A combined experimental and theoretical approach for doxycycline sensing using simple fluorescent probe with distinct fluorescence change in wide range of interferences

Overuse of doxycycline (DOXY) can cause serious problems to human health, environment and food quality. So, it is essential to develop a new sensing methodology that is both sensitive and selective for the quantitative detection of DOXY. In our current research, we synthesized a simple fluorescent probe 4,4'-bis(benzyloxy)-1,1'-biphenyl (BBP) for the highly selective detection of doxycycline by through fluorescence spectroscopy. The probe BBP displayed ultra-sensitivity towards doxycycline due to Forster resonance energy transfer (FRET). Fluorescence spectroscopy, density functional theory (DFT), 1H NMR titration, UV-Vis, and Job's plot were used to confirm the sensing mechanism. The charge transfer between the probe and analyte was further examined qualitatively by electron density differences (EDD) and quantitively by natural bond orbital (NBO) analyses. Whereas the non-covalent nature of probe BBP towards DOXY was verified by theoretical non-covalent interaction (NCI) analysis as along with Bader's quantum theory of atoms in molecules (QTAIM) analysis. Furthermore, probe BBP was also practically employed for the detection of doxycycline in fish samples, pharmaceutical wastewater and blood samples.

Extensive optical and DFT studies on novel AIE active fluorescent sensor for Colorimetric and fluorometric detection of nitrobenzene in Solid, solution and vapor phase

An electron rich isophthalamide based sensor IPA has been synthesized through a simple two-step reaction, containing noteworthy aggregation induced emission (AIE) properties. Considering the significant emission with λmax at 438 nm, sensor IPA has been employed for the sensing of nitrobenzene (NB) in solid, solution and vapor state with high sensitivity and selectivity. Sensor IPA showed noteworthy colorimetric and fluorometric quenching in fluorescence emission when exposed to NB. Small size of NB and involvement of photoinduced electron transfer (PET) lead to detection of NB down to 60 nM. IPA-NB interaction was studied through UV-Vis. spectroscopic studies along with fluorescence spectroscopy. Moreover, 1H and 13C NMR titration experiments provided additional support for determination of interaction type. Furthermore, by using density functional theory (DFT) calculations, thermodynamic stability was studied. Additionally, non-covalent interactions (NCI), frontier molecular orbitals (FMO), density of states (DOS), were investigated for providing further evidence of nitrobenzene sensing and its interaction with sensor. Natural bond orbital (NBO) analysis was carried out for charge transfer studies. Quantum theory of atom in molecule (QTAIM) and SAPT0 studies provided information about interaction points and binding energy. Additionally, IPA was investigated for NB sensing in real water samples, and its effective participation in solid state on-site detection as well as in solution phase was brought to light along with logic gate construction.

An extensive experimental and DFT studies on highly selective detection of nitrobenzene through deferasirox based new fluorescent sensor

A deferasirox based substituted triazole amine sensor TAD has been synthesized for the highly selective detection of nitrobenzene in real samples. Sensor TAD exhibited selective quenching response against nitrobenzene among the other nitroaromatic compounds (NACs). Photoinduced electron transfer (PET) process was devised as plausible sensing mechanisms which was supported via UV-visible and fluorescence spectroscopy, 1H NMR titration experiment, density functional theory (DFT) analysis and Job's plot. Non-covalent interaction (NCI) analysis and Bader's quantum theory of atoms in molecules (QTAIM) analysis were performed to investigate the presence of non-covalent interactions and symmetry perturbation theory (SAPT0) was performed for energy decomposition and quantitative analysis of interaction energies between sensor TAD and NB. Furthermore, sensor TAD was practically applied for the identification of NB in real samples.

Triazine based fluorescent sensor for sequential detection of Hg2+ and L-Cysteine in real samples and application in logic Gate: A combination of Extensive experimental and theoretical analysis

Triazine based fluorescent sensor TBT was rationally designed and synthesized to achieve sequential detection of Hg²⁺ and L-cysteine based on the presence of sulfur moiety and suitable cavity in the molecule. Sensor TBT exhibited excellent sensing potential for the selective detection of Hg²⁺ ions and L-cysteine (Cys) in real samples. Upon addition of Hg²⁺ to sensor TBT, enhancement in emission intensity of sensor TBT was observed which was accredited to the presence of sulfur moiety and size of cavity in the sensor. Upon interaction with Hg²⁺ blockage of intramolecular charge transfer (ICT) along with chelation-enhanced fluorescence (CHEF) resulted in the increase in fluorescence emission intensity of sensor TBT. Further, TBT-Hg²⁺ complex was employed for the selective detection of Cys through fluorescence quenching mechanism. This was attributed to the significantly stronger interaction of Cys with Hg²⁺, which resulted in the formation of Cys-Hg²⁺ complex and subsequently sensor TBT was released from TBT-Hg²⁺ complex. The nature of interaction between TBT-Hg²⁺ and Cys-Hg²⁺ complex was evaluated through ¹H NMR titration experimentations. Extensive DFT studies were also carried out which include thermodynamic stability, frontier molecular orbitals (FMO), density of states (DOS), non-covalent interaction (NCI), quantum theory of atom in molecule (QTAIM), electron density differences (EDD) and natural bond orbital (NBO) analyses. All the studies supported the non-covalent type of interaction between analytes and sensor TBT. The limit of detection for Hg²⁺ ions was found to be as low as 61.9 nM. Sensor TBT was also employed for the quantitative detection of Hg²⁺ and Cys in real samples. Additionally, logic gate was fabricated by using sequential detection strategy.

New fluorescent probe for sensing of mefenamic acid in aqueous medium: An integrated experimental and theoretical analysis

Abnormal levels of mefenamic acid (MFA) in living organisms can result in hepatic necrosis, liver, and gastrointestinal diseases. Therefore, development of accurate and effective method for detection of MFA is of great significance for the protection of public health. Herein, we designed a stilbene based sensor ECO for the sensitive and selective detection of mefenamic acid by employing fluorescence spectroscopy for the first time. The developed sensor ECO displayed fluorescence turn-off response towards MFA based on PET (photoinduced electron transfer) and hydrogen bonding. The sensing mechanism of MFA was investigated through ¹H NMR titration experiment and density functional theory (DFT) calculations. The presence of non-covalent interaction was confirmed through spectroscopic analysis and was further supported by non-covalent interaction (NCI) analysis and Bader's quantum theory of atoms in molecules (QTAIM) analysis. Additionally, the sensor ECO coated test strips were fabricated for on-site detection of mefenamic acid. Furthermore, the practical applicability of sensor ECO to detect MFA was also explored in human blood and artificial urine samples.

Theoretical and experimental studies on mechanochromic triphenylamine based fluorescent "ON-OFF-ON" sensor for sequential detection of Fe3+ and deferasirox

A novel triphenylamine (TPA) based sensor TTU was rationally designed and synthesized that exhibited reversible mechanochromic and aggregation induced emission enhancement (AIEE) properties. The AIEE active sensor was employed for fluorometric detection of Fe³⁺ in aqueous medium, with distinguished selectivity. The sensor showed a highly selective quenching response towards Fe³⁺ that is ascribed to complex formation with paramagnetic Fe³⁺. Subsequently, TTU-Fe³⁺ complex acted as a fluorescence sensor for the detection of deferasirox (DFX). The subsequent addition of DFX to TTU-Fe³⁺ complex led to the recovery of fluorescence emission intensity of sensor TTU that was attributed to the displacement of Fe³⁺ by DFX and release of sensor TTU. The proposed sensing mechanisms for Fe³⁺ and DFX was confirmed through ¹H NMR titration experiment and DFT calculations. Frontier molecular orbitals (FMO), density of states (DOS), natural bond orbital (NBO), non-covalent interaction (NCI) and electron density difference (EDD) analysis were performed using DFT calculations to support the experimental results. Moreover, sensor TTU displayed colorimetric detection of Fe³⁺. Further, the sensor was employed for the detection of Fe³⁺ and DFX in real water samples. Finally, logic gate was fabricated by using sequential detection strategy.

AIEE active J-aggregates of naphthalimide based fluorescent probe for detection of Nitrobenzene: Combined experimental and theoretical approaches for Non-covalent interaction analysis

A new naphthalimide-based fluorescent probe NS with exceptional J-aggregates based aggregation-induced emission enhancement (AIEE) properties was rationally synthesized through a single-step imidation reaction. Probe NS exhibited excellent AIEE properties in aqueous media through the formation of J-aggregates with remarkable red-shift. The AIEE active probe NS was used for selective and sensitive detection of nitrobenzene (NB) based on fluorescence quenching response. Formation of J-aggregates was assessed through fluorescence titration. These J-aggregates contributed significantly to produce favorable interaction between probe NS and NB. The highly selective fluorescence detection of NB was accredited to the adjustable smaller size of NB that can easily penetrate into interstitial spaces of probe molecules. Ability of sensor to detect NB in solid state was also accomplished through solid state fluorescence spectroscopy. Nature of interaction and sensitivity of probe NS for NB has also been investigated through ¹H NMR titration and density functional theory (DFT) including non-covalent interaction (NCI), quantum theory of atom in molecule (QTAIM), electron density differences (EDD), frontier molecular orbitals (FMO) and density of states (DOS) analysis. Advantageously, probe exhibited colorimetric and vapor phase detection of NB. Moreover, probe was quite sensitive for the trace detection of NB in real samples.

Abstract P5-02-02: Second harmonic generation in combination with nuclear morphometry in the evaluation of DCIS

Purpose/Objective: Collagen is a major extracellular matrix (ECM) constituent in normal breast and is extensively remodeled in breast carcinoma. Therefore, features of remodeled collagen in the stroma adjacent to ductal carcinoma in situ (DCIS) could indicate cancer progression. The major objective of this study is to identify potential tumor-associated collagen signatures unique to DCIS that will allow us to predict progression based on the collagen texture and nuclear morphology. In this present study, we develop two image analysis pipelines (SHG Texture Extraction and H&E Nuclear Morphology Extractor) to quantify 1) stromal changes, 2) collagen signatures and 3) nuclear morphology from normal breast to DCIS in order to predict local breast cancer recurrence.

Method: We used second harmonic generation (SHG) images and H&E to analyze collagen features and to study nuclear morphology using a data set of 336 patients (from which 310 normal and 327 DCIS regions were imaged). The 336 patients were a subset of patients with pure DCIS taken from a case-control study. Clinical-pathologic factors were associated with risk of subsequent ipsilateral cancer (DCIS or invasive). The SHG framework consisted of collagen segmentation using 1) adaptive thresholding and 2) morphological operations. The H&E framework consisted of nuclear segmentation using adaptive thresholding and a maker-controlled watershed algorithm; and nuclear feature extractions including intensity, texture and morphology. Overall, the SHG framework segments collagen regions and computes textural features specifically at collagen regions. Furthermore, the H&E framework segments nuclei and computes nuclei morphology and textural features. These features were used in L1-regularized logistic regression to construct classification models to discriminate normal vs DCIS regions; and to distinguish regions from DCIS patients with vs. without local recurrences.

Results: In first experiment, we performed L1-regularized logistic regression to construct a classification model to discriminate normal vs DCIS regions. Our results suggest that using only SHG collagen features, this logistic model selected 19 significant features to build a classification model that achieved area under curve (AUC) 90% and accuracy 83% using 5-Fold cross validation. When H&E nuclei features are used, the logistic model selected 88 significant features and achieved AUC 91% and accuracy 86%. By combined both SHG and H&E features, the model achieved classification AUC 93% and accuracy 88%. By using L1-regularized logistic model with combined significant SHG and H&E features, we achieved AUC 59% with an accuracy of 61% for DCIS and recurrent DCIS regions.

Conclusions: Our study suggests that SHG and nuclear morphology features extracted from H&E can improve the classification of normal and DCIS regions. Overall, these results suggest that second harmonic generation and H&E nuclear morphology analysis could aid in the assessment of prognosis and risk of progression to invasive breast cancer.

Citation Format: Park CC, Irshad H, Ziaee S, Martin-Tuite P, Habel L, Weaver VM, Schnitt SJ, Beck AH. Second harmonic generation in combination with nuclear morphometry in the evaluation of DCIS [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-02-02.

Crowdsourcing image annotation for nucleus detection and segmentation in computational pathology: evaluating experts, automated methods, and the crowd

The development of tools in computational pathology to assist physicians and biomedical scientists in the diagnosis of disease requires access to high-quality annotated images for algorithm learning and evaluation. Generating high-quality expert-derived annotations is time-consuming and expensive. We explore the use of crowdsourcing for rapidly obtaining annotations for two core tasks in com- putational pathology: nucleus detection and nucleus segmentation. We designed and implemented crowdsourcing experiments using the CrowdFlower platform, which provides access to a large set of labor channel partners that accesses and manages millions of contributors worldwide. We obtained annotations from four types of annotators and compared concordance across these groups. We obtained: crowdsourced annotations for nucleus detection and segmentation on a total of 810 images; annotations using automated methods on 810 images; annotations from research fellows for detection and segmentation on 477 and 455 images, respectively; and expert pathologist-derived annotations for detection and segmentation on 80 and 63 images, respectively. For the crowdsourced annotations, we evaluated performance across a range of contributor skill levels (1, 2, or 3). The crowdsourced annotations (4,860 images in total) were completed in only a fraction of the time and cost required for obtaining annotations using traditional methods. For the nucleus detection task, the research fellow-derived annotations showed the strongest concordance with the expert pathologist- derived annotations (F-M =93.68%), followed by the crowd-sourced contributor levels 1,2, and 3 and the automated method, which showed relatively similar performance (F-M = 87.84%, 88.49%, 87.26%, and 86.99%, respectively). For the nucleus segmentation task, the crowdsourced contributor level 3-derived annotations, research fellow-derived annotations, and automated method showed the strongest concordance with the expert pathologist-derived annotations (F-M = 66.41%, 65.93%, and 65.36%, respectively), followed by the contributor levels 2 and 1 (60.89% and 60.87%, respectively). When the research fellows were used as a gold-standard for the segmentation task, all three con- tributor levels of the crowdsourced annotations significantly outperformed the automated method (F-M = 62.21%, 62.47%, and 65.15% vs. 51.92%). Aggregating multiple annotations from the crowd to obtain a consensus annotation resulted in the strongest performance for the crowd-sourced segmentation. For both detection and segmentation, crowd-sourced performance is strongest with small images (400 × 400 pixels) and degrades significantly with the use of larger images (600 × 600 and 800 × 800 pixels). We conclude that crowdsourcing to non-experts can be used for large-scale labeling microtasks in computational pathology and offers a new approach for the rapid generation of labeled images for algorithm development and evaluation.

Loop-mediated isothermal amplification (RT-LAMP): a new approach for the detection of foot-and-mouth disease virus and its sero-types in Pakistan

Successful disease management requires a rapid and sensitive diagnosis method that can recognize early infection even before the manifestation of its clinical signs. The only available field diagnostic tests for foot-and-mouth disease (FMD) are lateral flow devices, commonly known as chromatographic strips. Low sensitivity and inability to detect FMD virus (FMDV) at the serotype level are limitations of lateral flow devices. Therefore, a reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) was standardized using universal and sero-type specific genes in a single tube. This test does not require sophisticated equipment and can detect FMDV at serotype level in about 60 min. In addition, the sensitivity and specificity of this test is comparable to conventional reverse transcriptase PCR and real time PCR (rRT-PCR).

Studies on the biology, chemotherapy and distribution of warble fly in Pakistan

This paper presents data on the prevalence, biology and control of warble fly infestation (WFI) in cattle and goats in Pakistan. A questionnaire for obtaining information on biology and prevalence was circulated amongst field veterinary staff and livestock farmers in all five provinces (Punjab, Sindh, Balochistan, Khyber Pakhtunkhwa [KPK] and Gilgit-Baltistan) and in the Federally Administered Tribal Areas of the country. A total of 1,019 questionnaires were received (Punjab = 296, Sindh = 246, KPK = 318, Balochistan = 151, Gilgit-Baltistan = 8). Warble fly infestation was reported from each province and from the federally administered tribal areas, particularly from hilly, semi-hilly and sandy desert areas (the Cholistan desert, which adjoins the Rehim Yar Khan, Bahawalpur and Bahawalnagar districts, and the Nara area of Sanghar district). Warbles (nodules) started appearing on the backs of the infested animals from September through December and disappeared from October through March. The prevalence of WFI varied from 5% to 75%. It was highest in hilly areas and gradually decreased towards the plains. A map was developed of warble fly-infested areas. Four field trials were conducted to study the efficacy of different drugs indicated for the control of warble fly infestation. A total of 2,094 cattle and 3,876 goats were given five different injectables (avermectins); namely, Ivomec, Endectin, Euvectin, Dectomax and Promectin (ivermectin) during the first three weeks of September. A control group was given normal saline. All the medicines were found to be effective in controlling infestation.

Epidemiology of Shiga toxin-producing Escherichia coli O157 in very young calves in the North Island of New Zealand

AIMS

To study the occurrence and spatial distribution of Shiga toxin-producing Escherichia coli (STEC) O157 in calves less than 1-week-old (bobby calves) born on dairy farms in the North Island of New Zealand, and to determine the association of concentration of IgG in serum, carcass weight, gender and breed with occurrence of E. coli O157 in these calves.

METHODS

In total, 309 recto-anal mucosal swabs and blood samples were collected from bobby calves at two slaughter plants in the North Island of New Zealand. The address of the farm, tag number, carcass weight, gender and breed of the sampled animals were recorded. Swabs were tested for the presence of E. coli O157 using real time PCR (RT-PCR). All the farms were mapped geographically to determine the spatial distribution of farms positive for E. coli O157. K function analysis was used to test for clustering of these farms. Multiplex PCR was used for the detection of Shiga toxin 1 (stx1), Shiga toxin 2 (stx2), E. coli attaching and effacing (eae) and Enterohaemolysin (ehxA) genes in E. coli O157 isolates. Genotypes of isolates from this study (n = 10) along with human (n = 18) and bovine isolates (n = 4) obtained elsewhere were determined using bacteriophage insertion typing for stx encoding.

RESULTS

Of the 309 samples, 55 (17.7%) were positive for E. coli O157 by RT-PCR and originated from 47/197 (23.8%) farms. E. coli O157 was isolated from 10 samples of which seven isolates were positive for stx2, eae and ehxA genes and the other three isolates were positive for stx1, stx2, eae and ehxA. Bacteriophage insertion typing for stx encoding revealed that 12/18 (67%) human and 13/14 (93%) bovine isolates belonged to genotypes 1 and 3. K function analysis showed some clustering of farms positive for E. coli O157. There was no association between concentration of IgG in serum, carcass weight and gender of the calves, and samples positive for E. coli O157, assessed using linear mixed-effects models. However, Jersey calves were less likely to be positive for E. coli O157 by RT-PCR than Friesian calves (p = 0.055).

CONCLUSIONS

Healthy bobby calves are an asymptomatic reservoir of E. coli O157 in New Zealand and may represent an important source of infection for humans. Carriage was not associated with concentration of IgG in serum, carcass weight or gender.

Sero-epidemiology of peste des petits ruminants (PPR) in Pakistan

A sero survey was conducted during 2005-2006 to estimate the sero prevalence of PPR in the small ruminant population of Pakistan. A total of 2798 samples were collected including goats (1979) and sheep (819) from villages in 27 randomly selected districts. These were tested by cELISA for PPRV and true prevalence estimates were calculated by Rogan and Gladen estimator. Overall, 1273 (45.5%) were found positive; 980 (49.5%) of 1979 samples from goats and 293 (35.8%) of 819 serum samples from sheep were positive. The true sero-prevalence of PPR was estimated to be 48.5% (95% CI, 46.6-50.3), and 52.9% (95% CI, 50.7-55.1) and 37.7 (95% CI, 34.4-41.0) for goats and sheep, respectively. PPR virus is widely distributed all across Pakistan and has become an endemic infection of small ruminants. Since it is one of the leading causes of morbidity and mortality in small ruminants, it poses a serious threat to food security and the rural economy in Pakistan.

The epidemiology of peste des petits ruminants in Pakistan

Peste des petits ruminants (PPR) is an acute and highly contagious viral disease of small ruminants, which is newly emerging in Pakistan. Information provided by participatory disease surveillance teams was used to develop a database for PPR outbreaks in Pakistan. Twenty-four villages were selected throughout the country and field investigations were conducted in each village to study the dynamics of the disease. In each area, flocks with a history of PPR were identified and serological sampling was conducted. Some 1,463 small ruminants (sheep and goats) were sampled and 1,096 tested positive for the presence of antibodies against PPR. These results clearly indicate that PPR is prevalent throughout Pakistan.

Inactivation of infectious bursal disease virus by binary ethylenimine and formalin

In this experiment conducted to study the inactivation dynamics of infectious bursal disease virus (IBDV) by binary ethylenimine (BEI) in comparison with formalin, IBDV was isolated from the bursa of infected chickens and its confirmation was done by agar gel precipitation test. Viral suspensions were subjected to inactivation with BEI and formalin for pre-set time intervals. BEI was employed at concentrations of 0.001 and 0.002 mol/L while formalin was used at 0.1% and 0.2%. Sampling was done at 6, 12, 24, 36 and 48 h of incubation and samples were tested for their inactivation status in 9-day-old embryonated eggs and 3-week-old broiler chickens. IBDV was completely inactivated by 0.001 and 0.002 mol/L BEI after 36 h of incubation at 37 degrees C, whereas formalin at 0.1% and 0.2% concentrations inactivated IBDV in 24 h.

Hepatitis C virus core and envelope proteins do not suppress the host's ability to clear a hepatic viral infection

Several hepatitis C virus (HCV) proteins have been shown in vitro to interact with host cellular components that are involved in immune regulation. However, there is a paucity of data supporting the relevance of these observations to the in vivo situation. To test the hypothesis that such an interaction suppresses immune responses, we studied a line of transgenic C57BL/6 mice that express the HCV core and envelope proteins in the liver. The potential effects of these proteins on the hepatic immune response were evaluated by challenging these mice with a hepatotropic adenovirus. Both transgenic and nontransgenic mice developed similar courses of infection and cleared the virus from the liver by 28 days postinfection. Both groups of mice mounted similar immunoglobulin G (IgG), IgG2a, interleukin-2, and tumor necrosis factor alpha responses against the virus. Additionally, BALB/c mice were able to clear infection with recombinant adenovirus that does or does not express the HCV core and envelope 1 proteins in the same manner. These data suggest that HCV core and envelope proteins do not inhibit the hepatic antiviral mechanisms in these murine experimental systems and thus favor a model in which HCV circumvents host responses through a mechanism that does not involve general suppression of intrahepatic immune responses.