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Article: Single patch super-resolution of histopathology whole slide images: a comparative study.

Afshari, Mehdi / Yasir, Saba / Keeney, Gary L / Jimenez, Rafael E / Garcia, Joaquin J / Tizhoosh, Hamid R

Journal of medical imaging (Bellingham, Wash.)

2023 Volume 10, Issue 1, Page(s) 17501

Abstract: Purpose: The latest generation of scanners can digitize histopathology glass slides for computerized image analysis. These images contain valuable information for diagnostic and prognostic purposes. Consequently, the availability of high digital ... ...

Abstract	Purpose: The latest generation of scanners can digitize histopathology glass slides for computerized image analysis. These images contain valuable information for diagnostic and prognostic purposes. Consequently, the availability of high digital magnifications like Approach: Over the past decade, the digital solution of enhancing images resolution has been addressed by the concept of super resolution (SR). In addition, deep learning has offered state-of-the-art results for increasing the image resolution after acquisition. In this study, multiple deep learning networks designed for image SR are trained and assessed for the histopathology domain. Results: We report quantitative and qualitative comparisons of the results using publicly available cancer images to shed light on the benefits and challenges of deep learning for extrapolating image resolution in histopathology. Three pathologists evaluated the results to assess the quality and diagnostic value of generated SR images. Conclusions: Pixel-level information, including structures and textures in histopathology images, are learnable by deep networks; hence improving the resolution quantity of scanned slides is possible by training appropriate networks. Different SR networks may perform best for various cancer sites and subtypes.
Language	English
Publishing date	2023-01-31
Publishing country	United States
Document type	Journal Article
ISSN	2329-4302
ISSN	2329-4302
DOI	10.1117/1.JMI.10.1.017501
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Article ; Online: Pathophysiological Implications of Interstitial Cajal-like Cells (ICC-like) in Uterus: A Comparative Study with Gastrointestinal ICCs.

López-Pingarrón, Laura / Almeida, Henrique / Pereboom-Maicas, Desirée / García, Joaquín J

Current issues in molecular biology

2023 Volume 45, Issue 9, Page(s) 7557–7571

Abstract: The main function of interstitial cells of Cajal (ICCs) is to regulate gastrointestinal peristalsis by acting as a "pacemaker" cell by generating spontaneous slow electrical waves. In 2005, electron microscopy revealed a cell type similar to ICCs (ICC- ... ...

Abstract	The main function of interstitial cells of Cajal (ICCs) is to regulate gastrointestinal peristalsis by acting as a "pacemaker" cell by generating spontaneous slow electrical waves. In 2005, electron microscopy revealed a cell type similar to ICCs (ICC-like) outside the gastrointestinal tract, with contractile activity and c-Kit
Language	English
Publishing date	2023-09-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2000024-8
ISSN	1467-3045 ; 1467-3037
ISSN (online)	1467-3045
ISSN	1467-3037
DOI	10.3390/cimb45090476
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Article: Melatonin as a Coadjuvant in the Treatment of Patients with Fibromyalgia.

González-Flores, David / López-Pingarrón, Laura / Castaño, María Yolanda / Gómez, María Ángeles / Rodríguez, Ana B / García, Joaquín J / Garrido, María

Biomedicines

2023 Volume 11, Issue 7

Abstract: Fibromyalgia syndrome (FMS) is a chronic widespread pain syndrome that is accompanied by fatigue, sleep disturbances, anxiety, depression, lack of concentration, and neurocognitive impairment. As the currently available drugs are not completely ... ...

Abstract	Fibromyalgia syndrome (FMS) is a chronic widespread pain syndrome that is accompanied by fatigue, sleep disturbances, anxiety, depression, lack of concentration, and neurocognitive impairment. As the currently available drugs are not completely successful against these symptoms and frequently have several side effects, many scientists have taken on the task of looking for nonpharmacological remedies. Many of the FMS-related symptoms have been suggested to be associated with an altered pattern of endogenous melatonin. Melatonin is involved in the regulation of several physiological processes, including circadian rhythms, pain, mood, and oxidative as well as immunomodulatory balance. Preliminary clinical studies have propounded that the administration of different doses of melatonin to patients with FMS can reduce pain levels and ameliorate mood and sleep disturbances. Moreover, the total antioxidant capacity, 6-sulfatoxymelatonin and urinary cortisol levels, and other biological parameters improve after the ingestion of melatonin. Recent investigations have proposed a pathophysiological relationship between mitochondrial dysfunction, oxidative stress, and FMS by looking at certain proteins involved in mitochondrial homeostasis according to the etiopathogenesis of this syndrome. These improvements exert positive effects on the quality of life of FMS patients, suggesting that the use of melatonin as a coadjuvant may be a successful strategy for the management of this syndrome.
Language	English
Publishing date	2023-07-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines11071964
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Article ; Online: Role of Oxidative Stress on the Etiology and Pathophysiology of Amyotrophic Lateral Sclerosis (ALS) and Its Relation with the Enteric Nervous System.

López-Pingarrón, Laura / Almeida, Henrique / Soria-Aznar, Marisol / Reyes-Gonzales, Marcos C / Terrón, María Pilar / García, Joaquín J

Current issues in molecular biology

2023 Volume 45, Issue 4, Page(s) 3315–3332

Abstract: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease affecting motor neurons in the spinal cord, cerebral cortex, and medulla oblongata. Most patients present a clinical phenotype of classic ALS-with predominant atrophy, muscle ... ...

Abstract	Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease affecting motor neurons in the spinal cord, cerebral cortex, and medulla oblongata. Most patients present a clinical phenotype of classic ALS-with predominant atrophy, muscle weakness, and fasciculations-and survival of 3 to 5 years following diagnosis. In the present review, we performed a literature search to provide an update on the etiology and pathophysiological mechanisms involved in ALS. There are two types of ALS: the familial form with genetic involvement, and the sporadic form with a multifactorial origin. ALS pathophysiology is characterized by involvement of multiple processes, including oxidative stress, glutamate excitotoxicity, and neuroinflammation. Moreover, it is proposed that conditioning risk factors affect ALS development, such as susceptibility to neurodegeneration in motor neurons, the intensity of performed physical activity, and intestinal dysbiosis with involvement of the enteric nervous system, which supports the existing theories of disease generation. To improve patients' prognosis and survival, it is necessary to further deepen our understanding of the etiopathogenesis of ALS.
Language	English
Publishing date	2023-04-07
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2000024-8
ISSN	1467-3045 ; 1467-3037
ISSN (online)	1467-3045
ISSN	1467-3037
DOI	10.3390/cimb45040217
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Article ; Online: Identification of SARS-CoV-2 from Human Lung Formalin-Fixed Paraffin-Embedded Tissue Sections Using Mass Spectrometry.

Mangalaparthi, Kiran K / Singh, Smrita / Garapati, Kishore / Garcia, Joaquin J / Kipp, Benjamin R / Roden, Anja C / Pandey, Akhilesh

Omics : a journal of integrative biology

2023 Volume 27, Issue 10, Page(s) 494–496

MeSH term(s)	Humans ; SARS-CoV-2 ; Paraffin Embedding/methods ; COVID-19 ; Lung ; Formaldehyde/chemistry ; Mass Spectrometry ; Tissue Fixation/methods
Chemical Substances	Formaldehyde (1HG84L3525)
Language	English
Publishing date	2023-10-09
Publishing country	United States
Document type	Letter
ZDB-ID	2030312-9
ISSN	1557-8100 ; 1536-2310
ISSN (online)	1557-8100
ISSN	1536-2310
DOI	10.1089/omi.2023.0157
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Article ; Online: Creating an atlas of normal tissue for pruning WSI patching through anomaly detection.

Nejat, Peyman / Alsaafin, Areej / Alabtah, Ghazal / Comfere, Nneka I / Mangold, Aaron R / Murphree, Dennis H / Zot, Patricija / Yasir, Saba / Garcia, Joaquin J / Tizhoosh, H R

Scientific reports

2024 Volume 14, Issue 1, Page(s) 3932

Abstract: Patching whole slide images (WSIs) is an important task in computational pathology. While most of them are designed to classify or detect the presence of pathological lesions in a WSI, the confounding role and redundant nature of normal histology are ... ...

Abstract	Patching whole slide images (WSIs) is an important task in computational pathology. While most of them are designed to classify or detect the presence of pathological lesions in a WSI, the confounding role and redundant nature of normal histology are generally overlooked. In this paper, we propose and validate the concept of an "atlas of normal tissue" solely using samples of WSIs obtained from normal biopsies. Such atlases can be employed to eliminate normal fragments of tissue samples and hence increase the representativeness of the remaining patches. We tested our proposed method by establishing a normal atlas using 107 normal skin WSIs and demonstrated how established search engines like Yottixel can be improved. We used 553 WSIs of cutaneous squamous cell carcinoma to demonstrate the advantage. We also validated our method applied to an external dataset of 451 breast WSIs. The number of selected WSI patches was reduced by 30% to 50% after utilizing the proposed normal atlas while maintaining the same indexing and search performance in leave-one-patient-out validation for both datasets. We show that the proposed concept of establishing and using a normal atlas shows promise for unsupervised selection of the most representative patches of the abnormal WSI patches.
MeSH term(s)	Humans ; Carcinoma, Squamous Cell ; Skin Neoplasms ; Biopsy ; Ascomycota ; Breast
Language	English
Publishing date	2024-02-16
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/s41598-024-54489-9
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Article ; Online: Democratizing Artificial Intelligence in Anatomic Pathology.

Flotte, Thomas J / Derauf, Stephanie A / Byrd, Rachel K / Kroneman, Trynda N / Bell, Debra A / Stetzik, Lucas / Lee, Seung-Yi / Samiei, Alireza / Hart, Steven N / Garcia, Joaquin J / Beamer, Gillian / Westerling-Bui, Thomas

Archives of pathology & laboratory medicine

2024

Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	194119-7
ISSN	1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
ISSN (online)	1543-2165
ISSN	0363-0153 ; 0096-8528 ; 0003-9985
DOI	10.5858/arpa.2023-0205-OA
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Article ; Online: Review of treatment modalities and outcomes of patients with basal cell adenocarcinoma.

Gutierrez, Claudia N / Chatzopoulos, Kyriakos / Garcia, Joaquin J / Janus, Jeffrey R

American journal of otolaryngology

2020 Volume 41, Issue 3, Page(s) 102414

Abstract: Purpose: This study summarizes the treatment modalities of basal cell adenocarcinoma (BCAC) of the parotid gland and subsequent outcome at a single institution to better define the treatment of this rare tumor.: Material and methods: A retrospective ... ...

Abstract	Purpose: This study summarizes the treatment modalities of basal cell adenocarcinoma (BCAC) of the parotid gland and subsequent outcome at a single institution to better define the treatment of this rare tumor. Material and methods: A retrospective review of patients treated for BCAC of the parotid gland from 1/01/1996 to 08/1/2018 was performed. Patients were identified using our institution's Cancer Registry. Results: A total of thirteen patients (46% female, median age of 56) treated for BCAC of the parotid gland were identified. Eight patients (57%) were staged as T1, four were staged as T2 (29%), and two were stage T4a (14%) due to tumor involvement of the facial nerve. None of the patients had nodal involvement or distant metastases. Three patients (21%) underwent radiation therapy ranging from 60-70Gy for positive margin or facial nerve involvement by tumor. Five patients (36%) underwent a neck dissection (ND) ranging from just a level IIb dissection up to levels IIa, IIb, and III with none of the nodes being positive for disease. The remainder of patients did not undergo a neck dissection. Follow-up was 8.1 ± 6.2 (mean ± SD) years with no local or regional recurrence at time of last follow-up in any patient cohort. Conclusions: Our review suggests that elective neck dissections are not necessary following resection of T1/T2N0M0 basal cell adenocarcinoma for the prevention of local or regional recurrence. No longer performing neck dissections for T1/T2N0M0 BCAC would reduce the morbidity associated with the treatment of this rare parotid tumor.
MeSH term(s)	Adenocarcinoma/diagnostic imaging ; Adenocarcinoma/radiotherapy ; Adenocarcinoma/surgery ; Adult ; Aged ; Aged, 80 and over ; Diffusion Magnetic Resonance Imaging ; Female ; Follow-Up Studies ; Humans ; Male ; Middle Aged ; Neck Dissection ; Neoplasm Recurrence, Local/prevention & control ; Parotid Neoplasms/diagnostic imaging ; Parotid Neoplasms/radiotherapy ; Parotid Neoplasms/surgery ; Retrospective Studies ; Time Factors ; Treatment Outcome ; Unnecessary Procedures
Language	English
Publishing date	2020-02-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	604541-8
ISSN	1532-818X ; 0196-0709
ISSN (online)	1532-818X
ISSN	0196-0709
DOI	10.1016/j.amjoto.2020.102414
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Article ; Online: SARS-CoV-2 RNA detection in Formalin-Fixed Paraffin-Embedded (FFPE) tissue by droplet digital PCR (ddPCR).

Majumdar, Ramanath / Vrana, Julie A / Koepplin, Justin W / Milosevic, Dragana / Roden, Anja C / Garcia, Joaquin J / Kipp, Benjamin R / Moyer, Ann M

Clinica chimica acta; international journal of clinical chemistry

2022 Volume 532, Page(s) 181–187

Abstract: Background: SARS-CoV-2 is an RNA virus that primarily causes respiratory disease; however, infection of other tissue has been reported. Evaluation of SARS-CoV-2 in tissue specimens may increase understanding of SARS-CoV-2 pathobiology.: Materials and ... ...

Abstract	Background: SARS-CoV-2 is an RNA virus that primarily causes respiratory disease; however, infection of other tissue has been reported. Evaluation of SARS-CoV-2 in tissue specimens may increase understanding of SARS-CoV-2 pathobiology. Materials and methods: A qualitative test for detection of SARS-CoV-2 in formalin-fixed paraffin-embedded (FFPE) tissues was developed and validated using droplet digital PCR (ddPCR), which has a lower limit of detection than reverse transcription (RT)-qPCR. After extraction of total RNA from unstained FFPE tissue, SARS-CoV-2 nucleocapsid (N1, N2) target sequences were amplified and quantified, along with human RPP30 as a control using the Bio-Rad SARS-CoV-2 ddPCR kit. Results: SARS-CoV-2 was detected in all 21 known positive samples and none of the 16 negative samples. As few as approximately 5 viral copies were reliably detected. Since January 2021, many tissue types have been clinically tested. Of the 195 clinical specimens, the positivity rate was 35% with placenta and fetal tissue showing the highest percentage of positive cases. Conclusion: This sensitive FFPE-based assay has broad clinical utility with applications as diverse as pregnancy loss and evaluation of liver transplant rejection. This assay will aid in understanding atypical presentations of COVID-19 as well as long-term sequelae.
MeSH term(s)	COVID-19/diagnosis ; Formaldehyde ; Humans ; Paraffin Embedding ; RNA, Viral/isolation & purification ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/genetics
Chemical Substances	RNA, Viral ; Formaldehyde (1HG84L3525)
Language	English
Publishing date	2022-05-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80228-1
ISSN	1873-3492 ; 0009-8981
ISSN (online)	1873-3492
ISSN	0009-8981
DOI	10.1016/j.cca.2022.05.007
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Article ; Online: HISTOLOGIC FINDINGS IN VITREORETINAL LYMPHOMA: Learning From Enucleation Specimens.

Albadri, Sam T / Pulido, Jose S / Macon, William R / Garcia, Joaquin J / Salomao, Diva R

Retina (Philadelphia, Pa.)

2020 Volume 40, Issue 2, Page(s) 391–398

Abstract: Purpose: We aimed to describe the clinical and histologic findings in a few enucleation cases with intraocular lymphoma.: Methods: Retrospective review of pathology files from a 22-year period identified cases with intraocular lymphoma among all ... ...

Abstract	Purpose: We aimed to describe the clinical and histologic findings in a few enucleation cases with intraocular lymphoma. Methods: Retrospective review of pathology files from a 22-year period identified cases with intraocular lymphoma among all enucleation specimens. Patient demographics, clinical findings, laboratory results, radiographic studies, and indication for enucleation were abstracted from electronic health records; slides were reviewed. Results: Four patients (three women and one man; age range, sixth through eighth decades of life) underwent enucleation with a final diagnosis of intraocular lymphoma. Two patients with primary vitreoretinal large B-cell lymphomas had been treated for refractory uveitis. Specimens showed retinal and subretinal infiltrates by atypical large B-lymphocytes and rare neoplastic cells in the vitreous. The remaining two patients had systemic lymphoproliferative disorders. One patient had chronic lymphocytic leukemia and floaters in his eye; vitreoretinal lymphoma developed, consistent with intraocular Richter transformation. The other had diffuse large B-cell lymphoma in remission; however, blurred vision developed, she was treated for panuveitis without improvement, and was later found to have ocular involvement by diffuse large B-cell lymphoma. Conclusion: Our series details the unusual circumstances when an eye is removed for intraocular lymphoma. Different patterns of ocular tissue involvement were observed when we compared primary and secondary lymphomas.
MeSH term(s)	Aged ; Aged, 80 and over ; Biopsy ; Diagnosis, Differential ; Eye Enucleation/methods ; Female ; Follow-Up Studies ; Humans ; Intraocular Lymphoma/diagnosis ; Intraocular Lymphoma/surgery ; Lymphoma, Large B-Cell, Diffuse/diagnosis ; Lymphoma, Large B-Cell, Diffuse/surgery ; Male ; Middle Aged ; Retina/pathology ; Retinal Neoplasms/diagnosis ; Retinal Neoplasms/surgery ; Retrospective Studies ; Tomography, Optical Coherence/methods ; Ultrasonography/methods ; Vitreous Body/pathology
Language	English
Publishing date	2020-01-22
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	603192-4
ISSN	1539-2864 ; 0275-004X
ISSN (online)	1539-2864
ISSN	0275-004X
DOI	10.1097/IAE.0000000000002676
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