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Article ; Online: Experiences of oncology researchers in the Veterans Health Administration during the COVID-19 pandemic.

Becker, Daniel J / Csehak, Kenneth / Barbaro, Alexander M / Roman, Stefanie D / Loeb, Stacy / Makarov, Danil V / Sherman, Scott / Lim, Sahnah

PloS one

2024 Volume 19, Issue 1, Page(s) e0290785

Abstract: The Veterans Health Administration is chartered "to serve as the primary backup for any health care services needed…in the event of war or national emergency" according to a 1982 Congressional Act. This mission was invoked during the COVID-19 pandemic to ...

Abstract	The Veterans Health Administration is chartered "to serve as the primary backup for any health care services needed…in the event of war or national emergency" according to a 1982 Congressional Act. This mission was invoked during the COVID-19 pandemic to divert clinical and research resources. We used an electronic mixed-methods questionnaire constructed using the Theoretical Domains Framework (TDF) and the Capability, Opportunity, and Motivation (COM-B) model for behavior change to study the effects of the pandemic on VHA researchers. The questionnaire was distributed electronically to 118 cancer researchers participating in national VHA collaborations. The questionnaire received 42 responses (36%). Only 36% did not feel that their research focus changed during the pandemic. Only 26% reported prior experience with infectious disease research, and 74% agreed that they gained new research skills. When asked to describe helpful support structures, 29% mentioned local supervisors, mentors, and research staff, 15% cited larger VHA organizations and 18% mentioned remote work. Lack of timely communication and remote work, particularly for individuals with caregiving responsibilities, were limiting factors. Fewer than half felt professionally rewarded for pursuing research related to COVID. This study demonstrated the tremendous effects of the COVID-19 pandemic on research activities of VHA investigators. We identified perceptions of insufficient recognition and lack of professional advancement related to pandemic-era research, yet most reported gaining new research skills. Individualizing the structure of remote work and ensuring clear and timely team communication represent high yield areas for improvement.
MeSH term(s)	Humans ; COVID-19/epidemiology ; Pandemics ; Veterans Health ; Research Personnel ; Medical Oncology
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0290785
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: FACTORS INFLUENCING THE TREATMENT OUTCOME OF INTENTIONAL REPLANTATION ON TEETH WITH PERIAPICAL PERIODONTITIS: A SYSTEMATIC REVIEW AND META-ANALYSIS.

Ong, Teng Kai / Lim, Daniel / Singh, Maharaj / Fial, Alissa V

The journal of evidence-based dental practice

2022 Volume 22, Issue 4, Page(s) 101722

Abstract: Objectives: The purpose of this review was to appraise the quality of evidence of the existing publications on IR, and to perform a meta-analysis on the treatment outcomes of IR.: Methods: The specific PIO questions were as follows: Population: ... ...

Abstract	Objectives: The purpose of this review was to appraise the quality of evidence of the existing publications on IR, and to perform a meta-analysis on the treatment outcomes of IR. Methods: The specific PIO questions were as follows: Population: Patients with periapical periodontitis either before or after non-surgical endodontic therapy. Intervention: IR performed with retrograde preparation and retrograde filling. Outcomes: the healing, treatment complications, and the factors influencing these outcomes after IR. Electronic and hand searches were performed in the Web of Science, PubMed, CINAHL, and Cochrane Library databases. Two authors independently screened the titles and abstracts for eligibility. The risk of bias was performed using the NIH Quality Assessment Tool, and each study was rated as "Good", "Fair" or "Poor". The analyses were performed on the treatment outcome (healing and complications), and the factors influencing the outcome of the procedure. Results: Fourteen articles were included in the qualitative and quantitative syntheses. One was a prospective cohort study, and the other 13 were retrospective cohort studies. Overall, the evidence of this review was of poor-to-fair quality. The pooled healing rate was 80.2%, and there was a 21.7% of complication rate. Longer follow-up period, the presence of perio-endo disease, the use of non-bioceramic material as retrograde filling, longer extraoral time, and maxillary molar were found to be associated with lower healing rates. However, the differences between the subgroups were not statistically significant. Conclusions: The present review showed IR yielded a good overall healing rate with a low complication rate. Taking the quality of evidence into account, more high-quality studies are required to evaluate the validity of the factors that may influence the treatment outcome of IR.
Language	English
Publishing date	2022-03-21
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2056058-8
ISSN	1532-3390 ; 1532-3382
ISSN (online)	1532-3390
ISSN	1532-3382
DOI	10.1016/j.jebdp.2022.101722
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Article: Developing Bioprospecting Strategies for Bioplastics Through the Large-Scale Mining of Microbial Genomes.

Vuong, Paton / Lim, Daniel J / Murphy, Daniel V / Wise, Michael J / Whiteley, Andrew S / Kaur, Parwinder

Frontiers in microbiology

2021 Volume 12, Page(s) 697309

Abstract: The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global ... ...

Abstract	The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global phylogenetic and ecological distribution of potential PHA producing bacteria and archaea was carried out by mining a global genome repository for PHA synthase (PhaC), a key enzyme involved in PHA biosynthesis. Bacteria from the phylum Actinobacteria were found to contain the PhaC Class II genotype which produces medium-chain length PHAs, a physiology until now only found within a few
Language	English
Publishing date	2021-07-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.697309
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Article ; Online: Adjunctive fixation of the humeral epicondyle in a lateral condylar fracture model: Ex vivo comparison of pins and plates with a novel composite (AdhFix).

Quinn, Robert J / Höglund, Odd V / Hutchinson, Daniel J / Opande, Lola / Lim, Edward / Birgersson, Ulrik / Granskog, Viktor / Malkoch, Michael

Veterinary surgery : VS

2023 Volume 53, Issue 2, Page(s) 311–319

Abstract: Objective: To compare the biomechanical properties of using a novel composite construct (AdhFix) to an interfragmentary Kirschner wire or a reconstruction plate as adjunctive epicondylar stabilization in simulated lateral unicondylar humeral fractures.!# ...

Abstract	Objective: To compare the biomechanical properties of using a novel composite construct (AdhFix) to an interfragmentary Kirschner wire or a reconstruction plate as adjunctive epicondylar stabilization in simulated lateral unicondylar humeral fractures. Study design: Cadaveric biomechanical assessment. Sample population: Paired humeri harvested from skeletally mature dogs (14-41 kg), nine cadavers per group. Methods: Simulated lateral unicondylar humeral fractures were stabilized with a transcondylar 4.5 mm cortical screw placed in lag fashion. Adjunct fixations consisting of a novel composite incorporating 2.7 mm cortical screws on one side, and either a 2.7 mm reconstruction plate or a 1.6 mm Kirschner wire on the contralateral side, were tested within paired humeri. Repaired humeri were axially loaded to failure and construct stiffness, yield load, and ultimate load were obtained from the load-deformation curves. Results: In pairwise comparison, yield load was significantly higher for AdhFix group compared to the pin group, p = .016. No statistical significance was seen in the comparison between AdhFix group and the plate group, p = .25. Conclusion: Adhfix was mechanically superior to K-wires, and comparable to plate fixation, for adjunctive fixation in a lateral humeral condylar model. Our results support further investigation of the novel composite for adjunct fracture fixation in lateral humeral condylar fractures. Clinical significance: The novel composite tested may be a viable alternative for adjunct fixation of humeral condylar fractures, a technique that circumvents plate contouring.
MeSH term(s)	Humans ; Animals ; Dogs ; Fracture Fixation, Internal/veterinary ; Fracture Fixation, Internal/methods ; Biomechanical Phenomena ; Humeral Fractures/surgery ; Humeral Fractures/veterinary ; Bone Nails/veterinary ; Bone Plates/veterinary ; Humerus/surgery ; Cadaver ; Dog Diseases
Language	English
Publishing date	2023-11-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491071-8
ISSN	1532-950X ; 0161-3499
ISSN (online)	1532-950X
ISSN	0161-3499
DOI	10.1111/vsu.14048
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Article ; Online: Contrastive learning-based pretraining improves representation and transferability of diabetic retinopathy classification models.

Alam, Minhaj Nur / Yamashita, Rikiya / Ramesh, Vignav / Prabhune, Tejas / Lim, Jennifer I / Chan, R V P / Hallak, Joelle / Leng, Theodore / Rubin, Daniel

Scientific reports

2023 Volume 13, Issue 1, Page(s) 6047

Abstract: Diabetic retinopathy (DR) is a major cause of vision impairment in diabetic patients worldwide. Due to its prevalence, early clinical diagnosis is essential to improve treatment management of DR patients. Despite recent demonstration of successful ... ...

Abstract	Diabetic retinopathy (DR) is a major cause of vision impairment in diabetic patients worldwide. Due to its prevalence, early clinical diagnosis is essential to improve treatment management of DR patients. Despite recent demonstration of successful machine learning (ML) models for automated DR detection, there is a significant clinical need for robust models that can be trained with smaller cohorts of dataset and still perform with high diagnostic accuracy in independent clinical datasets (i.e., high model generalizability). Towards this need, we have developed a self-supervised contrastive learning (CL) based pipeline for classification of referable vs non-referable DR. Self-supervised CL based pretraining allows enhanced data representation, therefore, the development of robust and generalized deep learning (DL) models, even with small, labeled datasets. We have integrated a neural style transfer (NST) augmentation in the CL pipeline to produce models with better representations and initializations for the detection of DR in color fundus images. We compare our CL pretrained model performance with two state of the art baseline models pretrained with Imagenet weights. We further investigate the model performance with reduced labeled training data (down to 10 percent) to test the robustness of the model when trained with small, labeled datasets. The model is trained and validated on the EyePACS dataset and tested independently on clinical datasets from the University of Illinois, Chicago (UIC). Compared to baseline models, our CL pretrained FundusNet model had higher area under the receiver operating characteristics (ROC) curve (AUC) (CI) values (0.91 (0.898 to 0.930) vs 0.80 (0.783 to 0.820) and 0.83 (0.801 to 0.853) on UIC data). At 10 percent labeled training data, the FundusNet AUC was 0.81 (0.78 to 0.84) vs 0.58 (0.56 to 0.64) and 0.63 (0.60 to 0.66) in baseline models, when tested on the UIC dataset. CL based pretraining with NST significantly improves DL classification performance, helps the model generalize well (transferable from EyePACS to UIC data), and allows training with small, annotated datasets, therefore reducing ground truth annotation burden of the clinicians.
MeSH term(s)	Humans ; Diabetic Retinopathy/diagnosis ; Neural Networks, Computer ; Algorithms ; Machine Learning ; Fundus Oculi ; Diabetes Mellitus
Language	English
Publishing date	2023-04-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-33365-y
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Article ; Online: Genomic epidemiology and transmission dynamics of recurrent Clostridioides difficile infection in Western Australia.

Knight, Daniel R / Imwattana, Korakrit / Collins, Deirdre A / Lim, Su-Chen / Hong, Stacey / Putsathit, Papanin / Riley, Thomas V

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

2023 Volume 42, Issue 5, Page(s) 607–619

Abstract: Recurrent cases of Clostridioides difficile infection (rCDI) remain one of the most common and serious challenges faced in the management of CDI. The accurate distinction between a relapse (caused by infection with the same strain) and reinfection ( ... ...

Abstract	Recurrent cases of Clostridioides difficile infection (rCDI) remain one of the most common and serious challenges faced in the management of CDI. The accurate distinction between a relapse (caused by infection with the same strain) and reinfection (caused by a new strain) has implications for infection control and prevention, and patient therapy. Here, we used whole-genome sequencing to investigate the epidemiology of 94 C. difficile isolates from 38 patients with rCDI in Western Australia. The C. difficile strain population comprised 13 sequence types (STs) led by ST2 (PCR ribotype (RT) 014, 36.2%), ST8 (RT002, 19.1%) and ST34 (RT056, 11.7%). Among 38 patients, core genome SNP (cgSNP) typing found 27 strains (71%) from initial and recurring cases differed by ≤ 2 cgSNPs, suggesting a likely relapse of infection with the initial strain, while eight strains differed by ≥ 3 cgSNPs, suggesting reinfection. Almost half of patients with CDI relapse confirmed by WGS suffered episodes that occurred outside the widely used 8-week cut-off for defining rCDI. Several putative strain transmission events between epidemiologically unrelated patients were identified. Isolates of STs 2 and 34 from rCDI cases and environmental sources shared a recent evolutionary history, suggesting a possible common community reservoir. For some rCDI episodes caused by STs 2 and 231, within-host strain diversity was observed, characterised by loss/gain of moxifloxacin resistance. Genomics improves discrimination of relapse from reinfection and identifies putative strain transmission events among patients with rCDI. Current definitions of relapse and reinfection based on the timing of recurrence need to be reconsidered.
MeSH term(s)	Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Western Australia/epidemiology ; Reinfection ; Clostridioides difficile/genetics ; Recurrence ; Clostridium Infections/drug therapy ; Clostridium Infections/epidemiology ; Clostridium Infections/microbiology ; Genomics
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-03-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	603155-9
ISSN	1435-4373 ; 0934-9723 ; 0722-2211
ISSN (online)	1435-4373
ISSN	0934-9723 ; 0722-2211
DOI	10.1007/s10096-023-04569-x
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Article ; Online: Elucidation of independently modulated genes in

Hirose, Yujiro / Poudel, Saugat / Sastry, Anand V / Rychel, Kevin / Lamoureux, Cameron R / Szubin, Richard / Zielinski, Daniel C / Lim, Hyun Gyu / Menon, Nitasha D / Bergsten, Helena / Uchiyama, Satoshi / Hanada, Tomoki / Kawabata, Shigetada / Palsson, Bernhard O / Nizet, Victor

mSystems

2023 Volume 8, Issue 3, Page(s) e0024723

Abstract: Streptococcus ... ...

Abstract	Streptococcus pyogenes
MeSH term(s)	Humans ; Streptococcus pyogenes/genetics ; Bacterial Proteins/genetics ; Virulence/genetics ; Toxins, Biological/metabolism ; Transcriptome
Chemical Substances	Bacterial Proteins ; Toxins, Biological
Language	English
Publishing date	2023-06-06
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00247-23
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Article ; Online: Caveolin-3 is required for regulation of transient outward potassium current by angiotensin II in mouse atrial myocytes.

Tyan, Leonid / Turner, Daniel / Komp, Karlie R / Medvedev, Roman Y / Lim, Evi / Glukhov, Alexey V

American journal of physiology. Heart and circulatory physiology

2021 Volume 320, Issue 2, Page(s) H787–H797

Abstract: Angiotensin II (AngII) is a key mediator of the renin-angiotensin system and plays an important role in the regulation of cardiac electrophysiology by affecting various cardiac ion currents, including transient outward potassium current, ...

Abstract	Angiotensin II (AngII) is a key mediator of the renin-angiotensin system and plays an important role in the regulation of cardiac electrophysiology by affecting various cardiac ion currents, including transient outward potassium current,
MeSH term(s)	Angiotensin II/pharmacology ; Animals ; Caveolin 3/deficiency ; Caveolin 3/genetics ; Caveolin 3/metabolism ; Female ; Heart Atria/drug effects ; Heart Atria/metabolism ; Male ; Membrane Potentials ; Mice, Inbred C57BL ; Mice, Knockout ; Myocytes, Cardiac/drug effects ; Myocytes, Cardiac/metabolism ; Potassium/metabolism ; Protein Kinase C/metabolism ; Receptor, Angiotensin, Type 1/agonists ; Receptor, Angiotensin, Type 1/metabolism ; Shal Potassium Channels/metabolism ; Mice
Chemical Substances	Cav3 protein, mouse ; Caveolin 3 ; Kcnd2 protein, mouse ; Kcnd3 protein, mouse ; Receptor, Angiotensin, Type 1 ; Shal Potassium Channels ; Angiotensin II (11128-99-7) ; Protein Kinase C (EC 2.7.11.13) ; Potassium (RWP5GA015D)
Language	English
Publishing date	2021-01-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	603838-4
ISSN	1522-1539 ; 0363-6135
ISSN (online)	1522-1539
ISSN	0363-6135
DOI	10.1152/ajpheart.00569.2020
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Article ; Online: Helicity and Polarization Gradient Optical Trapping in Evanescent Fields.

Lu, Jinsheng / Ginis, Vincent / Lim, Soon Wei Daniel / Capasso, Federico

Physical review letters

2023 Volume 131, Issue 14, Page(s) 143803

Abstract: Optical traps using nonconservative forces instead of conservative intensity-gradient forces expand the trap parameter space. Existing traps with nonconservative helicity-dependent forces are limited to chiral particles and fields with helicity gradients. ...

Abstract	Optical traps using nonconservative forces instead of conservative intensity-gradient forces expand the trap parameter space. Existing traps with nonconservative helicity-dependent forces are limited to chiral particles and fields with helicity gradients. We relax these constraints by proposing helicity and polarization gradient optical trapping of achiral particles in evanescent fields. We further propose an optical switching system in which a microsphere is trapped and optically manipulated around a microfiber using polarization gradients. Our Letter deepens the understanding of light-matter interactions in polarization gradient fields and expands the range of compatible particles and stable trapping fields.
Language	English
Publishing date	2023-10-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.131.143803
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Article ; Online: Comprehensive characterization of fetal and mature retinal cell identity to assess the fidelity of retinal organoids.

Kim, Hani Jieun / O'Hara-Wright, Michelle / Kim, Daniel / Loi, To Ha / Lim, Benjamin Y / Jamieson, Robyn V / Gonzalez-Cordero, Anai / Yang, Pengyi

Stem cell reports

2023 Volume 18, Issue 1, Page(s) 175–189

Abstract: Characterizing cell identity in complex tissues such as the human retina is essential for studying its development and disease. While retinal organoids derived from pluripotent stem cells have been widely used to model development and disease of the ... ...

Abstract	Characterizing cell identity in complex tissues such as the human retina is essential for studying its development and disease. While retinal organoids derived from pluripotent stem cells have been widely used to model development and disease of the human retina, there is a lack of studies that have systematically evaluated the molecular and cellular fidelity of the organoids derived from various culture protocols in recapitulating their in vivo counterpart. To this end, we performed an extensive meta-atlas characterization of cellular identities of the human eye, covering a wide range of developmental stages. The resulting map uncovered previously unknown biomarkers of major retinal cell types and those associated with cell-type-specific maturation. Using our retinal-cell-identity map from the fetal and adult tissues, we systematically assessed the fidelity of the retinal organoids in mimicking the human eye, enabling us to comprehensively benchmark the current protocols for retinal organoid generation.
MeSH term(s)	Adult ; Humans ; Retina/metabolism ; Pluripotent Stem Cells/metabolism ; Neurons ; Organoids ; Cell Differentiation ; Induced Pluripotent Stem Cells/metabolism
Language	English
Publishing date	2023-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2720528-9
ISSN	2213-6711 ; 2213-6711
ISSN (online)	2213-6711
ISSN	2213-6711
DOI	10.1016/j.stemcr.2022.12.002
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