cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Post-translational regulation of APOBEC3A in breast cancer
Creators: name: Collins, Christopher D.
Publisher: name: Washington State University
Year: 2024
Subjects: Cellular biology
APOBEC3A
APOBEC
Post-translational Regulation
Breast Cancer

description: Cancer is the 2nd leading cause of death in the US and is generally characterized by the accumulation of mutations that activate oncogenes or silence tumor suppressor genes. These mutations are the result of DNA damage with both endogenous and exogenous sources. Mutations that decrease the fidelity of DNA replication or repair machinery promote genome instability, which can promote further mutagenesis. This is especially problematic in tumors where accumulation of new mutations increases the heterogeneity, increasing the risk of clonal populations developing mechanisms for metastasis or evading therapies.
description: APOBEC mutations contribute significantly to mutagenesis in breast cancer, with APOBEC3A being identified as the primary source of these mutations. The research presented here attempts to further our understanding of how APOBEC3A is regulated in cells and how these mechanisms can become dysregulated in cancer. To do this we have investigated the role that post-translational modifications and protein interactions play in regulating APOBEC3A activity in breast cancer. Our inquiry led us to identify APOBEC3A Lys30 as a target for acetylation in a unique mechanism of regulation within the APOBEC3 subfamily, with inhibitory effects on mutagenic activity. We additionally identified proteins that likely play a role in this process, with data suggesting that both HAT1 and SIRT1 influence APOBEC3 activity in cells. Our investigation into APOBEC3A interactors uncovered the ubiquitin-proteasome system as a negative regulator of APOBEC3A transcription, although the mechanism by which this occurs is still largely uncharacterized. These findings not only offer new targets for early identification of APOBEC3A dysregulation in cancer patients, but we hope will also offer targets for the use of novel therapies.
Additional file 3 of Human periodontal ligament stem cell sheets activated by graphene oxide quantum dots repair periodontal bone defects by promoting mitochondrial dynamics dependent osteogenic differentiation
Creators: name: An, Na
name: Yan, Xiaoyuan
name: Qiu, Qiujing
name: Zhang, Zeying
name: Zhang, Xiyue
name: Zheng, Bowen
name: Zhao, Zhenjin
name: Guo, Jiajie
name: Liu, Yi
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: Science Policy
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 3: Figure S3. Biocompatibility evaluation in vivo.
Characterization and Development of Lateral Flow Assays for Automated Multi-step Processes and Point-of-care Cervical Cancer Detection
Creators: name: Newsham, Emilie I
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Medical devices
Industrial biotechnology diagnostics (incl. biosensors)
Medical biotechnology diagnostics (incl. biosensors)

description: Paper-fluidic devices are a popular platform for point-of-care diagnostics due to their low cost, ease of use, and equipment-free detection of target molecules. The most common example is the lateral flow assay, in which samples are added to a paper membrane and a colorimetric indicator provides a binary signal indicating whether the molecule of interest is present. A novel lateral flow assay was developed to detect a protein biomarker for early stage cervical cancer. Cervical cancer can be cured if detected and treated at an early stage, but approximately 90% of cervical cancer deaths occur in low and middle-income countries due to lack of accessible testing. Methods for detecting the biomarker, valosin-containing protein (VCP), were optimized using enzymatic and gold nanoparticle dot blots, then lateral flow assays were developed and validated using purified VCP and cervical cancer HeLa cells. Future validation with patient tissue samples will permit translation of this device to testing clinics in low-resource areas. Despite advantages for use in resource limited settings, lateral flow assays are limited by their inability to perform more complex or multi-step processes, such as nucleic acid amplification or enzymatic signal enhancement. Thermally actuated wax valves are one mechanism that provides complete control over fluid obstruction and release. To better understand how wax valves can be used in fully automated, self-contained lateral flow assays, different sizes and geometries of valves were tested to investigate their effects on actuation time, flow rate, and flow pattern. Another limitation in the understanding of lateral flow assays is the lack of experimental data describing the microscale flow within the pores of the paper membrane that drives the biophysical reactions in the assay. Mathematical models can be designed to explain macroscopic phenomena, but so far, no literature has compared microfluidic models to microfluidic data. To quantify microfluidic properties within lateral flow assays, fluorescent nanoparticles were imaged flowing through different areas of the membrane and their velocity was quantified using micro-particle image velocimetry (µPIV). Scanning electron microscope images were used to verify that this experimental model was reasonable for describing microfluidic properties of the lateral flow assay. Altogether, this document investigates how developing lateral flow assays for cervical cancer detection can save lives by improving the accessibility of an early diagnosis, and how more robust lateral flow assay characterization can expand their applicability to a broad range of detection processes.
Acceleration of PDE-based biological simulation through the development of neural network metamodels
Creators: name: Burzawa, Lukasz
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Knowledge representation and reasoning
Modelling and simulation

description: PDE models are a major tool used in quantitative modeling of biological and scientific phenomena. Their major shortcoming is the high computational complexity of solving each model. When scaling up to millions of simulations needed to find their optimal parameters we frequently have to wait days or weeks for results to come back. To cope with that we propose a neural network approach that can produce comparable results to a PDE model while being about 1000x faster. We quantitatively and qualitatively show the neural network metamodels are accurate and demonstrate their potential for multi-objective optimization in biology. We hope this approach can speed up scientific research and discovery in biology and beyond.
Rational design of an influenza-COVID-19 chimeric protective vaccine with S-RBD and HA-stalk
Creators: name: Li, Yulei
name: Liu, Peipei
name: Hao, Tianjiao
name: Liu, Sheng
name: Wang, Xi
name: Xie, Yufeng
name: Xu, Ke
name: Lei, Wenwen
name: Zhang, Cheng
name: Han, Pu
name: Li, Ying
name: Jin, Xiyue
name: Huan, Yu
name: Lu, Yafei
name: Zhang, Rong
name: Li, Xiaoyan
name: Zhao, Xin
name: Xu, Kun
name: Liao, Pu
name: Lu, Xuancheng
name: Bi, Yuhai
name: Song, Hao
name: Wu, Guizhen
name: Zhu, Baoli
name: Gao, George F.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Highly contagious respiratory illnesses like influenza and COVID-19 pose serious risks to public health. A two-in-one vaccine would be ideal to avoid multiple vaccinations for these diseases. Here, we generated a chimeric receptor binding domain of the spike protein (S-RBD) and hemagglutinin (HA)-stalk-based vaccine for both SARS-CoV-2 and influenza viruses. The S-RBD from SARS-CoV-2 Delta was fused to the headless HA from H1N1 (H1Delta), creating a chimera that forms trimers in solution. The cryo-electron microscopy structure of the chimeric protein complexed with the RBD-targeting CB6 and the HA-stalk-targeting CR9114 antibodies shows that the trimeric protein is stable and accessible for neutralizing antibody binding. Immunization with the vaccine elicited high and long-lasting neutralizing antibodies and effectively protected mice against the challenges of lethal H1N1 or heterosubtypic H5N8, as well as the SARS-CoV-2 Delta or Omicron BA.2 variants. Overall, this study offers a two-in-one universal vaccine design to combat infections caused by both SARS-CoV-2 variants of concern and influenza viruses.
sj-docx-1-jou-10.1177_14648849211036622 – Supplemental material for News media framing of social protests around racial tensions during the Donald Trump presidency
Creators: name: Ophir, Yotam
name: Forde, Devin K
name: Neurohr, Madison
name: Walter, Dror
name: Massignan, Virginia
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 200199 Communication and Media Studies not elsewhere classified
subject: FOS: Media and communications

description: Supplemental material, sj-docx-1-jou-10.1177_14648849211036622 for News media framing of social protests around racial tensions during the Donald Trump presidency by Yotam Ophir, Devin K Forde, Madison Neurohr, Dror Walter and Virginia Massignan in Journalism
Assessment of the Cepheid 3-gene Host Response Fingerstick Blood Test (MTB-HR) on rapid diagnosis of tuberculosis
Creators: name: Wu, Xiaocui
name: Tan, Guangkun
name: Ma, Jian
name: Yang, Juan
name: Guo, Yinjuan
name: Lu, Haiwen
name: Ke, Hui
name: Li, Mengran
name: Tang, Yi-Wei
name: Sha, Wei
name: Yu, Fangyou
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: The World Health Organization has identified high-priority target product profiles for new TB diagnostics which include rapid biomarker-based, non-sputum-based diagnostic testing, using an easily accessible sample. The Cepheid 3-gene Host Response Fingerstick Blood Prototype Test (MTB-HR) quantifies relative mRNA levels of a 3-gene signature (GBP5, DUSP3, and KLF2) from a whole-blood sample on the GeneXpert platform. The objective of the present study was to evaluate the performance of the MTB-HR to distinguish between active tuberculosis (ATB), latent Mycobacterium tuberculosis infection (LTBI), other pulmonary diseases, and healthy volunteers at a tertiary care centre. Among 653 participants enrolled in this study, 192 were diagnosed as having ATB, and the remaining 461 were classified as non-ATB, including 137 cases of LTBI, 224 cases of other pulmonary diseases, and 100 healthy volunteers. The corresponding AUCs of the MTB-HR in distinguishing untreated ATB from non-ATB, LTBI, other pulmonary diseases, and healthy volunteers were 0.814 (95% CI, 0.760-0.868, sensitivity 76.1%, specificity 71.6%), 0.739 (95% CI, 0.667-0.812, sensitivity 59.7%, specificity 78.1%), 0.825 (95% CI, 0.770-0.880, sensitivity 82.1%, specificity 65.6%), 0.892 (95% CI, 0.839-0.945, sensitivity 76.1%, specificity 88.0%), respectively. When only samples with TAT of less than 1 h were included, the AUC of the MTB-HR in distinguishing untreated ATB from non-ATB was largest, 0.920 (95% CI, 0.822-1.000, sensitivity 81.3%, specificity 87.7%). In conclusion, the MTB-HR assay shows potential as a rapid, blood-based screening and triage test for ATB, especially for untreated ATB, with the advantage of increased diagnostic yield since blood is more readily available.
Impact of the Northern Fowl Mite on Laying Hen Production and Welfare Beginning at 17 Weeks of Age
Creators: name: Jarrett, Rachel A
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Animal management

description: The northern fowl mite (Ornithonyssus sylviarum) is an obligate blood-feeding ectoparasite of poultry that can cause decreased egg production, profit loss, anemia, irritation to flocks and personnel, and death to hens in extreme cases. This study aimed to investigate the effects of the northern fowl mite (NFM) on laying hen performance and welfare quality beginning at 17 weeks of age. Two flocks (Trials 1 and 2) involved 800 Tetra Brown hens (n=200 per room) housed in four cage-free rooms at the Purdue University Poultry Unit. Two rooms were infested with NFM and two rooms served as controls. In Trial 1, initial NFM infestation occurred at 24 weeks on 2% (4 hens) in each of the NFM rooms. Because NFM populations were scarce, a second infestation on 2% of hens occurred at 35 weeks. A final attempt to infest with NFM occurred at 41 weeks with all hens in NFM rooms being infested. In Trial 2, initial NFM infestation occurred at 24 weeks on 2% (4 hens) in each of the NFM rooms and a second infestation took place on 2% of hens at 30 weeks of age to boost the NFM population. Egg production and mortality were recorded daily and case weights were recorded weekly. Monthly Welfare Quality® assessments were taken, as well as monthly mite counts on all birds beginning at 28 weeks. Mite checks were conducted periodically on 25% (50 hens) in all rooms between weeks 25 and 38. Data were analyzed in SAS® using the GLM procedure and an ANCOVA and all significant statistical differences were reported at P < 0.05. Proportion of hens with a mite infestation was treated as the covariate. In Trial 1, regardless of treatment, mortality increased dramatically after 21 weeks, leading to a loss of 473 hens by period 7. NFM hen-day production percentage (HD) was approximately 2% lower than the Tetra management guide and control HD was 7% higher than the Tetra management guide. In Trial 1, treatment had an effect on HD, case weights, and feather damage on the belly (P < 0.05). Proportion of hens infested with mites had an effect on percent shell and feather damage on the belly. Cannibalism and pecking in Trial 1 led to extreme feather loss, high mortality, and negatively impacted production parameters. Feather loss and high mortality contributed to the low NFM populations. In Trial 2, percent livability remained high (approximately 97% for both groups) and HD remained slightly lower than the Tetra management guide (9% and 8% lower for control and NFM), respectively. In Trial 2, treatment had an effect on eggs per hen housed, mortality, feather damage on the head and neck, and skin lesions (P < 0.05). Proportion of birds infested with mites had an effect on feather damage on the back, crop, head, and neck (P < 0.05).
Black Hole Shadows Modelling in Extended gravity: Rotation Accounting and coupled effects
Creators: name: Alexeyev, Stanislav
name: Zenin, Oleg
name: Baiderin, Artem
Publisher: name: arXiv
Year: 2025
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Using an improved version of the Newman-Janis algorithm, we obtain metrics of rotating black holes for a set of extended gravity theories that extend general relativity in different ways: the Horndeski model, the bumblebee model, the Gauss-Bonnet scalar gravity, the loop quantum gravity, the conformal gravity, and $f(Q)$ (symmetric teleparallel gravity STEGR). The obtained metrics are used to model black hole shadows. It is shown that for some models the critical values of the angular momentum $a_{crit}$ emerge. The previous conclusion that the extended gravity theory corrects by itself the effects of rotation in both directions is confirmed. This appears to be important for further modelling of shadow profiles taking into account the constantly increasing accuracy of black hole images. Thus, when rotation is taken into account black hole shadow images, as the GW170817 test or the post-Newtonian formalism, can serve as a meaningful way to test and constrain extended theories of gravity.
description: 14 pages, 4 figures
Stratigraphy, distribution, and geochemistry of the Newberry Volcano tephras
Creators: name: Kuehn, Stephen Christopher
Publisher: name: Washington State University
Year: 2002
Subjects: Volcanic ash, tuff, etc. -- Oregon -- Newberry Volcano
Newberry Volcano (Or.)

description: Newberry volcano has a long history of silicic pyroclastic volcanism and has produced many extensive tephra deposits. During the last approximately 550.000 years, the volcano has erupted at least 60 rhyolitic and dacitic tephras. These record a range of eruptive styles including plinian. sub-plinian. pyroclastic flows, and pyroclastic surges and both dry and phreatomagmatic activity. Tephra dispersal from individual eruptions ranges from very limited (i.e. small pumice rings a few hundred meters to a kilometer in extent) to extensive (i.e. plinian airfall deposits which have been recognized several hundred kilometers downwind). The most recent plinian eruption, the approximately 1250-1450 year old Newberry Pumice, produced an eruption column which reached a height of -25 km and was dispersed by unusually high velocity winds. Some Pleistocene eruptions, including tephra 9822B, may have sent pyroclastic material to heights of 40 km or more. Several deposits including Evans Well, 9822B. Qat/Qbt, 995B, and Qtae are compositionally heterogeneous and probably record the mixing of magmas before or during eruption. The similarity coefficient and discriminant function analysis have been used to compare electron microprobe determined glass compositions for proximal Newberry tephra deposits and distal ash layers. Newberry Pumice correlates to six distal locations in Oregon and Idaho. Paulina Creek, Ice Quarry, 9912D. 9920C. 984F, 984G5. 9917C, and 9881C correlate to ash layers at Summer Lake, Oregon. Paulina Creek tephra also correlates to several locations in northern California and is the source of the Olema ash bed. Tephra 9917C is highly similar to Pringle Falls tephras K and D. Lava Pass tephra correlates to a distal ash preserved at a depth of 142 m in the Knolls core in the Bonneville basin, Utah. A coarse 0.6 m thick deposit of Wono tephra has been located on the northwest flank of Newberry volcano. The large number of eruptions and established tephra correlations suggest that additional correlations of Newberry tephra are likely to be made to distal sites, both studied and yet to be studied. The volcano's extensive eruptive history and relatively recent activity also indicate that future large ash and pumice producing eruptions are likely.
SaeR as a novel target for antivirulence therapy against Staphylococcus aureus
Creators: name: Gao, Peng
name: Wei, Yuanxin
name: Hou, Suying
name: Lai, Pok-Man
name: Liu, Han
name: Tai, Sherlock Shing Chiu
name: Tang, Victor Yat Man
name: Prakash, Pradeep Halebeedu
name: Sze, Kong-Hung
name: Chen, Jonathan Hon Kwan
name: Sun, Hongzhe
name: Li, Xuechen
name: Kao, Richard Yi-Tsun
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Staphylococcus aureus is a major human pathogen responsible for a wide range of clinical infections. SaeRS is one of the two-component systems in S. aureus that modulate multiple virulence factors. Although SaeR is required for S. aureus to develop an infection, inhibitors have not been reported. Using an in vivo knockdown method, we demonstrated that SaeR is targetable for the discovery of antivirulence agent. HR3744 was discovered through a high-throughput screening utilizing a GFP-Lux dual reporter system driven by saeP1 promoter. The antivirulence efficacy of HR3744 was tested using Western blot, Quantitative Polymerase Chain Reaction, leucotoxicity, and haemolysis tests. In electrophoresis mobility shift assay, HR3744 inhibited SaeR-DNA probe binding. WaterLOGSY-NMR test showed HR3744 directly interacted with SaeR’s DNA-binding domain. When SaeR was deleted, HR3744 lost its antivirulence property, validating the target specificity. Virtual docking and mutagenesis were used to confirm the target’s specificity. When Glu159 was changed to Asn, the bacteria developed resistance to HR3744. A structure–activity relationship study revealed that a molecule with a slight modification did not inhibit SaeR, indicating the selectivity of HR3744. Interestingly, we found that SAV13, an analogue of HR3744, was four times more potent than HR3744 and demonstrated identical antivirulence properties and target specificity. In a mouse bacteraemia model, both HR3744 and SAV13 exhibited in vivo effectiveness. Collectively, we identified the first SaeR inhibitor, which exhibited in vitro and in vivo antivirulence properties, and proved that SaeR could be a novel target for developing antivirulence drugs against S. aureus infections.
CD1d facilitates African swine fever virus entry into the host cells via clathrin-mediated endocytosis
Creators: name: Chen, Xin
name: Zheng, Jun
name: Liu, Chuanxia
name: Li, Tingting
name: Wang, Xiao
name: Li, Xuewen
name: Bao, Miaofei
name: Li, Jiangnan
name: Huang, Li
name: Zhang, Zhaoxia
name: Bu, Zhigao
name: Weng, Changjiang
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: African swine fever (ASF) is a highly contagious and acute hemorrhagic viral disease with high morbidity and mortality in domestic pigs and wild boars. The disease has become a global threat to the pig production industry and has caused enormous economic losses in many countries in recent years. However, the molecular mechanism underlying ASF virus (ASFV) entry of the host cells is not fully understood, which restricts the development of vaccines and antiviral-drugs of ASFV. In this study, we found that the host protein CD1d acts as a host factor, which mediates ASFV entry into the host cells. As the main capsid protein on the surface of ASFV virions, p72 can mediate viral entry. Using IP-MS assay, CD1d was identified as a binding partner of p72 on surface of ASFV virions. Knockdown of CD1d expression and blocking the cells with anti-pCD1d antibody, or incubating ASFV virions with soluble CD1d protein could significantly inhibit ASFV infection. CD1d is located on the membrane surface of primary porcine alveolar macrophages (PAMs) and mediates the virus entry via binding to p72. CD1d knockout or CD1d knockdown assay showed that CD1d could facilitate ASFV virions internalization via clathrin-mediated endocytosis (CME). Furthermore, CD1d interacts with EPS15 to mediate ASFV entry via clathrin-mediated endocytosis. Overall, our findings revealed that CD1d is a novel host-entry factor involved in ASFV internalization via the EPS15-clathrin endocytosis axis and a potential target for antiviral intervention.
sj-pdf-1-ctj-10.1177_17407745211014493 – Supplemental material for Joint testing of overall and simple effects for the two-by-two factorialtrial design
Creators: name: Leifer, Eric S
name: Troendle, James F
name: Kolecki, Alexis
name: Follmann, Dean A
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
subject: FOS: Clinical medicine
subject: 160807 Sociological Methodology and Research Methods
subject: FOS: Sociology

description: Supplemental material, sj-pdf-1-ctj-10.1177_17407745211014493 for Joint testing of overall and simple effects for the two-by-two factorialtrial design by Eric S Leifer, James F Troendle, Alexis Kolecki and Dean A Follmann in Clinical Trials
Additional file 1 of Novel histotypes of sporadic Creutzfeldt–Jakob disease linked to 129MV genotype
Creators: name: Cracco, Laura
name: Puoti, Gianfranco
name: Cornacchia, Antonio
name: Glisic, Katie
name: Lee, Seong‑Ki
name: Wang, Zerui
name: Cohen, Mark L.
name: Appleby, Brian S.
name: Cali, Ignazio
Publisher: name: figshare
Year: 2024
Subjects: subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 1: Supplementary Materials. Table S1. Age at onset, disease duration, information on western blot (WB) analysis, histotypic and clinical determination in sCJDMV cases examined in this study. Table S2. Histopathological features of sCJD MV1 and MV1-2. Table S3. Lesion profiles statistical significance. Table S4. Histopathological features of sCJDMV2-1. Table S5. resPrPSc type prevalence. Table S6. Distribution of resPrPSc T1 and T2 in the brain of sCJDMV2-1.
SaeR as a Novel Target for Antivirulence Therapy against Staphylococcus aureus
Creators: name: Gao, Peng
name: Wei, Yuanxin
name: Hou, Suying
name: Lai, Pok-Man
name: Liu, Han
name: Tai, Sherlock Shing Chiu
name: Tang, Victor Yat Man
name: Prakash, Pradeep Halebeedu
name: Sze, Kong-Hung
name: Chen, Jonathan Hon Kwan
name: Sun, Hongzhe
name: Li, Xuechen
name: Kao, Richard Yi-Tsun
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Staphylococcus aureus is a major human pathogen responsible for a wide range of clinical infections. SaeRS is one of the two-component systems in S. aureus that modulate multiple virulence factors. Although SaeR is required for S. aureus to develop an infection, inhibitors have not been reported. Using an in vivo knockdown method, we demonstrated that SaeR is targetable for the discovery of antivirulence agent. HR3744 was discovered through a high-throughput screening utilising a GFP-Lux dual reporter system driven by saeP1 promoter. ,. The antivirulence efficacy of HR3744 was tested using Western blot, Quantitative Polymerase Chain Reaction, leucotoxicity, and hemolysis tests. In electrophoresis mobility shift assay, HR3744 inhibited SaeR-DNA probe binding. WaterLOGSY-NMR test showed HR3744 directly interacted with SaeR's DNA-binding domain When saeR was deleted, HR3744 lost its antivirulence property, validating the target specificity. Virtual docking and mutagenesis were used to confirm the target's specificity. When Glu159 was changed to Asn, the bacteria developed resistance to HR3744. A structure-activity relationship study revealed that a molecule with a slight modification did not inhibit SaeR, indicating the selectivity of HR3744. Interestingly, we found that SAV13, an analogue of HR3744, was four-times more potent than the HR3744 and demonstrated identical antivirulence property and target specificity. In a mouse bacteraemia model, both HR3744 and SAV13 exhibited in vivo effectiveness. Collectively, we identified the first SaeR inhibitor, which exhibited in vitro and in vivo antivirulence property, and proved that SaeR could be a novel target for developing antivirulence drugs against S. aureus infections.
sj-docx-1-jom-10.1177_01492063211029701 – Supplemental material for Founders’ Prior Shared International Experience, Time to First Foreign Market Entry, and New Venture Performance
Creators: name: Criaco, Giuseppe
name: Naldi, Lucia
name: Zahra, Shaker A.
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 150310 Organisation and Management Theory
subject: FOS: Economics and business

description: Supplemental material, sj-docx-1-jom-10.1177_01492063211029701 for Founders’ Prior Shared International Experience, Time to First Foreign Market Entry, and New Venture Performance by Giuseppe Criaco, Lucia Naldi and Shaker A. Zahra in Journal of Management
Solo Diners' Motives, Preferences, and Behavioral Intentions in Restaurant Dining
Creators: name: Her, EunSol
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Food and hospitality services
Hospitality management

description: Driven by a growth of single-person households and individualized lifestyles, solo dining in restaurants is an increasingly recognizable trend. However, little is known about solo diners’ motives and preferences in on- and off-premises restaurant dining and the subsequent behavioral intentions. In order to enhance the understanding of solo diners’ motives, preferences, and behavioral intentions in restaurant dining, this dissertation proposed and completed three studies related to solo (vs. group) diners’ menu-decision making process, solo (vs. group) diners’ service mode-decision making process, and a restaurant scale development for solo diner friendliness. Specifically, Study 1 examined the effect of dining social context (solo vs. group) on healthy or indulgent menu item decisions using self-control dilemmas and temporal construal theory as a theoretical framework. Findings revealed that solo diners showed less preferences for indulgent menu items because of a more utilitarian (i.e., less hedonic) consumption orientation than group diners, and that solo diners showed more preferences for healthy menu items than group diners when the menu included nutrition information such as calories, fat, and sodium. Study 2 examined the effect of dining social context (solo vs. group) on off-site over on-site dining intentions based on three mediators and the moderating role of self-determination using the self-determination theory. Findings revealed that, in the self-determined condition, solo diners showed more preferences for off-premises dining than group diners via greater convenience-seeking and polychronicity-seeking tendencies and lower anticipated enjoyment of on-premises dining. In the context-determined condition, solo diners showed more preferences for off-premises dining than group diners only via polychronicity-seeking and anticipated enjoyment of on-premises dining, and the effects were smaller. Lastly, Study 3 developed and validated a Solo Diner Friendliness (SoDF) scale that measured restaurant menu and service dimensions important for solo diners’ enjoyment as well as restaurant revisit intentions. The SoDF scale provided nine items under three factors, namely, Inconspicuousness, Proper Service, and Healthy Menu Items, that are valid and reliable measurements for future research and restaurant operators. Altogether, this dissertation offered theoretical and practical implications regarding how solo diners differed from group diners on various motivational and behavioral perspectives in on- and off-premises restaurant dining.
sj-pdf-1-cre-10.1177_02692155211035539 – Supplemental material for Exercise therapy for sarcopenia in rheumatoid arthritis: A meta-analysis and meta-regression of randomized controlled trials
Creators: name: Liao, Chun-De
name: Chen, Hung-Chou
name: Huang, Shih-Wei
name: Liou, Tsan-Hon
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 110904 Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: 110314 Orthopaedics
subject: 110604 Sports Medicine
subject: FOS: Health sciences

description: Supplemental material, sj-pdf-1-cre-10.1177_02692155211035539 for Exercise therapy for sarcopenia in rheumatoid arthritis: A meta-analysis and meta-regression of randomized controlled trials by Chun-De Liao, Hung-Chou Chen, Shih-Wei Huang and Tsan-Hon Liou in Clinical Rehabilitation
The spectrum of opportunistic infections and malignancies among women on antiretroviral therapy in Ethiopia
Creators: name: Getaneh, Yimam
name: Getnet, Fentabil
name: Rashid, Abdur
name: Kang, Li
name: Chu, Qingfei
name: Li, Sisi
name: Yi, Feng
name: Shao, Yiming
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Background: Women are disproportionally affected by HIV and are at greater risk of OIs and malignancies. This study investigated the spectrum of OIs and malignancies among women living with HIV (WLHIV) in Ethiopia. Methods: A retrospective longitudinal study was conducted among 3,817 WLHIV on Antiretroviral Treatment (ART) from 2007 to 2019 in Ethiopia. Data on OIs, malignancies, and clinical characteristics were retrieved from medical records. Prevalence, incidence, and mortality rates were measured over 13 years of follow-up. The Kaplan-Meier survival curve and multivariable Cox-proportional hazard regression were used to estimate incidence and identify predictors of OIs and malignancies, respectively. Result: The pooled prevalence of OIs or malignancies was 47%. OIs accounted for 39% and malignancies were 23.3%. The incidence of OIs and malignancies were 19.4 (95%CI:9.2-29.5) and 11.5 (95%CI:2.2-20.8) per 100 person-years of observation, respectively. Incidence of candidiasis was 14.1 per 100 person-years followed by Lymphoma (11.9), Cervical Cancer (11.5), and TB (10.9). The risk of OIs was higher in patients with baseline CD4 count ≤500 cells/mm3 [AHR (95%CI): 2.0 (1.8-2.3)] and VL>1000 copies/ml [AHR (95%CI): 1.5 (1.1-1.9)]. Overall, 24.6% died, and of them, 62.2% had a history of OIs or malignancies. The risk of death was higher among WLHIV with a history of Toxoplasmosis, TB and PCP. Conclusion: OIs and malignancies was recently increasing and two-thirds of all deaths were associated with these co-morbidities. The high rates of OIs and malignancies were attributed to poor treatment outcomes. The finding calls to enhance the diagnosis and treatment of these co-morbidities. AIDS: acquired immune deficiency syndrome; CI: confidence interval; EPHI: Ethiopian Public Health Institute; HAART: highly active antiretroviral therapy; HIV: human immunodeficiency virus; HR: hazard ratio; Mg/dl: milligram per deciliter; TB: tuberculosis; PCP: pneumocystis carinii pneumonia; ZJU: Zhejiang University
AIR-MIST SPRAY MODEL DEVELOPMENT IN STEEL SECONDARY COOLING PROCESS
Creators: name: Salazar, Edwin A Mosquera
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Mechanical engineering not elsewhere classified
Aerospace engineering not elsewhere classified

description: Continuous casting is an important process to transform molten metal into solid. Arrays of spray nozzles are used along the process to remove heat from the slab letting it solidify. Efficient and uniform heat removal without slab cracking is desired during steel continuous casting, and air-mist sprays could help to achieve this goal.Air-mist nozzles are one of the important keys for determining the quality of steel as well as energy consumption for pumping the water. Based on industrial data, it is estimated that a 1% reduction in scrapped production due to casting related defects can result in annual savings of 40.53 million dollars in the U.S. Computational simulations studies can minimize defects in steel such as cracks, inclusions, macro-segregations, porosity, and others, which are closely related to the heat transfer between water droplets and hot slab surface.
Conducting multiple spray experiments in order to find optimum operating conditions might be impractical and expensive in some cases. Thus, Computational Fluid Dynamics (CFD) simulation is aimed to be used for simulating the air-mist spray process. Because it is a challenging process due to strong air and water interaction, then numerical models have been developed to simulate water droplets. The first model involves air and water phases which then are transformed in single-phase water droplets. To do so, a Volume of Fraction (VOF) to the Discrete Phase Model (DPM) is used.

VOF-TO-DPM transition model involves the primary and secondary breakup which occurs in the water atomization process, starting with a single water core, followed by a smaller compact mass of water known as lumps or ligaments due to the interaction of air, and finally converted into water droplets.The second model is using the Nukiyama-Tanasawa function size distribution which injects water droplets based on defined size range and velocity profile. A validation of droplet size and velocity against experimental data has been accomplished. The models can avoid acquiring expensive equipment in order to understand nozzle spray performance, and droplets generated. Quality, water droplet velocity, size, energy, and water consumption are the core of the current study. Last but not least, the methodology for this model can be used in any other air-mist nozzle design.
Determining the N-representability of a reduced density matrix via unitary evolution and stochastic sampling
Creators: name: Massaccesi, Gustavo. E.
name: Oña, Ofelia. B.
name: Capuzzi, Pablo
name: Melo, Juan I.
name: Lain, Luis
name: Torre, Alicia
name: Peralta, Juan E.
name: Alcoba, Diego R.
name: Scuseria, Gustavo E.
Publisher: name: arXiv
Year: 2025
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The N-representability problem consists in determining whether, for a given p-body matrix, there exists at least one N-body density matrix from which the p-body matrix can be obtained by contraction, that is, if the given matrix is a p-body reduced density matrix (p-RDM). The knowledge of all necessary and sufficient conditions for a p-body matrix to be N-representable allows the constrained minimization of a many-body Hamiltonian expectation value with respect to the p-body density matrix and, thus, the determination of its exact ground state. However, the number of constraints that complete the N-representability conditions grows exponentially with system size, and hence the procedure quickly becomes intractable in practice. This work introduces a hybrid quantum-stochastic algorithm to effectively replace the N-representability conditions. The algorithm consists of applying to an initial N-body density matrix a sequence of unitary evolution operators constructed from a stochastic process that successively approaches the reduced state of the density matrix on a p-body subsystem, represented by a p-RDM, to a target p-body matrix, potentially a p-RDM. The generators of the evolution operators follow the adaptive derivative-assembled pseudo-Trotter method (ADAPT), while the stochastic component is implemented using a simulated annealing process. The resulting algorithm is independent of any underlying Hamiltonian, and it can be used to decide if a given p-body matrix is N-representable, establishing a criterion to determine its quality and correcting it. We apply this hybrid ADAPT algorithm to alleged reduced density matrices from a quantum chemistry electronic Hamiltonian, the reduced BCS model with constant pairing, and the Heisenberg XXZ spin model. In all cases, the proposed method behaves as expected for 1-RDMs and 2-RDMs, evolving the initial matrices towards different targets.
Infection and tissue distribution of highly pathogenic avian influenza A type H5N1 (clade 2.3.4.4b) in red fox kits (Vulpes vulpes)
Creators: name: Cronk, Brittany D.
name: Caserta, Leonardo Cardia
name: Laverack, Melissa
name: Gerdes, Rhea S.
name: Hynes, Kevin
name: Hopf, Cynthia R.
name: Fadden, Melissa A.
name: Nakagun, Shotaro
name: Schuler, Krysten L.
name: Buckles, Elizabeth L.
name: Lejeune, Manigandan
name: Diel, Diego G.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Avian influenza H5N1 is a highly pathogenic virus that primarily affects birds. However, it can also infect other animal species, including mammals. We report the infection of nine juvenile red foxes (Vulpes vulpes) with Highly Pathogenic Avian Influenza A type H5N1 (Clade 2.3.4.4b) in the spring of 2022 in the central, western, and northern regions of New York, USA. The foxes displayed neurologic signs, and examination of brain and lung tissue revealed lesions, with brain lesions ranging from moderate to severe meningoencephalitis. Analysis of tissue tropism using RT-PCR methods showed a comparatively lower Ct value in the brain, which was confirmed by in situ hybridization targeting Influenza A RNA. The viral RNA labelling was highly clustered and overlapped the brain lesions, observed in neurons, and grey matter. Whole viral genome sequences obtained from the affected foxes were subjected to phylogenetic and mutation analysis to determine influenza A clade, host specificity, and potential occurrence of viral reassortment. Infections in red foxes likely occurred due to preying on infected wild birds and are unlikely due to transmission between foxes or other mammals.
sj-docx-1-aut-10.1177_13623613211035936 – Supplemental material for COVID-19, social isolation and the mental health of autistic people and their families: A qualitative study
Creators: name: Pellicano, Elizabeth
name: Brett, Simon
name: den Houting, Jacquiline
name: Heyworth, Melanie
name: Magiati, Iliana
name: Steward, Robyn
name: Urbanowicz, Anna
name: Stears, Marc
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology
subject: 110319 Psychiatry (incl. Psychotherapy)
subject: FOS: Clinical medicine
subject: 111799 Public Health and Health Services not elsewhere classified
subject: FOS: Health sciences
subject: Education
subject: 130312 Special Education and Disability
subject: FOS: Educational sciences

description: Supplemental material, sj-docx-1-aut-10.1177_13623613211035936 for COVID-19, social isolation and the mental health of autistic people and their families: A qualitative study by Elizabeth Pellicano, Simon Brett, Jacquiline den Houting, Melanie Heyworth, Iliana Magiati, Robyn Steward, Anna Urbanowicz and Marc Stears in Autism
Spectrum of opportunistic infections and malignancies among women on Antiretroviral Therapy in Ethiopia
Creators: name: Getaneh, Yimam
name: Getnet, Fentabil
name: Rashid, Abdur
name: Kang, Li
name: Chu, Qingfei
name: Li, Sisi
name: Yi, Feng
name: Shao, Yiming
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Opportunistic infections (OIs) and malignancies are the major causes of morbidity and mortality among people living with HIV. Women are disproportionally affected by HIV and are at greater risk of OIs and malignancies. Despite advances in HIV diagnosis and treatment, prevalence, incidence and mortality associated with OIs and malignancies remains high. This study investigated the spectrum of OIs and malignancies among women living with HIV (WLHIV) in Ethiopia. A retrospective longitudinal study was conducted among 3,817 WLHIV on Antiretroviral Treatment (ART) from 2007 to 2019 in Ethiopia. Data on OIs, malignancies, and clinical and demographic characteristics were retrieved from medical records using abstraction tools between March and May 2020. Prevalence, incidence, and mortality rates were measured over 13 years of follow-up among WLHIV who initiated ART in 2007. The Kaplan-Meier survival curve and multivariable Cox-proportional hazard regression were used to estimate incidence and identify predictors of OIs and malignancies, respectively. The pooled prevalence of OIs or malignancies was 47% (95%CI:40.8-53.2). Briefly, OIs accounted for 39% and malignancies were 23.3%. The incidence of OIs and malignancies were 19.4 [95%CI = 9.2-29.5] and 11.5 [2.2-20.8] per 100 person-years of observation, respectively. Disaggregated by types, the incidence of oral candidiasis was 14.1 per 100 person-years followed by Lymphoma (11.9), Cervical Cancer (11.5), and TB (10.9). The risk of OIs was higher in patients with baseline CD4 count ≤500 cells/mm3 [AHR (95%CI): 2.0 (1.8-2.3)] and VL > 1000 copies/ml [AHR (95%CI): 1.5 (1.1-1.9)]. Over the 13-year follow-up, 24.6% died, and of them, 62.2% had a history of OIs or malignancies. The risk of death was higher among WLHIV with a history of Toxoplasmosis [AHR (95%CI):2.2(1.3-3.4)], TB [AHR (95%CI):2.1(1.7-2.6)] and PCP [AHR (95%CI):1.4(1.2-2.3)]. The burden of OIs and malignancies among WLHIV was recently increasing and two-thirds of all deaths were associated with these co-morbidities. The high rates of OIs and malignancies were attributed to poor treatment outcomes. The finding calls to enhance the diagnosis and treatment of these co-morbidities particularly TB, Toxoplasmosis, and cervical cancer during the clinical management.
Additional file 1 of Predicting moose behaviors from tri-axial accelerometer data using a supervised classification algorithm
Creators: name: Kirchner, Theresa M.
name: Devineau, Olivier
name: Chimienti, Marianna
name: Thompson, Daniel P.
name: Crouse, John
name: Evans, Alina L.
name: Zimmermann, Barbara
name: Eriksen, Ane
Publisher: name: figshare
Year: 2024
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Details on individual moose included in the study. Table S2. Ethogram used to record observations of captive moose including sample sizes and durations of all behaviors and grouping of behaviors to label accelerometer data intervals. Table S3. Variable importance of the random forest model. Importance of all predictor variables of the random forest model used to predict moose behavior from 3-s intervals of animal-borne accelerometer data. Table S4. Summary of the individual classification performance of the random forest model in predicting behavior from accelerometer data for each of the 14 moose in the study. Tables S5–S18. Confusion matrixes for the 14 moose. Values in columns represent the number of 3-s accelerometer data intervals predicted for each of the seven behaviors, split into rows based on the behavioral labels of the intervals recorded during the observations. Recall and precision quantify the classification performance of the model for each behavior of each individual. Prevalence indicates the contribution of each behavior to the total sample size of accelerometer data intervals for the respective individual.
sj-docx-1-cnr-10.1177_10547738211035456 for A Heideggerian Phenomenological Study of the Lived Experiences of Ghanaian Patients Living With End-Stage Renal Disease
Creators: name: Manookian, Arpi
name: Dehghan Nayeri, Nahid
name: Yakubu, Nicholas Danzima
name: Tabari, Fariba
name: Buunaaim, Alexis Dun Bo-Ib
name: Afoko, Vivian
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 111099 Nursing not elsewhere classified
subject: FOS: Health sciences

description: sj-docx-1-cnr-10.1177_10547738211035456 for A Heideggerian Phenomenological Study of the Lived Experiences of Ghanaian Patients Living With End-Stage Renal Disease by Arpi Manookian, Nahid Dehghan Nayeri, Nicholas Danzima Yakubu, Fariba Tabari, Alexis Dun Bo-Ib Buunaaim and Vivian Afoko in Clinical Nursing Research