bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a highly sensitive mouse monoclonal antibody for screening ALK‐rearrangements in lung cancers
Authors: Shen Yi , Jin Mulan , Wu Yipan , Zhang Yungang , Yuan Kehu , Chu Boyang , Qi Lili , Liu Huibo , Wang Chenlin , Wang Guangli , Shu Youmin , McDowell Julie , Wei Haitao , Chen Caiwei , Ma Donghui , He Weiwu , Chen Jian 
Published: June 2021

The anaplastic lymphoma kinase (ALK) rearrangements, mostly EML4‐ALK fusion, occur in 3‐7% of lung cancer patients and define a patient population that could respond to receptor tyrosine kinase inhibitor Crizotinib and Ceritinib. Currently, ALK testing is mostly conducted by either fluorescence in situ hybridization (FISH) or polymerase chain reaction (PCR) methods, either of which has its own limitations. The detection of the ALK protein in lung cancer patient tissues by IHC was found to be difficult mostly due to the low abundance of its fusion product. To overcome this limitation, we have developed an ALK mouse monoclonal antibody (clone 1A4) that is more sensitive than a current rabbit ALK antibody D5F3. Our initial analyses revealed that 1A4 can correctly identify all 5 EML4‐ALK positive samples that were previously confirmed by QPCR tests, while did not yield significant background on all 30 EML4‐ALK negative lung cancer samples. By using a different IHC detection system, we further tested 1A4 on 17 ALK‐positive and 10 ALK‐negative lung cancer biopsy specimens that have been validated by either FISH or PCR from another hospital. The IHC result of the antibody 100% agreed with the previous molecular diagnosis. The high concordance of the IHC results by the novel ALK antibody with other DNA/RNA based detection methods suggested that 1A4 could be used routinely for screening ALK‐rearrangement genetic events among patients.This research is partly supported by Chinese 863 research grant number 2014AA020909.
Intraductal Papillary Mucinous Neoplasms: Can Mesothelin Expression Help us to Classify them Better?
Authors: Avadhani Vaidehi , Ahrens Dagny , Kapur Varun , Brower Steven , Wayne Michael , Ghali Violette , Levi Gabriel 
Published: June 2021

Mesothelin is a cell surface protein and a differentiation antigen of mesothelial cells. Rcently, Mesothelin expression has been reported in mucinous neoplasms of the pancreas. The aim of this study is to study the expression of Mesothelin in Intraductal pancreatic mucinous neoplasms (IPMN) and to see if this can be used to identify lesions with increasing dysplasiaA retrospective search of our Surgical database from 2008‐2014 was done. 30 cases of mucinous cystic lesions of the pancreas were identified. Clinical data including the age, size of lesion, main or branch duct involvement and pathological features including size of lesion, presence of adenocarcinoma, histopathology of the lesion were collected. All the cases were reviewed to select a representative section with the worst lesion on histopathology. The block was recut to obtain 2 unstained slides per block. One was stained with Hematoxylin and Eosin and the other was stained for Mesothelin (Leica RTU Clone5B2). Mesothelin staining pattern was evaluated as shown:

Mesothelin stain

Pattern
Cytoplasmic
Luminal/Apical

Intensity
Weak, Intermediate, Strong
Weak, Intermediate, Strong

73% of the mucinous cystic lesions were IPMN, with 21 female patients and 9 male patients. The mean size of the lesion was 3.1 cm.

A. Histopathology
Number
Mesothelin positive
Apical stain positive

1. IPMN
16
13
4

2. IPMN with high grade dysplasia
3
3
3

3. IPMN with adenocarcinoma
3
2
2

4. Mucinous cystadenoma
2
1
0

5. Mucinous cystic neoplasm
6
1
0

B. Relation to duct

1. Main duct
8
7
6

2. Branch duct
8
6
2

3. Mixed
3
2
0

4. Not reported
3
2
1

Mesothelin shows strong luminal expression in IPMN associated with high grade dysplasia and adenocarcinoma. It can possibly be used to identify lesions which might recur or as a marker of poor prognosis, hence helpful in stratifying patients who need close follow up. It shows cytoplasmic granular positivity in neoplastic epithelium and is negative in benign pancreatic and duodenal epithelium, which may help in identifying lesional tissue. This feature may also be useful in stratifying FNA specimen which usually have scant cells. Long‐term follow up studies can be helpful to study association with recurrence and prognosis, and identify cases which require close follow‐up.
Expression of Wnt5a in urothelial carcinoma as potential prognostic marker
Authors: Saling Mark , Duckett Jordan , Jenkinson Scott , Malgor Ramiro 
Published: June 2021

Bladder cancer is the fourth most common cancer in males and the most common malignancy of the urinary tract. According to American Cancer Society 74,690 new cases and 15,580 deaths from bladder cancer are expected for 2014 in the US. Our group recently reported a positive correlation between the expression of Wnt5a, a member of the Wnt proteins family, and histopathological grade and stage of urothelial carcinoma (UC). The objective of the study was to analyze the correlation between the expression of Wnt5a, E‐cadherin, and β‐catenin and histopathological grade of the UC in human tissue samples. The expression of the receptor tyrosine kinase‐like orphan receptor 2 (Ror2) in the tumor as a mechanism of Wnt5a in the metastatic process was also exploredTissue samples were obtained via transurethral resection for diagnostic purposes, formalin fixed and paraffin embedded. Wnt5a, E‐cadherin, β‐catenin, and Ror‐2 expression was characterized in UC samples using immunohistochemistry (IHC). The histopathological grade of each sample was determined using H&E stained sections and applying International Society of Urological Pathology (ISUP) criteria.The IHC results show that low grade tumors show strong staining for E‐cadherin and β‐catenin and weak staining for Wnt5a while, high grade tumors show opposite result. Interestingly, high grade tumors that show invasion into the muscularis propria show strong immunostaining for both Wnt5a and Ror2 while in noninvasive tumors a weak staining for Ror2 was detected.These results are in agreement with previous reports from our laboratory and support the potential application of Wnt5a as a prognostic marker for UC. Based on our results, Wnt5a‐Ror2 signaling may play a role in the invasiveness of UC.
Using Protein Microarray Technology to Screen Anti‐PD‐1 Monoclonal Antibodies for Specificity and Applications in Anatomic Pathology
Authors: Chen Caiwei , Wei Haitao , Yuan Kehu , Wu Guiyin , Chen Jian , Chu Boyang , Wang Guangli , Shu Youmin , He Weiwu , Ma Donghui 
Published: June 2021

Programmed death‐1 (PD‐1) expresses in many tumors in response to inflammation. It is up‐regulated in activated T lymphocytes and inhibits T‐cell function upon binding to its ligands PD‐L1 and PDL2 and serves as a key checkpoint of the immune system. KEYTRUDA (pembrolizumab) is the first anti‐PD‐1 therapy approved in the United States and received FDA's Breakthrough Therapy designation for advanced melanoma. Thus, to evaluate PD1 protein levels in formalin‐fixed paraffin‐embedded tissue samples, a high quality monoclonal antibody validated for immunohistochemistry (IHC) is needed.To develop the best monoclonal antibody for PD‐1 IHC analysis, 41 monoclonal antibodies were generated. 8 of them work for IHC application on FFPE tissue sections. To identify clones that are mono‐specific on target, only two clones passed our high density protein microarray chip tests. Other immunoassays and species cross‐reactivity tests were also explored.In summary, two newly generated monoclonal antibodies demonstrated ultra‐specificity against PD‐1 protein and superior performance for IHC analyses. These two clones could be utilized as companion diagnostic reagents to stratify cancer patients before KEYTRUDA prescription.This research is partly supported by Chinese 863 research grant number 2014AA020909.
Identification of MicroRNA‐mRNA Dysregulations in Paroxysmal Atrial Fibrillation
Authors: Chiang David , Zhang Min , Voigt Niels , Alsina Katherina , Jakob Heinz , Martin James , Dobrev Dobromir , Wehrens Xander , Li Na 
Published: June 2021

BackgroundThe molecular mechanisms underlying the early development of atrial fibrillation remain poorly understood. Emerging evidence suggests that abnormal epigenetic modulation via microRNAs (miRNAs) may be involved in the pathogenesis of paroxysmal atrial fibrillation (pAF).ObjectiveTo identify key molecular changes associated with pAF, we conducted state‐of‐the‐art transcriptomic studies to identify the abnormal miRNA‐mRNA interactions potentially driving AF development.Methods and ResultsHigh quality total RNA including miRNA was isolated from atrial biopsies of age‐matched and sex‐matched pAF patients and control patients in sinus rhythm (SR; n=4 per group) and used for RNA‐sequencing and miRNA microarrays. 113 genes and 49 miRNAs were differentially expressed (DE) in pAF versus SR patients. Gene ontology analysis revealed an enrichment of DE genes in the “gonadotropin releasing hormone receptor pathway” and “p53 pathway”. Also, bioinformatic analyses identified 23 pairs of putative miRNA‐mRNA interactions that were altered in pAF (including 15 miRNAs and 17 mRNAs). Using quantitative real‐time (qRT)‐PCR and 3′UTR luciferase assays, the interaction between upregulation of miR‐199a‐5p and downregulation of FKBP5 was confirmed in pAF samples (P<0.05 vs. SR).ConclusionThis is the first transcriptomic and miRNA microarray study using samples from pAF patients. Combined with bioinformatics and molecular validation, we provide novel insights into the pathways and miRNA‐mRNA dysregulations that may drive AF development. This opens up new avenues of research into AF pathogenesis as well as therapeutic development.
Circulating CXCL‐9, ‐10 and ‐11 Levels Improve the Discrimination of Risk Prediction Models for Left Ventricular Dysfunction
Authors: Altara Raffaele , Gu Yumei , Struijker‐Boudier Harry , Staessen Jan , Blankesteijn W Matthijs 
Published: June 2021

IntroductionDetection of left ventricular dysfunction (LVD), a condition preceding heart failure, can be challenging. Because inflammation contributes to heart failure development, we measured serum levels of three related chemokines, CXCL‐9, ‐10 and ‐11, and NT‐proBNP in serum from subjects with LVD and controls and determined their improvement of risk prediction.MethodsSubjects with subclinical (n=17) or advanced (N=14) LVD and age‐ and sex‐matched controls (n=31) were recruited from the large‐scale family‐based study on the genetic epidemiology of cardiovascular phenotypes (FLEMENGHO). Cytokine levels were determined by ELISA. Integration Discrimination Improvement (IDI) and Net Reclassification Improvement (NRI) were determined using SAS software.ResultsIncreased serum levels of CXCL‐9, ‐10 and ‐11 were observed in the LVD groups (1.5, 1.3 and 1.8‐fold in the subclinical LVD and 2.2, 2.5 and 4‐fold in the advanced LVD group, respectively; p<0.01). NT‐proBNP was 1.5 and 1.8‐fold higher in the subclinical and advanced LVD groups; p<0.01). Adding the biomarker levels in a dichotomized way to a model already including established risk factors resulted in an improved NRI of 14.2% (P<0.01) and IDI of 155% (P<0.001)ConclusionAddition of CXCL‐9, ‐10 and ‐11 levels to established risk factors significantly improves the risk prediction models for LVD. This study underscores the importance of using a panel of biomarkers to better characterize subjects with LVD.
PKGIα Leucine Zipper Domain Mediates a Novel Interaction with MLK3, a Potential Anti‐Remodeling Substrate in the Heart
Authors: Calamaras Timothy , Baumgartner Robert , Wang Guang‐Rong , Lane Angela , Aronovitz Mark , Davis Roger , Mendelsohn Michael , Kass David , Karas Richard , Blanton Robert 
Published: June 2021

BackgroundHeart failure is a significant contributor to cardiovascular mortality. cGMP inhibits cardiac remodeling in part via cGMP‐dependent protein kinase G I α (PKGIα). Knock in mice with a mutant PKGIα Leucine Zipper (LZ) have both decreased cardiac function and JNK activity after transaortic constriction (TAC). JNK is regulated by MAPKs including mixed lineage kinase 3 (MLK3) which contains an LZ interacting motif. We hypothesized PKGIα interacts with MLK3 via the PKGIα LZ domain to regulate JNK.ResultsThe MLK3‐PKGIα interaction was observed in mouse heart by co‐immunoprecipitation of MLK3 and PKGIα (n=3). In Cos1 cells MLK3 co‐precipitated with PKGIα but was prevented by mutation of the PKGIα LZ domain (n=3). In cardiomyocytes JNK stimulation by 8‐Br‐cGMP was prevented in MLK3‐depleted cells (siRNA, n=3). The role of MLK3 in the heart was tested by subjecting MLK3 knockout mice (MLK3‐/‐) to TAC (7 days). Compared to WT littermates MLK3‐/‐ hearts had increased hypertrophy and LV end diastolic pressure indicating advanced cardiac dysfunction (n=8‐10)ConclusionThese data reveal a novel interaction between PKGIα‐MLK3 that requires the LZ domain. In cardiomyocytes MLK3 is necessary for cGMP dependent JNK activation. Loss of MLK3 in vivo promotes adverse cardiac remodeling.This work was supported by the NIH.
Entamoeba histolytica‐Induced Caspase‐4/11 Activation Elicits a Pro‐Inflammatory Response in Macrophages
Authors: Quach Jeanie , Mortimer Leanne , Moreau France , Chadee Kris 
Published: June 2021

Entamoeba histolytica (Eh) is a protozoan parasite that colonizes in/on the mucus layer and in 10% of individuals, Eh invades the colonic mucosa to cause amebic colitis. A hallmark of amebiasis is acute intestinal inflammation dominated by the secretion of pro‐inflammatory cytokines, interleukin (IL)‐1β and tumour necrosis factor (TNF)‐α. Eh in contact with macrophages activates caspase‐1 by the inflammasome complex resulting in the maturation of IL‐1β and ‐18. The role of inflammatory caspase‐4, ‐5, and ‐12 in humans are less understood. Caspase‐11, the murine homolog of caspase‐4, mediates non‐canonical inflammasome activation in response to particular pathogens, suggesting that caspase‐4 may have similar roles. As caspase‐4/11 might be an immune sensor in Eh infection the aim of this study was to identify a signature role for caspase‐4/11 in Eh‐induced macrophage responses. To determine if caspase‐4/11 was involved in inflammasome signalling, the gene was silenced with siRNA. Knockdown of caspase‐4/11 did not affect caspase‐1 activation or IL‐1β secretion in response to Eh. However, multiplex cytokine arrays showed marked up regulation of TNF‐α, MIP‐1β, and KC suggesting that caspase‐4/11 may have regulatory roles in the secretion of distinct cytokines/chemokines. Although there was no evidence for crosstalk between caspase‐4/11 and caspase‐1, these inflammatory caspases seem to play a critical role in regulating other cytokines/chemokines that shape the overall macrophage response towards Eh infection. Elucidating the role these inflammatory caspases play in Eh disease pathogenesis may shed light on new therapeutics to treat amebiasis.Grant Support: NSERC
How to teach physiology to 4th‐grade children? High Tech PhUn!
Authors: Gurovich Alvaro , Anthis Taylor , Barrett Emily , Brown Carson , Brown Jaylyn , Cole Shelby , Evans LeVisa , Fagg Breanna , Hamilton Shannon , Harpenau Olivia , Hayslip Rachel , Jarrett Steven , Majors Katharyn , Miller Breena , Thomas Destini 
Published: June 2021

Physiology Understanding (PhUn) week is the APS K‐12 outreach program that helps increasing awareness about STEM education. Here, we combined PhUn week, health education, and high technology to show 3 physiological systems: cardiovascular system (CV), neuromuscular (NM), and central nervous system (CNS). Three hands‐on activities were designed using a Biopac MP40 system. These activities were integrated into the 4th grade science curriculum. Five different sessions in two different days were completed, and 14 undergraduate students worked as facilitators, reaching 116 elementary school students. Each session was divided in 6 small 4‐student groups with the following general activity set‐up: 1) brief presentation about the activity, 2) measurement of HR during 3 different conditions (CV), reaction time on dominant and non‐dominant forearm (NM), and brain activity during 4 different activities (CNS), 3) analyzing collected data, and 4) discussing obtained results. Two children per group were connected to the Biopac MP40 system, one student per group controlled the computer, and the last member of the group recorded data on a data collection form. Collected data was later used in their science class to plot and compare values. Teaching physiology to 4th‐graders is not an easy task. Here, children had a great time and were able to understand better the effects of, for example, exercise on brain function and heart rate. Finally, we strongly suggest using applied high tech activities to strengthen science curricula while kids have ‘PhUn’.Supported by IU AHEC 14/15 #PIU081 and APS PhUn week program
Northwest Biosciences Network: Implementation of Vision and Change in Introductory Biology
Authors: Stavrianeas S. , Baumgartner E. , Brown J. , Duncan J. , Gaiser C , Kayes L. , Kiser S. , Kruchten A , Shriner W. 
Published: June 2021

The Northwest Biosciences Consortium (NWBC) is a diverse community of biology educators who embrace Vision and Change to create student‐centered, integrated, and investigative biology experiences for all students.Our faculty‐led approach aims to create introductory courses that train biologically literate students, while simultaneously aligning with upper division courses to ease transfers and improve retention.The NWBC aims to:· Develop Student Learning Outcomes (SLOs) that allow students to gain appreciation for the scientific process· Develop a series of customizable modules that can be incorporated into any introductory biology sequence that reflects our commitment to scientific literacy for all students.· Develop course descriptions aligned with Vision and Change to facilitate curriculum design and student transition, especially from 2‐ to 4‐year institutions· Foster professional development and legitimize need for change at our home institutions.The NWBC supports faculty development and collaborations within and between institutions. We benefit from an excellent working relationship with the NW PULSE Fellows and connections to other groups (i.e. BioQUEST, NABT, etc.) that help shape our efforts. Our learning curve on how to function as a network is leveling off, and we are taking steps to accomplish our goals. We look forward to learning from the experiences of others and share lessons learned with those who have similar aims.Supported by the NSFRCN‐UBE grant (DBI‐1248121).
Developing, Testing and Optimising a Mouse Hindlimb Musculoskeletal Model
Authors: Charles James , Cappellari Ornella , Spence Andrew , Wells Dominic , Hutchinson John 
Published: June 2021

Stability during locomotion arises from many complex interactions which are not yet fully understood. Studies into how sensory feedback from muscle spindles contributes to this have used neuromechanical simulations, however their accuracy is limited due to the lack of available physiological data. This presentation outlines the methods used to develop a musculoskeletal model of the mouse hindlimb, which will be used to predict responses to perturbations which occur with or without sensory feedback.The 3D musculoskeletal model, which represents bones, joints and 39 muscles of the mouse hindlimb, was created using SIMM (Musculographics, USA) through a combination of muscle architecture data and I2KI enhanced microCT scanning. Architecture data, such as muscle mass, pennation angle and fibre length were gathered from microdissections, while muscle geometry was determined using I2KI microCT scanning, a non‐destructive method of determining muscle paths and attachment points. Muscle moment arms predicted by the model were found to agree with measured data from previous studies.In future work, in vivo optogenetics will be used to characterise changes in gait and muscle forces which occur in free running mice in response to induced neural and mechanical perturbations with or without sensory feedback from hindlimb muscles. These physiological data will be used to update and refine the musculoskeletal model.
Anatomical Mapping of the Omental Vasculature to Refine its Optimal Use in Free Flap Transfer
Authors: McAndrew Darryl , Buckley Lisa , Ashford Bruce , Clark Jonathan 
Published: June 2021

Current clinical practice when harvesting an omental free flap is utilisation of the right gastroepiploic artery. This approach is time consuming and surgically demanding / invasive. The clinical use of omental free tissue transfer for reconstruction is based on arterial dimensions, capabilities of surgical instrumentation and surgeon experience. This study mapped the omental arterial distributions and the diameter of the branching omental arteries to determine the viability of alternative vessels for microvascular anastomosis. By establishing the dimensions, patterns and calibres of omental arcades, disruption to the gastroepiploic arterial distribution could be minimised and allow smaller and simpler omental flaps to be harvested.Mapping of the pattern of the omental vasculature and physical measurement of the arterial omental branches and primary gastroepiploic arteries occurred within 10 cadavers.Results indicate average arterial omental branch diameters of 0.71mm, compared to an average gastroepiploic artery diameter of 1.66mm. Vessel diameters do not support the reliable use of omental branches as candidates for microvascular anastomosis, and support the continued use of the larger, more proximal gastroepiploic artery.
Accuracy of Osteophyte Detection in Conventional Computed Tomography and Magnetic Resonance Imaging of Joints
Authors: Al‐Attar N , Venne G , Easteal R , Kunz M 
Published: June 2021

Osteophytes are bony spurs on normal bone that develop as an adaptive reparative process due to excessive stress at/near a joint. As osteophytes develop from normal bone, they are not always well depicted in common imaging techniques (e.g. CT, MRI). This creates a challenge for preoperative planning and image‐guided surgical methods that are commonly incorporated in the clinical routine of orthopedic surgery.The study examined the accuracy of osteophyte detection in clinical CT and MRI scans of varying types of joints.The investigation was performed on three fresh‐frozen ex‐vivo human resected joints identified as having a high potential for presentation of osteophytes. The specimens underwent varying imaging protocols for CT scanning and clinical protocols for MRI. After dissection of the joint, the specimens were subjected to structured 3D light scanning to establish a reference model of the anatomy. Scans from the imaging protocols were segmented and their 3D models were co‐registered to the light scanner models. The quality of the osteophyte images were evaluated by determining the Root Mean Square (RMS) error between the segmented osteophyte models and the light scan model.The mean RMS errors for CT and MRI scanning were 1.169 mm and 1.419 mm, respectively. Comparing the different CT parameters, significance was achieved with scanning at 120 kVp and 1.25 mm slice thickness to depict osteophytes; also, significance was also apparent at a lower voltage (100 kVp).Preliminary results demonstrate that osteophyte detection may be dependent on the degree of calcification of the osteophyte. They also illustrate that while some imaging parameters were more favorable than others, a more accurate osteophyte depiction may result from the combination of both MRI and CT scanning.