Journal: medRxiv

Article Title: A novel framework for quantifying the clinical impact of substandard and falsified antimicrobials: application to typhoid fever

doi: 10.1101/2025.07.08.25331006

Figure Lengend Snippet: Distribution of the %API for ciprofloxacin (top panel) and ofloxacin (bottom panel) collected in random surveys. – The dashed lines represent the tolerance limits for ciprofloxacin tablets as stated by the International Pharmacopeia (12 th Edition, 2025).

Article Snippet: When exploring how different levels of resistance modified dose effects, both outcomes showed no relationship with ofloxacin dose at MICs deemed susceptible to ofloxacin (i.e., MIC ≤ 0.125 mg/L) by the Clinical and Laboratory Standards Institute (CLSI) ( and ).

Techniques:

Journal: medRxiv

Article Title: A novel framework for quantifying the clinical impact of substandard and falsified antimicrobials: application to typhoid fever

doi: 10.1101/2025.07.08.25331006

Figure Lengend Snippet: Average treatment effect of different ofloxacin doses on fever clearance time (A) and failure probability (B) compared to a baseline total dose of 52 mg/kg. Effects were only estimated within the range of doses present in the data (13.8–172.4 mg/kg). All other parameters were kept at their baseline values for each individual. The grey shaded region represents a 90% credible interval. The horizontal dashed line represents no change from baseline. The vertical dashed line represents the average dose.

Article Snippet: When exploring how different levels of resistance modified dose effects, both outcomes showed no relationship with ofloxacin dose at MICs deemed susceptible to ofloxacin (i.e., MIC ≤ 0.125 mg/L) by the Clinical and Laboratory Standards Institute (CLSI) ( and ).

Techniques:

Journal: medRxiv

Article Title: A novel framework for quantifying the clinical impact of substandard and falsified antimicrobials: application to typhoid fever

doi: 10.1101/2025.07.08.25331006

Figure Lengend Snippet: Average treatment effect of different doses of ofloxacin at different MICs (panels) on fever clearance time compared to the average total dose of 52 mg/kg (vertical dashed line). Effects are only shown within the range of doses present in the data (13.8–172.4 mg/kg). All other parameters were kept at their baseline values for each individual. The grey shaded region represents a 90% credible interval. The horizontal dashed line represents no change compared to the average dose.

Article Snippet: When exploring how different levels of resistance modified dose effects, both outcomes showed no relationship with ofloxacin dose at MICs deemed susceptible to ofloxacin (i.e., MIC ≤ 0.125 mg/L) by the Clinical and Laboratory Standards Institute (CLSI) ( and ).

Techniques:

Journal: medRxiv

Article Title: A novel framework for quantifying the clinical impact of substandard and falsified antimicrobials: application to typhoid fever

doi: 10.1101/2025.07.08.25331006

Figure Lengend Snippet: Average treatment effect of different doses of ofloxacin at different MICs (panels) on failure probability compared to the average total dose of 52 mg/kg (vertical dashed line). Effects are only shown within the range of doses present in the data (13.8–172.4 mg/kg). All other parameters were kept at their baseline values for each individual. The grey shaded region represents a 90% credible interval. The horizontal dashed line represents no change compared to the average dose.

Article Snippet: When exploring how different levels of resistance modified dose effects, both outcomes showed no relationship with ofloxacin dose at MICs deemed susceptible to ofloxacin (i.e., MIC ≤ 0.125 mg/L) by the Clinical and Laboratory Standards Institute (CLSI) ( and ).

Techniques:

Journal: medRxiv

Article Title: A novel framework for quantifying the clinical impact of substandard and falsified antimicrobials: application to typhoid fever

doi: 10.1101/2025.07.08.25331006

Figure Lengend Snippet: Expected change in fever clearance time when patients take ofloxacin with %API distributed according to the ofloxacin distribution shown in compared to when they take ofloxacin with 100% API. Negative values indicate that the distribution decreased (i.e., improved) the fever clearance time. The shaded region shows 90% credible intervals. The panels show different target doses (i.e., the dose represented by 100% API). The vertical dashed line indicates the breakpoint for ofloxacin; MICs to the right of this line are considered non-susceptible.

Article Snippet: When exploring how different levels of resistance modified dose effects, both outcomes showed no relationship with ofloxacin dose at MICs deemed susceptible to ofloxacin (i.e., MIC ≤ 0.125 mg/L) by the Clinical and Laboratory Standards Institute (CLSI) ( and ).

Techniques:

Journal: medRxiv

Article Title: A novel framework for quantifying the clinical impact of substandard and falsified antimicrobials: application to typhoid fever

doi: 10.1101/2025.07.08.25331006

Figure Lengend Snippet: Expected change in fever clearance time when patients take ofloxacin with %API distributed according to the ciprofloxacin distribution shown in compared to when they take ofloxacin with 100% API. Negative values indicate that the distribution decreased (i.e., improved) the fever clearance time. The shaded region shows 90% credible intervals. The panels show different target doses (i.e., the dose represented by 100% API). The vertical dashed line indicates the breakpoint for ofloxacin; MICs to the right of this line are considered non-susceptible.

Article Snippet: When exploring how different levels of resistance modified dose effects, both outcomes showed no relationship with ofloxacin dose at MICs deemed susceptible to ofloxacin (i.e., MIC ≤ 0.125 mg/L) by the Clinical and Laboratory Standards Institute (CLSI) ( and ).

Techniques:

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Efficient in vivo presentation of Listeria monocytogenes- derived CD4 and CD8 T cell epitopes in the absence of IFN-gamma.

doi: 10.4049/jimmunol.168.4.1854

Figure Lengend Snippet: FIGURE 7. Up-regulation of MHC class I and II expression on DC after L. monocytogenes infection. The cytofluorometric analysis of MHC class I and II expression was performed after immunomagnetic isolation of DC from spleens of L. monocytogenes-infected wt or GKO mice. Cells were isolated 48 h after i.v. infection with 1 104 CFU L. monocytogenes (f) or from noninfected mice (). Isolated DC were stained with MHC class I- and II-specific mAb, respectively. Shown is the geometric mean fluo- rescence of gated CD11c cells.

Article Snippet: Cells were selected with paramagnetic microbeads conjugated to monoclonal hamster anti-mouse-CD11b (clone M1/70.15.11.5; Miltenyi Biotec, Bergisch Gladbach, Germany) and anti-mouse CD11c Abs (clone N418; Miltenyi Biotec), respectively.

Techniques: Expressing, Infection, Isolation, Staining

Journal: Nature Neuroscience

Article Title: Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding

doi: 10.1038/s41593-024-01615-5

Figure Lengend Snippet: a , Immunofluorescence (IF) images of primary cortical neurons immunostained for glial fibrillary acidic protein (GFAP) and oligodendrocyte transcription factor 2 (OLIG2) simultaneously with PSD95 to show that the cultures are devoid of glial cells or oligodendrocytes, respectively. DAPI for nuclei; PSD95 for excitatory neurons. Magnification, ×40. Scale bars, 50 μm. b , TurboID-PSD95 was cloned without (top row) and with (bottom row) its 5′ and 3′ UTRs and lentivirally expressed in primary cortical neurons. White dashed boxes are zoomed in areas in black&white images. DAPI for nuclei; MAP2 for dendrites; Flag for each TurboID. % dendritically localized TurboID-PSD95 is quantified by co-localization with MAP2 signal in ImageJ. 3 different areas of images per replicate ( n = 3). Magnification, ×20. Scale bars, 50 μm. Significance was derived from biological replicates, showing the center line at mean. c , IF images of TurboID-PSD95-transduced neurons immunostained for DAPI (blue, for nuclei), PSD95 (red, for endogenous PSD95) and TurboID-PSD95 (cyan, detected by Flag). Magnification, ×60. Scale bar, 50 μm. d , IF images show the expression of a presynaptic marker, Synaptophysin (cyan), and TurboID-PSD95 (red, detected by Flag antibody) in primary cortical neurons transduced with TurboID-PSD95. DAPI (blue) marker for nuclei. Three zoomed in regions are marked by the white boxes. Magnification, ×60. Scale bar, 10 μm. e , IF images show TurboID expression and biotinylation in primary cortical neurons transduced with TurboID-PSD95 or Pan-TurboID after 30 minutes of biotin incubation. DAPI (blue, nuclei); MAP2 (green, dendrites); Flag (red, TurboID); and Streptavidin (cyan, biotinylated proteins). Magnification, ×20. Scale bars, 50 μm. f , Western blots stained for Flag and β-Actin from Pan-TurboID and TurboID-PSD95-transduced neurons in the absence (−) or presence (+) of exogenous biotin shown to indicate the relative expression levels of TurboID proteins. Quantifications of TurboID protein levels normalized to β-Actin are shown on the right ( n = 3); relative levels are not significant by two-tailed, paired Student’s t -test. g , Western blots stained for streptavidin signal in inputs (‘in’) and streptavidin pulldowns (‘pd’) from Pan-TurboID or TurboID-PSD95-transduced neurons in the absence (−) or presence (+) of exogenous biotin. h , Streptavidin pulldowns shown for dendritic (SHANK3, GKAP, NLGN1 and HOMER1) and negative control (GAPDH) proteins from TurboID-PSD95-transduced neurons in the absence (−) or presence (+) of exogenous biotin. Flag signal indicates self-biotinylation of each construct. Loaded on the gel are 10% (by volume) of input and 50% (by volume) of pulldowns. Percent isolated by TurboID-PSD95 in each condition is calculated by dividing the signal in the pulldown lane by that of the input lane, after each is adjusted to total, and quantifications are shown as bar graphs ( n = 3). P values: Flag = 0.58, SHANK3 = 0.0061, GKAP = 0.018, NLGN1 = 0.00052, HOMER1 = 0.021, GAPDH = 0.42. i , Streptavidin pulldowns shown for dendritic (BAIAP2 and DLGAP3) and nuclear (TBR1, H4 and H2AX) proteins from Pan-TurboID and TurboID-PSD95-transduced neurons in the presence (+) of exogenous biotin. Loaded on the gel are 10% (by volume) of input and 50% (by volume) of pulldowns. Percent isolated by each TurboID is calculated as in (h) ( n = 3). P values: BAIAP2 = 0.0052, DLGAP3 = 0.0035, TBR1 = 0.0063, H4 = 0.018, H2AX = 0.0037. j , Phosphorylation of EEF2, eIF2α, ERK1/2 and IRE1 and total levels of ATF4 and CHOP are shown in resting (rest), activated (DHPG, Dep) and stressed (Sodium arsenite (NaAsO 2 )) cells by using phospho-specific and total antibodies. The amount of phosphorylated or total protein is shown in the bar graphs, calculated by dividing the phosphorylated signal to total and β-Actin for the phosphorylated proteins and by dividing the total to β-Actin for ATF4 and CHOP ( n = 3). Significance was calculated with respect to rest. P values: P-EEF2 (DHPG = 0.0088, Dep = 0.0023, NaAsO 2 = 0.039), P-eIF2α (DHPG = 0.018, Dep = 0.0034, NaAsO 2 = 0.028), P-ERK1/2 (DHPG = 0.015, Dep = 0.0067, NaAsO 2 = 0.00084), P-IRE1 (DHPG = 0.06, Dep = 0.37, NaAsO 2 = 0.0027), ATF4 (DHPG = 0.038, Dep = 0.42, NaAsO 2 = 0.016), CHOP (DHPG = 0.044, Dep = 0.18, NaAsO 2 = 0.024). k , Quantitative PCR (qPCR) results shown for immediate early genes, Arc , Fos and Jun . The fold changes for each gene are calculated by first normalizing to the house-keeping gene β-Actin in each condition, then dividing the value of each condition by that of the resting state ( n = 3). l , Dendritic spine size in resting and KCl-depolarized neurons are measured using the Keyence microscope. Red squares are examples of spines that are counted ( n = 3, 12 spines from each biological replicate are counted as technical replicates). Significance was derived from the biological replicates using the two-tailed, unpaired Student’s t -test. Box plots show the min and max, with the center line at median. Magnification, ×100. Scale bars, 5 μm. m , Fluo-4-AM staining in resting, KCl-depolarized and DHPG-depolarized cells. Fluo4-AM was loaded in resting cells and measurements were taken at indicated time points after Fluo4-AM removal. In depolarized cells, the dye was loaded during silencing. After silencing, fluorescence was measured during stimulus at 10, 30 and 60-minute time points for the KCl treatment and at 10-minute for the DHPG-induced activation. Fluorescence was also measured 60 minutes after the stimulus removal (60′post KCl and 60′post DHPG). Circles represent data from 2 biological and 3 technical replicates. Below: Examples of Fluo4-AM fluorescence are shown in resting, 10-minute KCl-treated and 10-minute DHPG-treated neurons. Fluo4-AM loading (45 minutes) was performed during the last 45 minutes of the silencing step prior to stimulus addition for the KCl and DHPG treatment and simultaneously for the resting neurons. Imaging was performed 10 minutes after the stimulus was added. Scale bars, 50 μm. (b,f,h-k,m) Data are mean ± s.d. Significance was calculated using the two-tailed, paired Student’s t -test. P values: ns (not significant) >0.05; * <0.05; ** <0.01; *** <0.001; **** <0.0001. n indicates the number of biologically independent samples.

Article Snippet: Puromycin (1:3,000, mouse, Kerafast, EQ0001, RRID: AB_2620162), Flag (1:3,000, mouse, Sigma-Aldrich, F1804, RRID: AB_262044), β-Actin antibody (1:2,500, mouse, Sigma-Aldrich, A1978, RRID: AB_476692), RPL10A (1:1,000, rabbit, Abcam, ab174318), MAP2 (1:2,500, guinea pig, Synaptic Systems, 188004, RRID: AB_2138181), GFAP (1:500, rabbit, Abcam, ab7260, RRID: AB_305808), OLIG2 (1:500, rabbit, Proteintech, 13999-1-AP, RRID: AB_2157541), PSD95 (1:500, mouse, Millipore, MABN68, RRID: AB_10807979), Synaptophysin (1:300, mouse, Abcam, ab8049, RRID: AB_2198854), SHANK3 (1:500, mouse, Novus, NBP1-47610, RRID: AB_10010567), GKAP (1:500, rabbit, Novus, NBP1-76911, RRID: AB_11017331), NLGN1 (1:200, mouse, Novus, NBP2-42192), HOMER1 (1:1,000, rabbit, Proteintech, 12433-1-AP, RRID: AB_2295573), GAPDH (1:5,000, mouse, Thermo Fisher Scientific, AM4300, RRID: AB_2536381), BAIAP2 (1:500, rabbit, Proteintech, 11087-2-AP, RRID: AB_2063075), DLGAP3 (1:500, rabbit, Proteintech, 55056-1-AP, RRID: AB_10858793), TBR1 (1:500, rabbit, Proteintech, 20932-1-AP, RRID: AB_10695502), H4 (1:1,000, mouse, Abcam, ab31830, RRID: AB_1209246), H2A.X (1:1,000, rabbit, Proteintech, 10856-1-AP, RRID: AB_2114985), EEF2 (1:1,000, rabbit, Cell Signaling Technology, 2332, RRID:AB_10693546), P-EEF2 (1:1,000, rabbit, Cell Signaling Technology, 2331, RRID: AB_10015204), eIF2α (1:1,000, rabbit, Cell Signaling Technology, 9722, RRID: AB_2230924), P-eIF2α (1:1,000, rabbit, Cell Signaling Technology, 3398, RRID: AB_2096481), p42/44 MAPK (1:1,000, rabbit, Cell Signaling Technology, 4695, RRID: AB_390779), P-p42/44 MAPK (1:1,000, rabbit, Cell Signaling Technology, 9101, RRID: AB_331646), P-IRE1 (1:500, rabbit, Novus, NB100-2323SS, RRID: AB_10145203), IRE1 (1:500, rabbit, Novus, NB100-2324SS, RRID: AB_10000972), CHOP (1:1,000, mouse, Cell Signaling, 2895T, RRID: AB_2089254), ATF4 (1:1,000, rabbit, Cell Signaling Technology, 11815S, RRID: AB_2616025), MPHOSPH (1:300, rabbit, Biorbyt, orb100446), KCNJ9 (1:300, rabbit, LSBio, LS-C352416), KCNJ9 (1:300, mouse, Antibodies Incorporated, 75-445, RRID: AB_2686912), eIF4G2 (1:1,000, rabbit, Cell Signaling Technology, RRID: AB_10622189 and rabbit, Cell Signaling Technology, RRID: AB_2261993), NSUN3 (1:250, rabbit, LSBio, LS-C163024), MTF1 (1:300, rabbit, Novus, NBP1-86380, RRID: AB_11011361), ZFP64 (1:300, rabbit, Proteintech, 17187-1-AP, RRID: AB_2218826) and KATNBL1 (1:250, rabbit, Proteintech, 24795-1-AP, RRID: AB_2879730).

Techniques: Immunofluorescence, Clone Assay, Derivative Assay, Expressing, Marker, Transduction, Incubation, Western Blot, Staining, Two Tailed Test, Negative Control, Construct, Isolation, Real-time Polymerase Chain Reaction, Microscopy, Fluorescence, Activation Assay, Imaging

Journal: PLoS Pathogens

Article Title: Receptor-Targeted Nipah Virus Glycoproteins Improve Cell-Type Selective Gene Delivery and Reveal a Preference for Membrane-Proximal Cell Attachment

doi: 10.1371/journal.ppat.1005641

Figure Lengend Snippet: ( A ) Cell entry is EpCAM dependent but independent of ephrin-B2. Representative flow cytometry plots out of three independent experiments of CHO-K1, CHO-EpCAM, CHO-ephrin-B2 cells, and of a mixed culture composed of CHO-EpCAM and CHO-ephrin-B2 (1:1 ratio) monitored 72 h after transduction with NiVmut EpCAM -LV, NiVwt-LV or VSV-LV (MOI of 1). EpCAM expression was detected by an APC-coupled human EpCAM specific antibody. ( B ) To ascertain stability of transduction with the EpCAM-targeted vector, CHO-EpCAM cells were cultivated for further 30 days after transduction with the indicated MOIs. The percentage of GFP-positive cells was determined by flow cytometry at the indicated time points. One representative out of three independent experiments is shown.

Article Snippet: Human EpCAM was detected by an Allophycocyanin (APC) labeled mouse anti-EpCAM antibody (clone HEA-125, Miltenyi Biotec, Bergisch Gladbach, Germany, dilution 1:100).

Techniques: Flow Cytometry, Transduction, Expressing, Plasmid Preparation