kossenkov Andrew V , Liu Heng , Zhou Wei , Herlyn Meenhard , Lin Jianhuang , Zhang Rugang
Published: May 2023

Reverse Phase Protein Assay (RPPA) analysis in control and CARM1 knockout PEO4 cells.