Toxicologic Pathology Forum: A Roadmap for Building State-of-the-Art Digital Image Data Resources for Toxicologic Pathology in the Pharmaceutical Industry

Digitization of histologic slides brings with it the promise of enhanced toxicologic pathology practice through the increased application of computational methods. However, the development of these advanced methods requires access to substrate image data, that is, whole slide images (WSIs). Deep learning methods, in particular, rely on extensive training data to develop robust algorithms. As a result, pharmaceutical companies interested in leveraging computational methods in their digital pathology workflows must first invest in data infrastructure to enable data access for both data scientists and pathologists. The process of building robust image data resources is challenging and includes considerations of generation, curation, and storage of WSI files, and WSI access including via linked metadata. This opinion piece describes the collective experience of building resources for WSI data in the Roche group. We elaborate on the challenges encountered and solutions developed with the goal of providing examples of how to build a data resource for digital pathology analytics in the pharmaceutical industry.

[Clinical efficacy and safety of endobronchial one-way valves for the treatment of bronchopleural fistula]

Objective: To investigate the efficacy and safety of interventional endobronchial one-way valves (EBV) for the treatment of peripheral bronchopleural fistula (BPF). Methods: A total of 33 patients with peripheral BPF who underwent EBV implantation in Endoscopy Center of Shanghai Pulmonary Hospital from August 2017 to December 2021 were selected as the research objects. All the patients were diagnosed with peripheral BPF before the implantation surgery. The detailed medical records of the patients were collected, and the etiology, lesion location, treatment method and operation process, treatment efficacy and postoperative complications were analyzed to evaluate the efficacy and safety of EBV implantation. Results: Of the 33 patients in our study, 26 were male and 7 were female. The median age was 54.7 (28-86) years. There were 18 cases of BPF after thoracic surgery (54.5%), 6 cases of chronic obstructive pulmonary disease complicated with spontaneous pneumothorax (18.2%), and 12 cases of pulmonary tuberculosis and non-tuberculous mycobacterial infection with spontaneous pneumothorax (36.4%). A total of 63 valves were inserted in the 33 cases, and a maximum of valves and at least one were inserted in a single case. The lesions were located in the right lower lobe in 16 cases (48.5%) and the left upper lobe in 12 cases (36.4%). Of the 33 patients undergoing EBV placement, 22 (66.7%) were successful, with chest drainage tube indwelling duration of (88.5±36.6) days and (29.6±11.4) days, respectively, before and after EBV treatment. The time from EBV placement to successful withdrawal of EBV was (102.2±31.3) days. During a postoperative follow-up of 6 months after EBV treatment, the main complications were 29 cases with attachment of secretions to the EBV (90.6%) and 13 cases (40.6%) with mild granulation proliferation. In addition, there were five patients with moderate to severe granulation proliferation (15.6%), one with valve displacement or shedding (3.1%), and one with bleeding (3.1%). Conclusions: In this study, the success rate of EBV placement and occlusion was 66.7%. Transbronchoscopic EBV placement in the treatment of peripheral BPF is a effective treatment with relatively minor complications.

[Effect of porous zirconia ceramics on proliferation and differentiation of osteoblasts]

OBJECTIVE

To investigate the effect of porous surface morphology of zirconia on the proliferation and differentiation of osteoblasts.

METHODS

According to different manufacturing and pore-forming methods, the zirconia specimens were divided into 4 groups, including milled sintering group (M-Ctrl), milled porous group (M-Porous), 3D printed sintering group (3D-Ctrl) and 3D printed porous group (3D-Porous). The surface micromorphology, surface roughness, contact angle and surface elements of specimens in each group were detected by scanning electron microscope (SEM), 3D laser microscope, contact angle measuring device and energy-dispersion X-ray analysis, respectively. MC3T3-E1 cells were cultured on 4 groups of zirconia discs. The cell morphology of MC3T3-E1 cells on zirconia discs was eva-luated on 1 and 7 days by SEM. The cell proliferation was detected on 1, 3 and 5 days by cell counting kit-8 (CCK-8). After osteogenic induction for 14 days, the relative mRNA expression of alkaline phosphatase (ALP), type Ⅰ collagen (Colla1), Runt-related transcription factor-2 (Runx2) and osteocalcin (OCN) in MC3T3-E1 cells were detected by real-time quantitative polymerase chain reaction.

RESULTS

The pore size [(419.72±6.99) μm] and pore depth [(560.38±8.55) μm] of 3D-Porous group were significantly larger than the pore size [(300.55±155.65) μm] and pore depth [(69.97±31.38) μm] of M-Porous group (P < 0.05). The surface of 3D-Porous group appeared with more regular round pores than that of M-Porous group. The contact angles of all the groups were less than 90°. The contact angles of 3D-Ctrl (73.83°±5.34°) and M-Porous group (72.7°±2.72°) were the largest, with no significant difference between them (P>0.05). Cells adhered inside the pores in M-Porous and 3D-Porous groups, and the proliferation activities of them were significantly higher than those of M-Ctrl and 3D-Ctrl groups after 3 and 5 days' culture (P < 0.05). After 14 days' incubation, ALP, Colla1, Runx2 and OCN mRNA expression in 3D-Porous groups were significantly lower than those of M-Ctrl and 3D-Ctrl groups (P < 0.05). Colla1, Runx2 and OCN mRNA expressions in M-Porous group were higher than those of 3D-Porous group (P < 0.05).

CONCLUSION

The porous surface morphology of zirconia can promote the proliferation and adhesion but inhibit the differentiation of MC3T3-E1 cells.

[Pathogen distribution and antimicrobial resistance among lower respiratory tract infections in patients with hematological malignancies]

Objective: To investigate the pathogen distribution and antimicrobial resistance among lower respiratory tract infections in patients with hematological malignancies. Methods: Sputum samples were collected from 967 patients with hematological malignancies and lower respiratory tract infections in Department of Hematology,the Second Hospital of Shanxi Medical University from January 2017 to July 2020. The pathogens and drug sensitivity reports were carried out by automatic bacterial identification instruments. WHONET 5.6 and SPSS 20.0 softwares were used for statistical analysis. Results: A total of 961 strains of pathogens were isolated, 516 (53.7%) pathogens were Gram-negative bacteria, mainly 118 strains of Klebsiella pneumonia (12.3%), 68 strains of Pseudomonas aeruginosa (7.1%), 67 strains of Acinetobacter baumannii (7.0%),52 strains of Stenotrophomonas maltophilia (5.4%), 43 strains of Escherichia coli (4.5%), and 42 strains of Enterbacter cloacae (4.4%). There were 171 (17.8%) strains of Gram-positive bacteria and 274 (28.5%) fungi. The drug resistance rates of Pseudomonas aeruginosa and Acinetobacter baumannii to carbapenem were 22.1%-31.3%. Stenotrophomonas maltophilia was sensitive to levofloxacin, compound sulfamethoxazole and minocycline. The antimicrobial resistance rates of these three enterobacteria to carbapenems, cefoperazone/sulbactam, piperacillin/tazobactam were low (<10%). The resistant Gram-positive bacteria to ticoplanin, vancomycin and linazolamide were not detected. Conclusion: The major pathogens related to lower respiratory tract infections in patients with hematological malignancies are gram-negative bacteria in our centre. Different pathogens appear different characteristics of antimicrobial resistance.

High-yield strain of fusidic acid obtained by atmospheric and room temperature plasma mutagenesis and the transcriptional changes involved in improving its production in fungus Fusidium coccineum

AIMS

To obtain the high-yield strain of fusidic acid, which is produced from fungus Fusidium coccineum and is the only fusidane-type antibiotic that has been used clinically, and confirm the changes in the transcription levels involved in increasing its production.

METHODS AND RESULTS

By using the atmospheric and room temperature plasma mutagenesis technology, a high-yield mutant strain of fusidic acid-producing fungus F. coccineum was obtained. Using the genomic analysis of the original strain based on biosynthetic pathways of ergosterol and helvolic acid, we demonstrate that the pathway involved in the biosynthesis of 2,3-oxidosqualene from acetyl coenzyme A was shared by fusidic acid and ergosterol, and fusidic acid was finally synthesized by the catalysis of multiple cytochrome P450s and short-chain dehydrogenase/reductase from 2,3-oxidosqualene. Then, through the transcriptomic analysis of the original and mutagenized strain, it revealed that the proposed pathway from sucrose to fusidic acid was the most significantly up-regulated in the transcription levels of the mutant strain.

CONCLUSIONS

The changes in the transcription levels of fusidic acid during its biosynthesis might result in high-yield of fusidic acid in the mutant strain. This is the first report on the whole biosynthetic pathway of fusidic acid in F. coccineum.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study obtain the genetic basis for the biosynthesis of fusidic acid which could be beneficial for the molecular modifications of F. coccineum to further increase its yield by fermentation in future, and established the foundation to reveal the mechanism of the high-yield of the mutant strain.

[Clinical analysis of 234 esophageal foreign bodies]

Objective: To explore the clinical characteristics and treatment methods of esophageal foreign body. Method: The clinical data of 234 patients with esophageal foreign bodies admitted to our department from January 2015 to August 2018 were retrospectively analyzed, including course time, foreign body types, surgical methods, imaging manifestations and treatment related complications. Result: The diagnosis of esophageal foreign bodies was confirmed by esophageal CT or esophageal barium meal X-ray examination before operation in 234 patients. Course time varied from 3 hours to 7 days, and the jujube nucleus was the most common food-borne foreign body.223 patients underwent esophagoscopic exploration and foreign body removal under general intravenous anesthesia, 11 of them had no definite esophageal foreign body, 22 had esophageal perforation and periesophagitis. After removal of foreign body, the nasogastric feeding tube was inserted. About 10 days later, the nasogastric feeding tube was removed when they got healthy. Nine cases underwent cervical abscess incision and drainage under general anesthesia. The average postoperative hospital day was 11 days. Conclusion: The rigid esophagoscopy is a safe and effective method for the esophageal foreign bodies. And neck abscess incision must be necessary,when they suffered from esophageal perforation with neck abscess and other serious complications.

[The diagnosis and treatment of neck abscess and mediastinal abscess following esophageal perforation induced by esophageal foreign body]

Objective:The aim of this study is to discuss the clinical presentation, imaging examination and treatment of neck abscess and mediastinal abscess following esophageal perforation induced by esophageal foreign body. Method:Six patients all underwent lateral neck incision and drainage of neck abscess. Simultaneously, mediastinal abscess drainage was performed in 3 cases with mediastinal abscess. Result:All 6 patients were cured. The median time of extraction of gastric tube was 11 days (7-30 days). All patients were not treated with tracheotomy. Conclusion:Neck and chest CT should be done as soon as possible for suspected patients to definite the location of foreign body and the relationship between foreign body and surrounding structures. Patient who were suspected with neck abscess and mediastinal abscess should undergo surgery to remove foreign body and drain the infectious deep neck and mediastinal spaces as early as possible.

[Comparison of the secretory related molecules expression in stem cells from the pulp of human exfoliated deciduous teeth and dental pulp stem cells]

Objective: To compare the general biological characteristics and the expressions of proteins involved in secretion in stem cells from the pulp of human exfoliated deciduous teeth (SHED) and dental pulp stem cells (DPSC). Methods: SHED and DPSC were cultured and collected at passage 4 (P4) and P7. The submandibular gland epithelial and interstitial cells were cultured with tissue culture method. The cell morphology was observed using a phase contrast microscope. Flow cytometry was used to detect stem cell surface markers. Cell counting kit-8 (CCK-8) and IncuCyte ZOOM were used to evaluate cell proliferation. Quantitative real-time PCR (qPCR) was performed to examine the mRNA expressions of proteins involved in fluid and protein secretion. Results: P4 and P7 SHED and DPSC were spindle-shaped. There was no difference in cell morphology among the 4 group cells. P4 and P7 SHED and DPSC expressed CD29, CD44, CD73, and CD90, the mesenchymal stem cell markers, while, CD49f and CD117, the epithelium markers were undetected. There was no difference in cell proliferation among the 4 group cells. Compared with P4 SHED, the expressions of muscarinic cholinergic receptor 1 (MR1), MR3, aquaporin 5 (AQP5), β1-adrenoceptor (β1-AR), α-amylase, and mucin 5B in SHED were not different, while β2-AR expression was decreased (P<0.05). Compared with P4 DPSC, the expressions of MR3, β2-AR, and α-amylase in P7 DPSC were not different, while, the expressions of MR1, AQP5, β1-AR, and mucin 5B were decreased (P<0.05). Compared with primary cultured submandibular gland epithelial cells and gland tissues from a child, the expressions of proteins involved in secretion were all decreased. Compared with submandibular epithelial cells from adults, the expression of AQP5 in P4 DPSC was decreased (P<0.05), while other proteins were not different. The expressions of AQP5, β1-AR, α-amylase and mucin 5B in P7 DPSC were increased (P<0.05), while other proteins were not different. In P4 and P7 DPSC, all the protein expression levels were decreased, compared with those in submandibular gland tissues (P<0.01). Conclusions: Compared with DPSC, SHED have stable growth and the expressions of protein involved fluid and protein secretion are low. Based on its extensive sources and easy separation, SHED can be used as the ideal seed cell for salivary gland tissue engineering and the treatment of salivary gland hypofunction, and the P4 to P7 SHED can be used for experimental study.

[Risk factors of central neck lymph node metastasis in cN0 papillary thyroid carcinoma]

Objective:To investigate the risk factors of central neck lymph node metastasis (CNLNM) in cN0 papillary thyroid carcinoma. Method:Retrospective analysis of 114 patients with papillary thyroid carcinoma in stage of cN0 who underwent primary treatment. Collected the clinical and pathological data, used the univariate and multivariate analysis to investigate the risk factors of central neck lymph node metastasis and high volume central neck lymph node metastasis.Result:In the univariate analysis, age (48.2% in<45 years vs 27.6% in≥45 years), multifocal (51% with vs 27.7% without), nodular goiter (58.8% with vs 28.7% without), showed significant difference in prevalence of CNLNM. Age (14.3% in<45 years vs 1.7% in≥45 years), tumor size (19.2% >1 cm vs 4.5%≤1 cm) showed significant difference in prevalence of high volume CNLNM. Inmultivariate analysis, age (RR= 0.304), multifocal (RR= 3.637) and nodular goiter (RR= 4.132) showed the independent risk factor of CNLNM.Conclusion:For cN0 patients with thyroid papillary carcinoma, if the age is younger than 45 years old, the tumor is multifocal, or associatedwith nodular goiter, the surgery should be more aggressive in the prophylactic central neck dissection.

[Assessment right atrial function in patients with systemic lupus erythematosus by speckle tracking and three-dimensional echocardiography]

Objective: To evaluate right atrial function in systemic lupus erythematosus (SLE) with normal pulmonary pressure by using two dimensional-speckle tracking imaging (2D-STI) and real-time three-dimensional echocardiography(RT-3DE). Methods: A totoal of 40 patients with SLE and 40 control subjects were collected between December 2011 and May 2014 from Ningbo Medical Treatment Center Lihuili Hospital. Right atrial global longitudinal strain (RAGLS) and all kinds of right atrium volume index (RAVI) were detected. Relationship between tricuspid annular plane systolic excursion(TAPSE), tricuspid annulus systolic peak velocity (S'), right ventricular myocardial performance index (RVMPI), E_TV/e'_TV and the right atrium parameters were analyzed. Results: SLE group's right atrium maximal volume index(RAVImax)(33.5±11.1) ml/m^2, right atrium minimal volume index (RAVImin)(13.2±4.5) ml/m^2, right atrium presystolic volume index (RAVIpre) (2.57±10.2) ml/m^2, right atrium total emptying volume index(RAVIt)(20.2±8.1)ml/m^2, right atrium active emptying volume index (RAVIa)(12.5±7.5) ml/m²) were increased .But right atrium passive emptying volume index(RAVIp)( 7.8±2.7) ml/m² and right atrial global longitudinal strain (RAGLS) (38.2%±7.7% ) were decreased (both P<0.05). RAGLS was positive correlated with S' and TAPSE, the r value were 0.565 and 0.445 respectively (both P<0.01). E_TV/e'_TV was positive correlated with RAVIpre, RAVIa, the r value were 0.469 and 0.481 respectively (both P<0.05). Conclusion: Detecting right atrial function by 2D-STI and RT-3DE could diagnose right atrial dysfunction in early stage of SLE patients with normal pulmonary pressure. The method is simple, has significant clinical value.

Characterization of 19 microsatellite loci in the clonal monkshood Aconitum kusnezoffii (Ranunculaceae)

PREMISE OF THE STUDY

Microsatellite loci were isolated and characterized from Aconitum kusnezoffii (Ranunculaceae) to estimate male and female reproductive success and evaluate the effects of clonal growth on sexual reproduction.

METHODS AND RESULTS

A genomic enrichment approach was used to develop microsatellite markers. In three investigated A. kusnezoffii populations, a total of 19 microsatellite loci were successfully amplified, and 13 of these loci were polymorphic. Most of the primer pairs designed for the identified loci also amplified corresponding microsatellite loci in A. barbatum var. puberulum and A. alboviolaceum.

CONCLUSIONS

The identified microsatellite loci will be useful for quantifying male and female fitness in A. kusnezoffii and evaluating the effects of clonal growth on sexual reproduction.

Induction of long-term oscillations in the γ frequency band by nAChR activation in rat hippocampal CA3 area

The hippocampal neuronal network oscillation at γ frequency band (γ oscillation) is generated by the precise interaction between interneurons and principle cells. γ oscillation is associated with attention, learning and memory and is impaired in the diseased conditions such as Alzheimer's disease (AD) and schizophrenia. Nicotinic acetylcholine receptor (nAChR) plays an important role in the regulation of hippocampal neurotransmission and network activity. It is not known whether nicotine modulates plasticity of network activity at γ oscillations in the hippocampus. In this study we investigated the effects of nicotine on the long-term changes of KA-induced γ oscillations. We found that hippocampal γ oscillations can be enhanced by a low concentration of nicotine (1μM), such an enhancement lasts for hours after washing out of nicotine, suggesting a form of synaptic plasticity, named as long-term oscillation at γ frequency band (LTOγ). Nicotine-induced LTOγ was mimicked by the selective α4β2 but not by α7 nAChR agonist and was involved in N-methyl-d-aspartate (NMDA) receptor activation as well as depended on excitatory and inhibitory neurotransmission. Our results indicate that nAChR activation induced plasticity in γ oscillation, which may be beneficial for the improvement of cognitive deficiency in AD and schizophrenia.

Association of the TNF-α+489 G/A polymorphism with chronic obstructive pulmonary disease risk in Asians: meta-analysis

The association between the TNF-α +489 G/A polymorphism and chronic obstructive pulmonary disease (COPD) remains controversial because of small group size and varied design among different studies. In the present study, a meta-analysis was conducted to assess the association between the +489 G/A polymorphism and COPD risk. A comprehensive search was conducted to identify articles that have reported an association between the TNF-α +489 G/A polymorphism and COPD risk. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated under both dominant (AA+GA vs GG genotypes) and allele (A vs G) models. Heterogeneity was assessed, as well as publication bias. Nine articles with ten eligible studies were included in this analysis. Significant association between the +489 G/A polymorphism and COPD was identified in Asians under the allele model (OR = 1.582, 95%CI = 1.035-2.419). However, no significant difference was found in the Caucasian groups. Strong evidence for between-study heterogeneity was identified under both models, and no publication bias was detected. Our results indicated a potential role of the A allele of the TNF-α +489 G/A polymorphism in increasing COPD risk in Asians, but not in Caucasians. Additional studies will be necessary to verify this conclusion.

Association of -238G/A and -863C/A polymorphisms in the TNF-α gene with chronic obstructive pulmonary disease based on a meta-analysis

Chronic obstructive pulmonary disease (COPD) is a chronic systemic inflammatory disease; increasing evidence indicates that the TNF-α polymorphism is associated with progression of this disease. Few studies have focused upon association between TNF-α -238G/A or -863C/A polymorphism and COPD risk. Reported associations have been controversial because of small sample size and varied study design among the different studies. We performed a meta-analysis to assess the correlation of these two polymorphisms in the TNF-α gene with COPD risk. A comprehensive search was conducted to identify all published articles on the association between TNF-α -238G/A or -863C/A polymorphism and COPD risk from different databases. Pooled odds ratios (ORs) with 95% confidence intervals (CI) were calculated, and the heterogeneity and publication bias were assessed. Eight articles with 10 eligible studies met our inclusion criteria; six studies were of the -238G/A polymorphism and the others involved the -863C/A polymorphism. In the case of the -863C/A polymorphism, significant association was detected only in Asians in the A allele carriers (GA+AA versus GG genotype) and allele (A versus G allele) model (OR = 0.505, 95%CI = 0.321-0.795 and OR = 0.560, 95%CI = 0.368-0.851, respectively). However, no significant association was detected for the -238G/A polymorphism. No evidence of between-study heterogeneity and publication bias was detected. We suggest a potentially protective role of the A allele in the TNF-α -863C/ A polymorphism against developing COPD in Asians. This hypothesis needs further studies for confirmation.

Association of the G403A polymorphism in the RANTES gene with coronary artery disease: a meta-analysis

The G403A polymorphism in the RANTES (regulated on activation normal T cell expressed and secreted) gene has a key role in the expression of RANTES, which has been detected in a range of cells in atherosclerotic plaque. However, the association of this polymorphism with the risk of coronary artery disease (CAD) remains controversial. A meta-analysis was performed to assess the association of the G403A polymorphism in the RANTES gene with the risk of CAD. A comprehensive search was conducted to identify all studies published on the association of the RANTES gene G403A polymorphism with CAD risk. The fixed or random-effect pooled measure was adopted based on a heterogeneity test among studies, which was evaluated using I(2). Potential sources of between-study heterogeneity were explored using meta-regression analysis. Publication bias was estimated with Begg's rank correlation method. Eight articles were included in this meta-analysis, with 4601 CAD cases and 2522 controls. No significant association of RANTES gene G403A polymorphism with CAD was identified in any of the codominant, dominant, recessive, homozygote, or heterozygote inheritance models. No evidence of publication bias was detected. The meta-analysis suggested that the A allele of the G403A polymorphism in the RANTES gene has no effect on the risk of CAD. This relationship needs to be confirmed by further studies.

[Analysis of 138 cases of superior oblique muscle paralysis]

Congenital or early infantile paralysis of the superior oblique muscle is primarily caused by congenital anomaly of the ocular muscles or by birth trauma, while the acquired is mostly caused by trauma, influenza, or acute infection. The diagnosis is done by Lancaster's test, the synoptophore, and the cover test in combination with prisms. For incooperative children, Park's three step test may be used. The angle of strabismus can be measured with the cover test and prisms, or by the synoptophore. For treatment, the patients were divided into (1) the group of prism correction, (2) the group of inferior oblique attenuation in the same eye, (3) the group of inferior rectus attenuation in the other eye, (4) the group of inferior oblique attenuation in the same eye combined with inferior rectus attenuation in the other eye, and (5) the group of superior oblique paralysis complicated with horizontal heterotropia. The immediate and longterm curative effect had been satisfactory. It is important to differentiate congenital cases from the acquired, the primary torticollis from that of ophthalmic origin, and the paralysis of superior oblique in one eye from the paralysis of the superior rectus in the other eye.