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Article ; Online: State of Charge-Dependent Impedance Spectroscopy as a Helpful Tool to Identify Reasons for Fast Capacity Fading in All-Solid-State Batteries.

Wiche, Miguel / Yusim, Yuriy / Vettori, Kilian / Ruess, Raffael / Henss, Anja / Elm, Matthias T

ACS applied materials & interfaces

2024 Volume 16, Issue 3, Page(s) 3253–3259

Abstract: Thiophosphate-based all-solid-state batteries (ASSBs) are considered the most promising candidate for the next generation of energy storage systems. However, thiophosphate-based ASSBs suffer from fast capacity fading with nickel-rich cathode materials. ... ...

Abstract	Thiophosphate-based all-solid-state batteries (ASSBs) are considered the most promising candidate for the next generation of energy storage systems. However, thiophosphate-based ASSBs suffer from fast capacity fading with nickel-rich cathode materials. In many reports, this capacity fading is attributed to an increase of the charge transfer resistance of the composite cathode caused by interface degradation and/or chemo-mechanical failure. The change in the charge transfer resistance is typically determined using impedance spectroscopy after charging the cells. In this work, we demonstrate that large differences in the long-term cycling performance also arise in cells, which exhibit a comparable charge transfer resistance at the cathode side. Our results confirm that the charge transfer resistance of the cathode is not necessarily responsible for capacity fading. Other processes, such as resistive processes on the anode side, can also play a major role. Since these processes usually depend on the state of charge, they may not appear in the impedance spectra of fully charged cells; i.e., analyzing the impedance spectra of charged cells alone is insufficient for the identification of major resistive processes. Thus, we recommend measuring the impedance at different potentials to get a complete understanding of the reasons for capacity fading in ASSBs.
Language	English
Publishing date	2024-01-09
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c13160
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Article ; Online: Re: increasing hospital admission rates for urological complications after transrectal ultrasound guided prostate biopsy: R. K. Nam, R. Saskin, Y. Lee, Y. Liu, C. Law, L. H. Klotz, D. A. Loblaw, J. Trachtenberg, A. Stanimirovic, A. E. Simor, A. Seth, D. R. Urbach and S. A. Narod J Urol 2010; 183: 963-969.

Neulander, Endre Z / Yusim, I / Kaneti, J

The Journal of urology

2010 Volume 184, Issue 5, Page(s) 2216–7; author reply 2217

MeSH term(s)	Biopsy/adverse effects ; Biopsy/methods ; Humans ; Male ; Patient Admission/statistics & numerical data ; Prostate/diagnostic imaging ; Prostate/pathology ; Rectum ; Ultrasonography, Interventional ; Urologic Diseases/etiology ; Urologic Diseases/therapy
Language	English
Publishing date	2010-11
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	3176-8
ISSN	1527-3792 ; 0022-5347
ISSN (online)	1527-3792
ISSN	0022-5347
DOI	10.1016/j.juro.2010.06.121
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Article ; Online: Evaluation of the optimal strategy in men with a single unilateral suspicious lesion on MRI undergoing transperineal MRI/ultrasound fusion prostate biopsy.

Yusim, Igor / Mazor, Elad / Frumkin, Einat / Jabareen, Muhammad / Hefer, Ben / Elsaraya, Nimer / Li, Sveta / Rouvinov, Keren / Novack, Victor / Mabjeesh, Nicola J

The Prostate

2023 Volume 83, Issue 13, Page(s) 1255–1262

Abstract: Background: Targeting biopsy (TBx) of suspicious lesions combined with random systematic biopsy (SBx) improves detection rates of prostate cancer (PCa) during magnetic resonance imaging (MRI)/ultrasound (US) fusion prostate biopsy. However, this ... ...

Abstract	Background: Targeting biopsy (TBx) of suspicious lesions combined with random systematic biopsy (SBx) improves detection rates of prostate cancer (PCa) during magnetic resonance imaging (MRI)/ultrasound (US) fusion prostate biopsy. However, this combination increases the number of biopsy cores, prolongs the procedure time, and increases complications and costs, leading to the overdiagnosis of clinically insignificant PCa (ciPCa). This study aims to evaluate the optimal sampling design to achieve a detection rate of clinically significant PCa (csPCa) equal to standard TBx with SBx with fewer biopsy cores. Materials and methods: Of 508 consecutive men who underwent transperineal MRI/US fusion prostate biopsy at our center between January 2020 and December 2022, 364 patients with a single unilateral suspicious lesion on MRI were included in the study. Three biopsy strategies were randomly selected to evaluate the diagnostic accuracy of PCa detection: (1) TBx with ipsilateral SBx, (2) TBx with contralateral SBx, and (3) TBx only. The PCa detection sensitivity for selected biopsy strategies was compared with the reference standards. The significance of differences in cancer detection between sampling schemes was determined using McNemar's test. Results: PCa was diagnosed in 182 of 364 men using TBx with bilateral SBx. International Society of Urological Pathology grade group (ISUP GG) ≥ 2 and ISUP GG ≥ 3 PCa was detected in 84/364 (23.1%) and 42/364 (11.5%), respectively, while ISUP GG 1 PCa was diagnosed in 98/364 (26.9%). Combining TBx with ipsilateral SBx detected 94.5% of all, 98.8% of ISUP GG ≥ 2, 100% of ISUP GG ≥ 3, and 89.8% of ISUP GG 1 PCa. TBx with contralateral SBx detected fewer csPCa (91.7% vs. 98.8%, p = 0.03), as did TBx alone (90.5 vs. 98.8, p = 0.008). Conclusions: Our study demonstrates that TBx with ipsilateral SBx performed around the multiparametric MRI-suspected lesion in transperineal MRI/US biopsy of the prostate achieves a very high detection rate for csPCa (ISUP ≥ 2) without compromising the detection of increased risk PCa (ISUP ≥ 3). In addition, this strategy reduces the number of biopsy cores by 8-10 per patient, procedure time, and pathology processing costs and decreases ciPCa detection.
MeSH term(s)	Humans ; Male ; Image-Guided Biopsy/methods ; Magnetic Resonance Imaging/methods ; Prostate/diagnostic imaging ; Prostate/pathology ; Prostatic Neoplasms/pathology ; Retrospective Studies ; Ultrasonography
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Clinical Trial ; Journal Article
ZDB-ID	604707-5
ISSN	1097-0045 ; 0270-4137
ISSN (online)	1097-0045
ISSN	0270-4137
DOI	10.1002/pros.24585
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Article ; Online: Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens.

Stromberg, Zachary R / Theiler, James / Foley, Brian T / Myers Y Gutiérrez, Adán / Hollander, Attelia / Courtney, Samantha J / Gans, Jason / Deshpande, Alina / Martinez-Finley, Ebany J / Mitchell, Jason / Mukundan, Harshini / Yusim, Karina / Kubicek-Sutherland, Jessica Z

PLOS global public health

2022 Volume 2, Issue 2, Page(s) e0000207

Abstract: Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, ... ...

Abstract	Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire group of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.
Language	English
Publishing date	2022-02-24
Publishing country	United States
Document type	Journal Article
ISSN	2767-3375
ISSN (online)	2767-3375
DOI	10.1371/journal.pgph.0000207
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Article ; Online: Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA.

Courtney, Samantha J / Stromberg, Zachary R / Myers Y Gutiérrez, Adán / Jacobsen, Daniel / Stromberg, Loreen R / Lenz, Kiersten D / Theiler, James / Foley, Brian T / Gans, Jason / Yusim, Karina / Kubicek-Sutherland, Jessica Z

Biosensors

2021 Volume 11, Issue 10

Abstract: Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone ... ...

Abstract	Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to influenza diagnostics. Here, we analyzed the Fast Evaluation of Viral Emerging Risks (FEVER) pipeline on ultrasensitive detection platforms, including a waveguide-based optical biosensor and a flow cytometry bead-based assay. The pipeline was also evaluated in silico for sequence coverage in comparison to the U.S. Centers for Disease Control and Prevention's (CDC) influenza A and B diagnostic assays. The influenza FEVER probe design had a higher tolerance for mismatched bases than the CDC's probes, and the FEVER probes altogether had a higher detection rate for influenza isolate sequences from GenBank. When formatted for use as molecular beacons, the FEVER probes detected influenza RNA as low as 50 nM on the waveguide-based optical biosensor and 1 nM on the flow cytometer. In addition to molecular beacons, which have an inherently high background signal we also developed an exonuclease selection method that could detect 500 pM of RNA. The combination of high-coverage probes developed using the FEVER pipeline coupled with ultrasensitive optical biosensors is a promising approach for future influenza diagnostic and biosurveillance applications.
MeSH term(s)	Biosensing Techniques ; Humans ; Influenza, Human ; Nucleic Acid Amplification Techniques ; Orthomyxoviridae ; RNA ; Sensitivity and Specificity
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2021-09-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662125-3
ISSN	2079-6374 ; 2079-6374
ISSN (online)	2079-6374
ISSN	2079-6374
DOI	10.3390/bios11100367
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Article ; Online: Epigraph: A Vaccine Design Tool Applied to an HIV Therapeutic Vaccine and a Pan-Filovirus Vaccine.

Theiler, James / Yoon, Hyejin / Yusim, Karina / Picker, Louis J / Fruh, Klaus / Korber, Bette

Scientific reports

2016 Volume 6, Page(s) 33987

Abstract: Epigraph is an efficient graph-based algorithm for designing vaccine antigens to optimize potential T-cell epitope (PTE) coverage. Epigraph vaccine antigens are functionally similar to Mosaic vaccines, which have demonstrated effectiveness in preliminary ...

Abstract	Epigraph is an efficient graph-based algorithm for designing vaccine antigens to optimize potential T-cell epitope (PTE) coverage. Epigraph vaccine antigens are functionally similar to Mosaic vaccines, which have demonstrated effectiveness in preliminary HIV non-human primate studies. In contrast to the Mosaic algorithm, Epigraph is substantially faster, and in restricted cases, provides a mathematically optimal solution. Epigraph furthermore has new features that enable enhanced vaccine design flexibility. These features include the ability to exclude rare epitopes from a design, to optimize population coverage based on inexact epitope matches, and to apply the code to both aligned and unaligned input sequences. Epigraph was developed to provide practical design solutions for two outstanding vaccine problems. The first of these is a personalized approach to a therapeutic T-cell HIV vaccine that would provide antigens with an excellent match to an individual's infecting strain, intended to contain or clear a chronic infection. The second is a pan-filovirus vaccine, with the potential to protect against all known viruses in the Filoviradae family, including ebolaviruses. A web-based interface to run the Epigraph tool suite is available (http://www.hiv.lanl.gov/content/sequence/EPIGRAPH/epigraph.html).
Language	English
Publishing date	2016-10-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep33987
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Article ; Online: Trivalent mosaic or consensus HIV immunogens prime humoral and broader cellular immune responses in adults.

Cohen, Kristen W / Fiore-Gartland, Andrew / Walsh, Stephen R / Yusim, Karina / Frahm, Nicole / Elizaga, Marnie L / Maenza, Janine / Scott, Hyman / Mayer, Kenneth H / Goepfert, Paul A / Edupuganti, Srilatha / Pantaleo, Giuseppe / Hutter, Julia / Morris, Daryl E / De Rosa, Stephen C / Geraghty, Daniel E / Robb, Merlin L / Michael, Nelson L / Fischer, Will /

Giorgi, Elena E / Malhi, Harman / Pensiero, Michael N / Ferrari, Guido / Tomaras, Georgia D / Montefiori, David C / Gilbert, Peter B / McElrath, M Juliana / Haynes, Barton F / Korber, Bette T / Baden, Lindsey R

The Journal of clinical investigation

2023 Volume 133, Issue 4

Abstract: BACKGROUNDMosaic and consensus HIV-1 immunogens provide two distinct approaches to elicit greater breadth of coverage against globally circulating HIV-1 and have shown improved immunologic breadth in nonhuman primate models.METHODSThis double-blind ... ...

Abstract	BACKGROUNDMosaic and consensus HIV-1 immunogens provide two distinct approaches to elicit greater breadth of coverage against globally circulating HIV-1 and have shown improved immunologic breadth in nonhuman primate models.METHODSThis double-blind randomized trial enrolled 105 healthy HIV-uninfected adults who received 3 doses of either a trivalent global mosaic, a group M consensus (CON-S), or a natural clade B (Nat-B) gp160 env DNA vaccine followed by 2 doses of a heterologous modified vaccinia Ankara-vectored HIV-1 vaccine or placebo. We performed prespecified blinded immunogenicity analyses at day 70 and day 238 after the first immunization. T cell responses to vaccine antigens and 5 heterologous Env variants were fully mapped.RESULTSEnv-specific CD4+ T cell responses were induced in 71% of the mosaic vaccine recipients versus 48% of the CON-S recipients and 48% of the natural Env recipients. The mean number of T cell epitopes recognized was 2.5 (95% CI, 1.2-4.2) for mosaic recipients, 1.6 (95% CI, 0.82-2.6) for CON-S recipients, and 1.1 (95% CI, 0.62-1.71) for Nat-B recipients. Mean breadth was significantly greater in the mosaic group than in the Nat-B group using overall (P = 0.014), prime-matched (P = 0.002), heterologous (P = 0.046), and boost-matched (P = 0.009) measures. Overall T cell breadth was largely due to Env-specific CD4+ T cell responses.CONCLUSIONPriming with a mosaic antigen significantly increased the number of epitopes recognized by Env-specific T cells and enabled more, albeit still limited, cross-recognition of heterologous variants. Mosaic and consensus immunogens are promising approaches to address global diversity of HIV-1.TRIAL REGISTRATIONClinicalTrials.gov NCT02296541.FUNDINGUS NIH grants UM1 AI068614, UM1 AI068635, UM1 AI068618, UM1 AI069412, UL1 RR025758, P30 AI064518, UM1 AI100645, and UM1 AI144371, and Bill & Melinda Gates Foundation grant OPP52282.
MeSH term(s)	Animals ; Consensus ; Immunity, Cellular ; Vaccination ; Vaccinia virus ; HIV Infections ; AIDS Vaccines ; HIV Antibodies ; Vaccines, DNA
Chemical Substances	AIDS Vaccines ; HIV Antibodies ; Vaccines, DNA
Language	English
Publishing date	2023-02-15
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI163338
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Article ; Online: Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens

Stromberg, Zachary R / Theiler, James / Foley, Brian T / Myers y Gutiérrez, Adán / Hollander, Attelia / Courtney, Samantha J / Deshpande, Alina / Martinez-Finley, Ebany J / Mitchell, Jason / Mukundan, Harshini / Yusim, Karina / Kubicek-Sutherland, Jessica Z

medRxiv

Abstract: Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA ... ...

Abstract	Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire class of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.
Keywords	covid19
Language	English
Publishing date	2021-05-27
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.05.25.21257811
Database	COVID19

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Article: Theory of fast neurotransmitter release control based on voltage-dependent interaction between autoreceptors and proteins of the exocytotic machinery.

Yusim, K / Parnas, H / Segel, L

Bulletin of mathematical biology

2007 Volume 61, Issue 4, Page(s) 701–725

Abstract: A molecular-level theory is constructed for the control of fast neurotransmitter release, based on recent experimental findings that depolarization shifts presynaptic autoreceptors to a low affinity state and that an autoreceptor must be bound to a ... ...

Abstract	A molecular-level theory is constructed for the control of fast neurotransmitter release, based on recent experimental findings that depolarization shifts presynaptic autoreceptors to a low affinity state and that an autoreceptor must be bound to a transmitter before it can become associated with the exocytotic apparatus. It is assumed that such an association blocks release; experimental support for this assumption is cited. The theory provides mechanisms for key experimental results concerning the essence of the matter, what controls the time course of evoked release? The same general model can account for both evoked and spontaneous release. The new theory can be regarded as a molecular implementation of the (phenomenological) calcium-voltage hypothesis that was suggested earlier.
MeSH term(s)	Animals ; Autoreceptors/physiology ; Calcium Signaling ; Exocytosis ; Mathematics ; Membrane Potentials ; Models, Neurological ; Nerve Tissue Proteins/physiology ; Neurotransmitter Agents/metabolism
Chemical Substances	Autoreceptors ; Nerve Tissue Proteins ; Neurotransmitter Agents
Language	English
Publishing date	2007-08-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	184905-0
ISSN	1522-9602 ; 0092-8240 ; 0007-4985
ISSN (online)	1522-9602
ISSN	0092-8240 ; 0007-4985
DOI	10.1006/bulm.1999.0107
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Article ; Online: The hepatitis C sequence database in Los Alamos.

Kuiken, Carla / Hraber, Peter / Thurmond, James / Yusim, Karina

Nucleic acids research

2007 Volume 36, Issue Database issue, Page(s) D512–6

Abstract: The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. Presently, approximately 50 000 HCV ... ...

Abstract	The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. Presently, approximately 50 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide. The HCV sequence database collects and annotates sequence data, and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org.
MeSH term(s)	Databases, Genetic ; Genes, Viral ; Genotype ; Hepacivirus/genetics ; Hepatitis C/virology ; Humans ; Internet ; Sequence Analysis, Protein ; Sequence Analysis, RNA ; Software ; Viral Proteins/chemistry ; Viral Proteins/genetics
Chemical Substances	Viral Proteins
Language	English
Publishing date	2007-11-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkm962
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