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Article ; Online: Connecting cohorts of Finnish biobanks creates a research resource for the study of healthy ageing.

Eklund, Niina / Pätsi, Salla-Maaria / Lehtiniemi, Heli / Rohkimainen, Samppa / Kivelä, Juha / Öhman, Hanna / Sauramo, Minttu / Sutinen, Kyösti / Keskinarkaus, Anja / Terho, Perttu / Seppänen, Tapio / Nyberg, Pia / Männikkö, Minna / Silander, Kaisa

Scandinavian journal of public health

2024 , Page(s) 14034948241228482

Language	English
Publishing date	2024-03-04
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1475054-5
ISSN	1651-1905 ; 1403-4948
ISSN (online)	1651-1905
ISSN	1403-4948
DOI	10.1177/14034948241228482
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Zs.A 884: Show issues

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Article ; Online: Invasion depth estimation of carcinoma cells using adaptive stain normalization to improve epidermis segmentation accuracy.

Hoque, Md Ziaul / Keskinarkaus, Anja / Nyberg, Pia / Xu, Hongming / Seppänen, Tapio

Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society

2023 Volume 108, Page(s) 102276

Abstract: Submucosal invasion depth is a significant prognostic factor when assessing lymph node metastasis and cancer itself to plan proper treatment for the patient. Conventionally, oncologists measure the invasion depth by hand which is a laborious, subjective, ...

Abstract	Submucosal invasion depth is a significant prognostic factor when assessing lymph node metastasis and cancer itself to plan proper treatment for the patient. Conventionally, oncologists measure the invasion depth by hand which is a laborious, subjective, and time-consuming process. The manual pathological examination by measuring accurate carcinoma cell invasion with considerable inter-observer and intra-observer variations is still challenging. The increasing use of medical imaging and artificial intelligence reveals a significant role in clinical medicine and pathology. In this paper, we propose an approach to study invasive behavior and measure the invasion depth of carcinoma from stained histopathology images. Specifically, our model includes adaptive stain normalization, color decomposition, and morphological reconstruction with adaptive thresholding to separate the epithelium with blue ratio image. Our method splits the image into multiple non-overlapping meaningful segments and successfully finds the homogeneous segments to measure accurate invasion depth. The invasion depths are measured from the inner epithelium edge to outermost pixels of the deepest part of particles in image. We conduct our experiments on skin melanoma tissue samples as well as on organotypic invasion model utilizing myoma tissue and oral squamous cell carcinoma. The performance is experimentally compared to three closely related reference methods and our method provides a superior result in measuring invasion depth. This computational technique will be beneficial for the segmentation of epithelium and other particles for the development of novel computer-aided diagnostic tools in biobank applications.
MeSH term(s)	Humans ; Carcinoma, Squamous Cell ; Artificial Intelligence ; Mouth Neoplasms/diagnostic imaging ; Epidermis ; Epidermal Cells ; Coloring Agents
Chemical Substances	Coloring Agents
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639451-6
ISSN	1879-0771 ; 0895-6111
ISSN (online)	1879-0771
ISSN	0895-6111
DOI	10.1016/j.compmedimag.2023.102276
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Zs.A 1323: Show issues

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Article ; Online: Insights into Preservation of Blood Biomarkers in Biobank Samples.

Juurikka, Krista / Åström, Pirjo / Pekkala, Tiina / Öhman, Hanna / Sorsa, Timo / Tervahartiala, Taina / Salo, Tuula / Lehenkari, Petri / Nyberg, Pia

Biopreservation and biobanking

2022 Volume 20, Issue 3, Page(s) 297–301

MeSH term(s)	Biological Specimen Banks ; Biomarkers ; Preservation, Biological
Chemical Substances	Biomarkers
Language	English
Publishing date	2022-01-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2593993-2
ISSN	1947-5543 ; 1947-5535
ISSN (online)	1947-5543
ISSN	1947-5535
DOI	10.1089/bio.2021.0096
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Article ; Online: Computerized cognitive interventions for adults with ADHD: A systematic review and meta-analysis.

Elbe, Pia / Bäcklund, Christian / Vega-Mendoza, Mariana / Sörman, Daniel / Malmberg Gavelin, Hanna / Nyberg, Lars / Ljungberg, Jessica K

Neuropsychology

2023 Volume 37, Issue 5, Page(s) 519–530

Abstract: Objective: Treatments for adults with attention-deficit hyperactivity disorder (ADHD) are understudied, compared to children and adolescents with the same condition. In this systematic review and random-effects meta-analysis, we aim to evaluate the ... ...

Abstract	Objective: Treatments for adults with attention-deficit hyperactivity disorder (ADHD) are understudied, compared to children and adolescents with the same condition. In this systematic review and random-effects meta-analysis, we aim to evaluate the outcomes of computerized cognitive training (CCT) interventions in randomized controlled trials (RCTs) including adults with ADHD. Method: Cognitive outcomes and ADHD symptom severity were analyzed separately. In addition, the Cattell-Horn-Carroll (CHC) theory of cognitive abilities was used to categorize outcome variables into subdomains, which were analyzed separately in a subsequent analysis. Results: The results revealed a small positive change in overall cognitive functioning, a measure of all cognitive outcomes in each study, for individuals who took part in CCT compared to controls ( Conclusions: We analyzed the risk of bias in the chosen studies and discuss the findings in terms of effect size. It is concluded that CCT has a small positive effect in adults with ADHD. Due to the lack of heterogeneity in intervention designs across the included studies, increased heterogeneity in future studies could help inform clinicians about the aspects of CCT, such as training type and length, that are most beneficial for this group. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
MeSH term(s)	Child ; Adolescent ; Adult ; Humans ; Attention Deficit Disorder with Hyperactivity/complications ; Attention Deficit Disorder with Hyperactivity/therapy ; Cognition ; Executive Function ; Memory, Short-Term
Language	English
Publishing date	2023-03-09
Publishing country	United States
Document type	Meta-Analysis ; Systematic Review ; Journal Article
ZDB-ID	1042412-x
ISSN	1931-1559 ; 0894-4105
ISSN (online)	1931-1559
ISSN	0894-4105
DOI	10.1037/neu0000890
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Zs.A 3002: Show issues

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Article ; Online: Whole slide image registration via multi-stained feature matching.

Hoque, Md Ziaul / Keskinarkaus, Anja / Nyberg, Pia / Mattila, Taneli / Seppänen, Tapio

Computers in biology and medicine

2022 Volume 144, Page(s) 105301

Abstract: In the recent decade, medical image registration and fusion process has emerged as an effective application to follow up diseases and decide the necessary therapies based on the conditions of patient. For many of the considerable diagnostic analyses, it ... ...

Abstract	In the recent decade, medical image registration and fusion process has emerged as an effective application to follow up diseases and decide the necessary therapies based on the conditions of patient. For many of the considerable diagnostic analyses, it is common practice to assess two or more different histological slides or images from one tissue sample. A specific area analysis of two image modalities requires an overlay of the images to distinguish positions in the sample that are organized at a similar coordinate in both images. In particular cases, there are two common challenges in digital pathology: first, dissimilar appearances of images resulting due to staining variances and artifacts; second, large image size. In this paper, we develop algorithm to overcome the fact that scanners from different manufacturers have variations in the images. We propose whole slide image registration algorithm where adaptive smoothing is employed to smooth the stained image. A modified scale-invariant feature transform is applied to extract common information and a joint distance helps to match keypoints correctly by eliminating position transformation error. Finally, the registered image is obtained by utilizing correct correspondences and the interpolation of color intensities. We validate our proposal using different images acquired from surgical resection samples of lung cancer (adenocarcinoma). Extensive feature matching with apparently increasing correct correspondences and registration performance on several images demonstrate the superiority of our method over state-of-the-art methods. Our method potentially improves the matching accuracy that might be beneficial for computer-aided diagnosis in biobank applications.
MeSH term(s)	Algorithms ; Artifacts ; Diagnosis, Computer-Assisted ; Humans ; Image Processing, Computer-Assisted/methods ; Staining and Labeling
Language	English
Publishing date	2022-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.105301
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Zs.A 653: Show issues

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Article ; Online: Retinex model based stain normalization technique for whole slide image analysis.

Hoque, Md Ziaul / Keskinarkaus, Anja / Nyberg, Pia / Seppänen, Tapio

Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society

2021 Volume 90, Page(s) 101901

Abstract: Medical imaging provides the means for diagnosing many of the medical phenomena currently studied in clinical medicine and pathology. The variations of color and intensity in stained histological slides affect the quantitative analysis of the ... ...

Abstract	Medical imaging provides the means for diagnosing many of the medical phenomena currently studied in clinical medicine and pathology. The variations of color and intensity in stained histological slides affect the quantitative analysis of the histopathological images. Moreover, stain normalization utilizing color for the classification of pixels into different stain components is challenging. The staining also suffers from variability, which complicates the automatization of tissue area segmentation with different staining and the analysis of whole slide images. We have developed a Retinex model based stain normalization technique in terms of area segmentation from stained tissue images to quantify the individual stain components of the histochemical stains for the ideal removal of variability. The performance was experimentally compared to reference methods and tested on organotypic carcinoma model based on myoma tissue and our method consistently has the smallest standard deviation, skewness value, and coefficient of variation in normalized median intensity measurements. Our method also achieved better quality performance in terms of Quaternion Structure Similarity Index Metric (QSSIM), Structural Similarity Index Metric (SSIM), and Pearson Correlation Coefficient (PCC) by improving robustness against variability and reproducibility. The proposed method could potentially be used in the development of novel research as well as diagnostic tools with the potential improvement of accuracy and consistency in computer aided diagnosis in biobank applications.
MeSH term(s)	Coloring Agents ; Diagnosis, Computer-Assisted ; Image Processing, Computer-Assisted ; Reproducibility of Results ; Staining and Labeling
Chemical Substances	Coloring Agents
Language	English
Publishing date	2021-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639451-6
ISSN	1879-0771 ; 0895-6111
ISSN (online)	1879-0771
ISSN	0895-6111
DOI	10.1016/j.compmedimag.2021.101901
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Zs.A 1323: Show issues

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Article: The AxBioTick Study:

Carlströmer Berthén, Nellie / Tompa, Eszter / Olausson, Susanne / Nyberg, Clara / Nyman, Dag / Ringbom, Malin / Perander, Linda / Svärd, Joel / Lindgren, Per-Eric / Forsberg, Pia / Wilhelmsson, Peter / Sjöwall, Johanna / Nordberg, Marika

Microorganisms

2023 Volume 11, Issue 5

Abstract: The AxBioTick study was initiated to investigate the prevalence of ticks and tick-borne pathogens and their impact on antibody and clinical responses in tick-bitten individuals on the Aland Islands. This geographical area is hyperendemic for both Lyme ... ...

Abstract	The AxBioTick study was initiated to investigate the prevalence of ticks and tick-borne pathogens and their impact on antibody and clinical responses in tick-bitten individuals on the Aland Islands. This geographical area is hyperendemic for both Lyme borreliosis (LB) and Tick-borne encephalitis (TBE). Blood samples and ticks were collected from 100 tick-bitten volunteers. A total of 425 ticks was collected, all determined to
Language	English
Publishing date	2023-04-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms11051100
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Article ; Online: Human α1 type IV collagen NC1 domain exhibits distinct antiangiogenic activity mediated by α1β1 integrin.

Sudhakar, Akulapalli / Nyberg, Pia / Keshamouni, Venkateshwar G / Mannam, Arjuna P / Li, Jian / Sugimoto, Hikaru / Cosgrove, Dominic / Kalluri, Raghu

The Journal of clinical investigation

2020 Volume 130, Issue 1, Page(s) 552

Language	English
Publishing date	2020-02-06
Publishing country	United States
Document type	Journal Article ; Retraction of Publication
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI135305
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Ua VI Zs.184: Show issues

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Article ; Online: 'It's a matter of patient safety': understanding challenges in everyday clinical practice for achieving good care on the surgical ward - a qualitative study.

Jangland, Eva / Nyberg, Berit / Yngman-Uhlin, Pia

Scandinavian journal of caring sciences

2017 Volume 31, Issue 2, Page(s) 323–331

Abstract: Background: Surgical care plays an important role in the acute hospital's delivery of safe, high-quality patient care. Although demands for effectiveness are high in surgical wards quality of care and patient safety must also be secured. It is therefore ...

Abstract	Background: Surgical care plays an important role in the acute hospital's delivery of safe, high-quality patient care. Although demands for effectiveness are high in surgical wards quality of care and patient safety must also be secured. It is therefore necessary to identify the challenges and barriers linked to quality of care and patient safety with a focus on this specific setting. Aim: To explore situations and processes that support or hinder good safe patient care on the surgical ward. Method: This qualitative study was based on a strategic sample of 10 department and ward leaders in three hospitals and six surgical wards in Sweden. Repeated reflective interviews were analysed using systematic text condensation. Findings: Four themes described the leaders' view of a complex healthcare setting that demands effectiveness and efficiency in moving patients quickly through the healthcare system. Quality of care and patient safety were often hampered factors such as a shift of care level, with critically ill patients cared for without reorganisation of nurses' competencies on the surgical ward. Conclusions: There is a gap between what is described in written documents and what is or can be performed in clinical practice to achieve good care and safe care on the surgical ward. A shift in levels of care on the surgical ward without reallocation of the necessary competencies at the patient's bedside show consequences for quality of care and patient safety. This means that surgical wards should consider reviewing their organisation and implementing more advanced nursing roles in direct patient care on all shifts. The ethical issues and the moral stress on nurses who lack the resources and competence to deliver good care according to professional values need to be made more explicit as a part of the patient safety agenda in the surgical ward.
Language	English
Publishing date	2017-06
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	639217-9
ISSN	1471-6712 ; 0283-9318
ISSN (online)	1471-6712
ISSN	0283-9318
DOI	10.1111/scs.12350
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Zs.A 2274: Show issues

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Article ; Online: The Role of MMP8 in Cancer: A Systematic Review.

Juurikka, Krista / Butler, Georgina S / Salo, Tuula / Nyberg, Pia / Åström, Pirjo

International journal of molecular sciences

2019 Volume 20, Issue 18

Abstract: Matrix metalloproteinases (MMPs) have traditionally been considered as tumor promoting enzymes as they degrade extracellular matrix components, thus increasing the invasion of cancer cells. It has become evident, however, that MMPs can also cleave and ... ...

Abstract	Matrix metalloproteinases (MMPs) have traditionally been considered as tumor promoting enzymes as they degrade extracellular matrix components, thus increasing the invasion of cancer cells. It has become evident, however, that MMPs can also cleave and alter the function of various non-matrix bioactive molecules, leading to both tumor promoting and suppressive effects. We applied systematic review guidelines to study MMP8 in cancer including the use of MMP8 as a prognostic factor or as a target/anti-target in cancer treatment, and its molecular mechanisms. A total of 171 articles met the inclusion criteria. The collective evidence reveals that in breast, skin and oral tongue cancer, MMP8 inhibits cancer cell invasion and proliferation, and protects patients from metastasis via cleavage of non-structural substrates. Conversely, in liver and gastric cancers, high levels of MMP8 worsen the prognosis. Expression and genetic alterations of MMP8 can be used as a prognostic factor by examination of the tumor and serum/plasma. We conclude, that MMP8 has differing effects on cancers depending on their tissue of origin. The use of MMP8 as a prognostic factor alone, or with other factors, seems to have potential. The molecular mechanisms of MMP8 in cancer further emphasize its role as an important regulator of bioactive molecules.
MeSH term(s)	Animals ; Biomarkers, Tumor/metabolism ; Epigenesis, Genetic ; Humans ; Matrix Metalloproteinase 8/blood ; Matrix Metalloproteinase 8/metabolism ; Neoplasms/blood ; Neoplasms/enzymology ; Neoplasms/genetics ; Polymorphism, Single Nucleotide/genetics ; Prognosis
Chemical Substances	Biomarkers, Tumor ; Matrix Metalloproteinase 8 (EC 3.4.24.34)
Language	English
Publishing date	2019-09-11
Publishing country	Switzerland
Document type	Journal Article ; Systematic Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms20184506
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